Comparative genomics of the Bifidobacterium breve taxon View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2014-03-01

AUTHORS

Francesca Bottacini, Mary O’Connell Motherway, Justin Kuczynski, Kerry Joan O’Connell, Fausta Serafini, Sabrina Duranti, Christian Milani, Francesca Turroni, Gabriele Andrea Lugli, Aldert Zomer, Daria Zhurina, Christian Riedel, Marco Ventura, Douwe van Sinderen

ABSTRACT

BACKGROUND: Bifidobacteria are commonly found as part of the microbiota of the gastrointestinal tract (GIT) of a broad range of hosts, where their presence is positively correlated with the host's health status. In this study, we assessed the genomes of thirteen representatives of Bifidobacterium breve, which is not only a frequently encountered component of the (adult and infant) human gut microbiota, but can also be isolated from human milk and vagina. RESULTS: In silico analysis of genome sequences from thirteen B. breve strains isolated from different environments (infant and adult faeces, human milk, human vagina) shows that the genetic variability of this species principally consists of hypothetical genes and mobile elements, but, interestingly, also genes correlated with the adaptation to host environment and gut colonization. These latter genes specify the biosynthetic machinery for sortase-dependent pili and exopolysaccharide production, as well as genes that provide protection against invasion of foreign DNA (i.e. CRISPR loci and restriction/modification systems), and genes that encode enzymes responsible for carbohydrate fermentation. Gene-trait matching analysis showed clear correlations between known metabolic capabilities and characterized genes, and it also allowed the identification of a gene cluster involved in the utilization of the alcohol-sugar sorbitol. CONCLUSIONS: Genome analysis of thirteen representatives of the B. breve species revealed that the deduced pan-genome exhibits an essentially close trend. For this reason our analyses suggest that this number of B. breve representatives is sufficient to fully describe the pan-genome of this species. Comparative genomics also facilitated the genetic explanation for differential carbon source utilization phenotypes previously observed in different strains of B. breve. More... »

PAGES

170

Journal

TITLE

BMC Genomics

ISSUE

1

VOLUME

15

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2164-15-170

DOI

http://dx.doi.org/10.1186/1471-2164-15-170

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1014252423

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/24581150


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Bifidobacterium", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Carbohydrate Metabolism", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Cluster Analysis", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Computational Biology", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA Transposable Elements", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Order", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genetic Association Studies", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genetic Variation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genome, Bacterial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genomics", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "High-Throughput Nucleotide Sequencing", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Metabolome", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Metabolomics", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Molecular Sequence Data", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Multigene Family", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Phylogeny", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland", 
          "id": "http://www.grid.ac/institutes/grid.7872.a", 
          "name": [
            "Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Bottacini", 
        "givenName": "Francesca", 
        "id": "sg:person.0750360565.04", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0750360565.04"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland", 
          "id": "http://www.grid.ac/institutes/grid.7872.a", 
          "name": [
            "Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Motherway", 
        "givenName": "Mary O\u2019Connell", 
        "id": "sg:person.01024643735.40", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01024643735.40"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Second Genome, Bioinformatics Department, San Bruno, CA USA", 
          "id": "http://www.grid.ac/institutes/grid.452682.f", 
          "name": [
            "Second Genome, Bioinformatics Department, San Bruno, CA USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Kuczynski", 
        "givenName": "Justin", 
        "id": "sg:person.01242576526.02", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01242576526.02"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland", 
          "id": "http://www.grid.ac/institutes/grid.7872.a", 
          "name": [
            "Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland"
          ], 
          "type": "Organization"
        }, 
        "familyName": "O\u2019Connell", 
        "givenName": "Kerry Joan", 
        "id": "sg:person.0775502015.36", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0775502015.36"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy", 
          "id": "http://www.grid.ac/institutes/grid.10383.39", 
          "name": [
            "Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Serafini", 
        "givenName": "Fausta", 
        "id": "sg:person.01160541054.33", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01160541054.33"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy", 
          "id": "http://www.grid.ac/institutes/grid.10383.39", 
          "name": [
            "Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Duranti", 
        "givenName": "Sabrina", 
        "id": "sg:person.01347407206.63", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01347407206.63"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy", 
          "id": "http://www.grid.ac/institutes/grid.10383.39", 
          "name": [
            "Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Milani", 
        "givenName": "Christian", 
        "id": "sg:person.0627060310.50", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0627060310.50"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland", 
          "id": "http://www.grid.ac/institutes/grid.7872.a", 
          "name": [
            "Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Turroni", 
        "givenName": "Francesca", 
        "id": "sg:person.01050617006.18", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01050617006.18"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy", 
          "id": "http://www.grid.ac/institutes/grid.10383.39", 
          "name": [
            "Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Lugli", 
        "givenName": "Gabriele Andrea", 
        "id": "sg:person.0743306710.38", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0743306710.38"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands", 
          "id": "http://www.grid.ac/institutes/grid.10417.33", 
          "name": [
            "Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Zomer", 
        "givenName": "Aldert", 
        "id": "sg:person.01226157015.13", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01226157015.13"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany", 
          "id": "http://www.grid.ac/institutes/grid.6582.9", 
          "name": [
            "Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Zhurina", 
        "givenName": "Daria", 
        "id": "sg:person.01347473767.06", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01347473767.06"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany", 
          "id": "http://www.grid.ac/institutes/grid.6582.9", 
          "name": [
            "Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Riedel", 
        "givenName": "Christian", 
        "id": "sg:person.01126521167.34", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01126521167.34"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy", 
          "id": "http://www.grid.ac/institutes/grid.10383.39", 
          "name": [
            "Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Ventura", 
        "givenName": "Marco", 
        "id": "sg:person.01356325510.28", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01356325510.28"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland", 
          "id": "http://www.grid.ac/institutes/grid.7872.a", 
          "name": [
            "Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland"
          ], 
          "type": "Organization"
        }, 
        "familyName": "van Sinderen", 
        "givenName": "Douwe", 
        "id": "sg:person.01310212310.93", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01310212310.93"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1038/nrmicro2047", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024437688", 
          "https://doi.org/10.1038/nrmicro2047"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/gb-2004-5-2-r12", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022585853", 
          "https://doi.org/10.1186/gb-2004-5-2-r12"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-1-61779-603-6_5", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014239867", 
          "https://doi.org/10.1007/978-1-61779-603-6_5"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00018-013-1318-0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032404552", 
          "https://doi.org/10.1007/s00018-013-1318-0"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1475-2859-10-s1-s16", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037912010", 
          "https://doi.org/10.1186/1475-2859-10-s1-s16"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2014-03-01", 
    "datePublishedReg": "2014-03-01", 
    "description": "BACKGROUND: Bifidobacteria are commonly found as part of the microbiota of the gastrointestinal tract (GIT) of a broad range of hosts, where their presence is positively correlated with the host's health status. In this study, we assessed the genomes of thirteen representatives of Bifidobacterium breve, which is not only a frequently encountered component of the (adult and infant) human gut microbiota, but can also be isolated from human milk and vagina.\nRESULTS: In silico analysis of genome sequences from thirteen B. breve strains isolated from different environments (infant and adult faeces, human milk, human vagina) shows that the genetic variability of this species principally consists of hypothetical genes and mobile elements, but, interestingly, also genes correlated with the adaptation to host environment and gut colonization. These latter genes specify the biosynthetic machinery for sortase-dependent pili and exopolysaccharide production, as well as genes that provide protection against invasion of foreign DNA (i.e. CRISPR loci and restriction/modification systems), and genes that encode enzymes responsible for carbohydrate fermentation. Gene-trait matching analysis showed clear correlations between known metabolic capabilities and characterized genes, and it also allowed the identification of a gene cluster involved in the utilization of the alcohol-sugar sorbitol.\nCONCLUSIONS: Genome analysis of thirteen representatives of the B. breve species revealed that the deduced pan-genome exhibits an essentially close trend. For this reason our analyses suggest that this number of B. breve representatives is sufficient to fully describe the pan-genome of this species. Comparative genomics also facilitated the genetic explanation for differential carbon source utilization phenotypes previously observed in different strains of B. breve.", 
    "genre": "article", 
    "id": "sg:pub.10.1186/1471-2164-15-170", 
    "inLanguage": "en", 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.3984108", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.3983930", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.3982843", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1023790", 
        "issn": [
          "1471-2164"
        ], 
        "name": "BMC Genomics", 
        "publisher": "Springer Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "15"
      }
    ], 
    "keywords": [
      "pan-genome", 
      "comparative genomics", 
      "gene-trait matching analysis", 
      "sortase-dependent pili", 
      "host health status", 
      "hypothetical genes", 
      "human gut microbiota", 
      "genome sequence", 
      "latter genes", 
      "biosynthetic machinery", 
      "gene cluster", 
      "genome analysis", 
      "metabolic capabilities", 
      "foreign DNA", 
      "genetic variability", 
      "breve species", 
      "utilization phenotype", 
      "silico analysis", 
      "genes", 
      "host environment", 
      "mobile elements", 
      "exopolysaccharide production", 
      "species", 
      "genomics", 
      "carbohydrate fermentation", 
      "genetic explanation", 
      "breve strains", 
      "gut colonization", 
      "gut microbiota", 
      "different strains", 
      "different environments", 
      "gastrointestinal tract", 
      "Bifidobacterium breve", 
      "health status", 
      "microbiota", 
      "genome", 
      "machinery", 
      "pili", 
      "DNA", 
      "strains", 
      "phenotype", 
      "colonization", 
      "human milk", 
      "host", 
      "breve", 
      "sequence", 
      "representatives", 
      "broad range", 
      "invasion", 
      "fermentation", 
      "adaptation", 
      "matching analysis", 
      "identification", 
      "sorbitol", 
      "analysis", 
      "bifidobacteria", 
      "clear correlation", 
      "production", 
      "environment", 
      "clusters", 
      "vagina", 
      "tract", 
      "variability", 
      "presence", 
      "components", 
      "status", 
      "protection", 
      "elements", 
      "number", 
      "milk", 
      "part", 
      "study", 
      "explanation", 
      "utilization", 
      "correlation", 
      "range", 
      "close trend", 
      "reasons", 
      "trends", 
      "capability", 
      "alcohol-sugar sorbitol", 
      "deduced pan-genome", 
      "breve representatives", 
      "differential carbon source utilization phenotypes", 
      "carbon source utilization phenotypes", 
      "source utilization phenotypes"
    ], 
    "name": "Comparative genomics of the Bifidobacterium breve taxon", 
    "pagination": "170", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1014252423"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/1471-2164-15-170"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "24581150"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/1471-2164-15-170", 
      "https://app.dimensions.ai/details/publication/pub.1014252423"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2021-11-01T18:22", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20211101/entities/gbq_results/article/article_628.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1186/1471-2164-15-170"
  }
]
 

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.10.1186/1471-2164-15-170'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-15-170'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-15-170'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-15-170'


 

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

340 TRIPLES      22 PREDICATES      133 URIs      120 LITERALS      23 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/1471-2164-15-170 schema:about N08758a9ca777467d88b6e0384abf4aa3
2 N119241b832744486b561df8afe2f0f80
3 N13d638ddb528414a96d735ff8b4aa586
4 N13d70c9cd322406989abd91ef2a2d8a4
5 N403c627a244144e583692aefe1012aa8
6 N4af54324ca08498f9891542a6ab2d0a9
7 N5140c945b9a648249634f7f8a1a20970
8 N5545e7fef8be4745a993153e0796a5d0
9 N6a49de5495014217b6dd30b96259553d
10 N7785e16ce51343a4834ceba4f33da0b4
11 N7977a4dcbcb040e48afe05cfbc38f1c0
12 N851fd47c5a784980be83f4c3410d9d86
13 Na96d923c163d4ceabaca0c917fd5a6c9
14 Nb28343dc916841189c216c6c9a56bb6b
15 Nbde8c7550f9f4a639b5f6e3d79305c04
16 Nefe1064df03e4b56b2601e25618c2261
17 anzsrc-for:06
18 anzsrc-for:0604
19 schema:author N34d6037391bd49dba5b220e3842e7df0
20 schema:citation sg:pub.10.1007/978-1-61779-603-6_5
21 sg:pub.10.1007/s00018-013-1318-0
22 sg:pub.10.1038/nrmicro2047
23 sg:pub.10.1186/1475-2859-10-s1-s16
24 sg:pub.10.1186/gb-2004-5-2-r12
25 schema:datePublished 2014-03-01
26 schema:datePublishedReg 2014-03-01
27 schema:description BACKGROUND: Bifidobacteria are commonly found as part of the microbiota of the gastrointestinal tract (GIT) of a broad range of hosts, where their presence is positively correlated with the host's health status. In this study, we assessed the genomes of thirteen representatives of Bifidobacterium breve, which is not only a frequently encountered component of the (adult and infant) human gut microbiota, but can also be isolated from human milk and vagina. RESULTS: In silico analysis of genome sequences from thirteen B. breve strains isolated from different environments (infant and adult faeces, human milk, human vagina) shows that the genetic variability of this species principally consists of hypothetical genes and mobile elements, but, interestingly, also genes correlated with the adaptation to host environment and gut colonization. These latter genes specify the biosynthetic machinery for sortase-dependent pili and exopolysaccharide production, as well as genes that provide protection against invasion of foreign DNA (i.e. CRISPR loci and restriction/modification systems), and genes that encode enzymes responsible for carbohydrate fermentation. Gene-trait matching analysis showed clear correlations between known metabolic capabilities and characterized genes, and it also allowed the identification of a gene cluster involved in the utilization of the alcohol-sugar sorbitol. CONCLUSIONS: Genome analysis of thirteen representatives of the B. breve species revealed that the deduced pan-genome exhibits an essentially close trend. For this reason our analyses suggest that this number of B. breve representatives is sufficient to fully describe the pan-genome of this species. Comparative genomics also facilitated the genetic explanation for differential carbon source utilization phenotypes previously observed in different strains of B. breve.
28 schema:genre article
29 schema:inLanguage en
30 schema:isAccessibleForFree true
31 schema:isPartOf N0fff5c733fee4e68bff3a72fd6332058
32 Nb7bd436978eb471e9c85b0c698f4fecc
33 sg:journal.1023790
34 schema:keywords Bifidobacterium breve
35 DNA
36 adaptation
37 alcohol-sugar sorbitol
38 analysis
39 bifidobacteria
40 biosynthetic machinery
41 breve
42 breve representatives
43 breve species
44 breve strains
45 broad range
46 capability
47 carbohydrate fermentation
48 carbon source utilization phenotypes
49 clear correlation
50 close trend
51 clusters
52 colonization
53 comparative genomics
54 components
55 correlation
56 deduced pan-genome
57 different environments
58 different strains
59 differential carbon source utilization phenotypes
60 elements
61 environment
62 exopolysaccharide production
63 explanation
64 fermentation
65 foreign DNA
66 gastrointestinal tract
67 gene cluster
68 gene-trait matching analysis
69 genes
70 genetic explanation
71 genetic variability
72 genome
73 genome analysis
74 genome sequence
75 genomics
76 gut colonization
77 gut microbiota
78 health status
79 host
80 host environment
81 host health status
82 human gut microbiota
83 human milk
84 hypothetical genes
85 identification
86 invasion
87 latter genes
88 machinery
89 matching analysis
90 metabolic capabilities
91 microbiota
92 milk
93 mobile elements
94 number
95 pan-genome
96 part
97 phenotype
98 pili
99 presence
100 production
101 protection
102 range
103 reasons
104 representatives
105 sequence
106 silico analysis
107 sorbitol
108 sortase-dependent pili
109 source utilization phenotypes
110 species
111 status
112 strains
113 study
114 tract
115 trends
116 utilization
117 utilization phenotype
118 vagina
119 variability
120 schema:name Comparative genomics of the Bifidobacterium breve taxon
121 schema:pagination 170
122 schema:productId N23858049eb6841838e1aba5047366e3b
123 Nc6677dddb516462087bd676ed546f5ee
124 Nee71b81f77c34ae2ad764ae508c67ca8
125 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014252423
126 https://doi.org/10.1186/1471-2164-15-170
127 schema:sdDatePublished 2021-11-01T18:22
128 schema:sdLicense https://scigraph.springernature.com/explorer/license/
129 schema:sdPublisher Nbebd718d25054d9681d6a663ba35b0e6
130 schema:url https://doi.org/10.1186/1471-2164-15-170
131 sgo:license sg:explorer/license/
132 sgo:sdDataset articles
133 rdf:type schema:ScholarlyArticle
134 N08758a9ca777467d88b6e0384abf4aa3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
135 schema:name Computational Biology
136 rdf:type schema:DefinedTerm
137 N0fff5c733fee4e68bff3a72fd6332058 schema:volumeNumber 15
138 rdf:type schema:PublicationVolume
139 N119241b832744486b561df8afe2f0f80 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
140 schema:name Multigene Family
141 rdf:type schema:DefinedTerm
142 N13d638ddb528414a96d735ff8b4aa586 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
143 schema:name Genetic Association Studies
144 rdf:type schema:DefinedTerm
145 N13d70c9cd322406989abd91ef2a2d8a4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
146 schema:name Metabolomics
147 rdf:type schema:DefinedTerm
148 N185f0a37bf0647a38a76e0ce9200bafa rdf:first sg:person.01242576526.02
149 rdf:rest Nc78c9fa331e74a43bc74a0ab952db5bc
150 N1ea6f6a64a124023bd9b2d8f0fdbe90c rdf:first sg:person.01160541054.33
151 rdf:rest Ne67976e518fd49958bcfa56dbfde004b
152 N23858049eb6841838e1aba5047366e3b schema:name doi
153 schema:value 10.1186/1471-2164-15-170
154 rdf:type schema:PropertyValue
155 N25c94482eadd47d4aa453f842f8b88d7 rdf:first sg:person.01226157015.13
156 rdf:rest Naf5b6a6ef1fd44c381435e4276f1a8b5
157 N320664642c1a4f6da234119880b0ba7f rdf:first sg:person.0627060310.50
158 rdf:rest Nb9c7de89d6c14233be28b5b7dca5dad3
159 N34d6037391bd49dba5b220e3842e7df0 rdf:first sg:person.0750360565.04
160 rdf:rest N810a47e378164672868c2b73dda9a127
161 N403c627a244144e583692aefe1012aa8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
162 schema:name Gene Order
163 rdf:type schema:DefinedTerm
164 N441f37c7514342b4a99f9a724da9d865 rdf:first sg:person.01126521167.34
165 rdf:rest Nf1619e73d3de4c4dbda93793385e396e
166 N4af54324ca08498f9891542a6ab2d0a9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
167 schema:name High-Throughput Nucleotide Sequencing
168 rdf:type schema:DefinedTerm
169 N5140c945b9a648249634f7f8a1a20970 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
170 schema:name Bifidobacterium
171 rdf:type schema:DefinedTerm
172 N5545e7fef8be4745a993153e0796a5d0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
173 schema:name Phylogeny
174 rdf:type schema:DefinedTerm
175 N6a49de5495014217b6dd30b96259553d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
176 schema:name Molecular Sequence Data
177 rdf:type schema:DefinedTerm
178 N7785e16ce51343a4834ceba4f33da0b4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
179 schema:name Carbohydrate Metabolism
180 rdf:type schema:DefinedTerm
181 N7977a4dcbcb040e48afe05cfbc38f1c0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
182 schema:name DNA Transposable Elements
183 rdf:type schema:DefinedTerm
184 N810a47e378164672868c2b73dda9a127 rdf:first sg:person.01024643735.40
185 rdf:rest N185f0a37bf0647a38a76e0ce9200bafa
186 N851fd47c5a784980be83f4c3410d9d86 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
187 schema:name Genomics
188 rdf:type schema:DefinedTerm
189 Na147fa3ee239425dad69153d9cb13f32 rdf:first sg:person.01310212310.93
190 rdf:rest rdf:nil
191 Na96d923c163d4ceabaca0c917fd5a6c9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
192 schema:name Cluster Analysis
193 rdf:type schema:DefinedTerm
194 Naf5b6a6ef1fd44c381435e4276f1a8b5 rdf:first sg:person.01347473767.06
195 rdf:rest N441f37c7514342b4a99f9a724da9d865
196 Nb28343dc916841189c216c6c9a56bb6b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
197 schema:name Genome, Bacterial
198 rdf:type schema:DefinedTerm
199 Nb7bd436978eb471e9c85b0c698f4fecc schema:issueNumber 1
200 rdf:type schema:PublicationIssue
201 Nb9c7de89d6c14233be28b5b7dca5dad3 rdf:first sg:person.01050617006.18
202 rdf:rest Ne212bbc23ccd4991bad854db06d91e18
203 Nbde8c7550f9f4a639b5f6e3d79305c04 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
204 schema:name Genetic Variation
205 rdf:type schema:DefinedTerm
206 Nbebd718d25054d9681d6a663ba35b0e6 schema:name Springer Nature - SN SciGraph project
207 rdf:type schema:Organization
208 Nc6677dddb516462087bd676ed546f5ee schema:name pubmed_id
209 schema:value 24581150
210 rdf:type schema:PropertyValue
211 Nc78c9fa331e74a43bc74a0ab952db5bc rdf:first sg:person.0775502015.36
212 rdf:rest N1ea6f6a64a124023bd9b2d8f0fdbe90c
213 Ne212bbc23ccd4991bad854db06d91e18 rdf:first sg:person.0743306710.38
214 rdf:rest N25c94482eadd47d4aa453f842f8b88d7
215 Ne67976e518fd49958bcfa56dbfde004b rdf:first sg:person.01347407206.63
216 rdf:rest N320664642c1a4f6da234119880b0ba7f
217 Nee71b81f77c34ae2ad764ae508c67ca8 schema:name dimensions_id
218 schema:value pub.1014252423
219 rdf:type schema:PropertyValue
220 Nefe1064df03e4b56b2601e25618c2261 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
221 schema:name Metabolome
222 rdf:type schema:DefinedTerm
223 Nf1619e73d3de4c4dbda93793385e396e rdf:first sg:person.01356325510.28
224 rdf:rest Na147fa3ee239425dad69153d9cb13f32
225 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
226 schema:name Biological Sciences
227 rdf:type schema:DefinedTerm
228 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
229 schema:name Genetics
230 rdf:type schema:DefinedTerm
231 sg:grant.3982843 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2164-15-170
232 rdf:type schema:MonetaryGrant
233 sg:grant.3983930 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2164-15-170
234 rdf:type schema:MonetaryGrant
235 sg:grant.3984108 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2164-15-170
236 rdf:type schema:MonetaryGrant
237 sg:journal.1023790 schema:issn 1471-2164
238 schema:name BMC Genomics
239 schema:publisher Springer Nature
240 rdf:type schema:Periodical
241 sg:person.01024643735.40 schema:affiliation grid-institutes:grid.7872.a
242 schema:familyName Motherway
243 schema:givenName Mary O’Connell
244 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01024643735.40
245 rdf:type schema:Person
246 sg:person.01050617006.18 schema:affiliation grid-institutes:grid.7872.a
247 schema:familyName Turroni
248 schema:givenName Francesca
249 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01050617006.18
250 rdf:type schema:Person
251 sg:person.01126521167.34 schema:affiliation grid-institutes:grid.6582.9
252 schema:familyName Riedel
253 schema:givenName Christian
254 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01126521167.34
255 rdf:type schema:Person
256 sg:person.01160541054.33 schema:affiliation grid-institutes:grid.10383.39
257 schema:familyName Serafini
258 schema:givenName Fausta
259 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01160541054.33
260 rdf:type schema:Person
261 sg:person.01226157015.13 schema:affiliation grid-institutes:grid.10417.33
262 schema:familyName Zomer
263 schema:givenName Aldert
264 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01226157015.13
265 rdf:type schema:Person
266 sg:person.01242576526.02 schema:affiliation grid-institutes:grid.452682.f
267 schema:familyName Kuczynski
268 schema:givenName Justin
269 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01242576526.02
270 rdf:type schema:Person
271 sg:person.01310212310.93 schema:affiliation grid-institutes:grid.7872.a
272 schema:familyName van Sinderen
273 schema:givenName Douwe
274 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01310212310.93
275 rdf:type schema:Person
276 sg:person.01347407206.63 schema:affiliation grid-institutes:grid.10383.39
277 schema:familyName Duranti
278 schema:givenName Sabrina
279 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01347407206.63
280 rdf:type schema:Person
281 sg:person.01347473767.06 schema:affiliation grid-institutes:grid.6582.9
282 schema:familyName Zhurina
283 schema:givenName Daria
284 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01347473767.06
285 rdf:type schema:Person
286 sg:person.01356325510.28 schema:affiliation grid-institutes:grid.10383.39
287 schema:familyName Ventura
288 schema:givenName Marco
289 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01356325510.28
290 rdf:type schema:Person
291 sg:person.0627060310.50 schema:affiliation grid-institutes:grid.10383.39
292 schema:familyName Milani
293 schema:givenName Christian
294 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0627060310.50
295 rdf:type schema:Person
296 sg:person.0743306710.38 schema:affiliation grid-institutes:grid.10383.39
297 schema:familyName Lugli
298 schema:givenName Gabriele Andrea
299 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0743306710.38
300 rdf:type schema:Person
301 sg:person.0750360565.04 schema:affiliation grid-institutes:grid.7872.a
302 schema:familyName Bottacini
303 schema:givenName Francesca
304 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0750360565.04
305 rdf:type schema:Person
306 sg:person.0775502015.36 schema:affiliation grid-institutes:grid.7872.a
307 schema:familyName O’Connell
308 schema:givenName Kerry Joan
309 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0775502015.36
310 rdf:type schema:Person
311 sg:pub.10.1007/978-1-61779-603-6_5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014239867
312 https://doi.org/10.1007/978-1-61779-603-6_5
313 rdf:type schema:CreativeWork
314 sg:pub.10.1007/s00018-013-1318-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032404552
315 https://doi.org/10.1007/s00018-013-1318-0
316 rdf:type schema:CreativeWork
317 sg:pub.10.1038/nrmicro2047 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024437688
318 https://doi.org/10.1038/nrmicro2047
319 rdf:type schema:CreativeWork
320 sg:pub.10.1186/1475-2859-10-s1-s16 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037912010
321 https://doi.org/10.1186/1475-2859-10-s1-s16
322 rdf:type schema:CreativeWork
323 sg:pub.10.1186/gb-2004-5-2-r12 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022585853
324 https://doi.org/10.1186/gb-2004-5-2-r12
325 rdf:type schema:CreativeWork
326 grid-institutes:grid.10383.39 schema:alternateName Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
327 schema:name Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
328 rdf:type schema:Organization
329 grid-institutes:grid.10417.33 schema:alternateName Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
330 schema:name Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
331 rdf:type schema:Organization
332 grid-institutes:grid.452682.f schema:alternateName Second Genome, Bioinformatics Department, San Bruno, CA USA
333 schema:name Second Genome, Bioinformatics Department, San Bruno, CA USA
334 rdf:type schema:Organization
335 grid-institutes:grid.6582.9 schema:alternateName Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
336 schema:name Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
337 rdf:type schema:Organization
338 grid-institutes:grid.7872.a schema:alternateName Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland
339 schema:name Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland
340 rdf:type schema:Organization
 




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


...