Heterogeneity of the gut microbiome in mice: guidelines for optimizing experimental design
Identifieur interne : 000067 ( Pmc/Curation ); précédent : 000066; suivant : 000068Heterogeneity of the gut microbiome in mice: guidelines for optimizing experimental design
Auteurs : Debby Laukens [Belgique] ; Brigitta M. Brinkman [Belgique] ; Jeroen Raes [Belgique] ; Martine De Vos [Belgique] ; Peter Vandenabeele [Belgique]Source :
- FEMS Microbiology Reviews [ 0168-6445 ] ; 2015.
Abstract
Targeted manipulation of the gut flora is increasingly being recognized as a means to improve human health. Yet, the temporal dynamics and intra- and interindividual heterogeneity of the microbiome represent experimental limitations, especially in human cross-sectional studies. Therefore, rodent models represent an invaluable tool to study the host–microbiota interface. Progress in technical and computational tools to investigate the composition and function of the microbiome has opened a new era of research and we gradually begin to understand the parameters that influence variation of host-associated microbial communities. To isolate true effects from confounding factors, it is essential to include such parameters in model intervention studies. Also, explicit journal instructions to include essential information on animal experiments are mandatory. The purpose of this review is to summarize the factors that influence microbiota composition in mice and to provide guidelines to improve the reproducibility of animal experiments.
Url:
DOI: 10.1093/femsre/fuv036
PubMed: 26323480
PubMed Central: 4703068
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Brinkman</name><affiliation wicri:level="1"><nlm:aff id="aff2">Inflammation Research Center, VIB, B-9052 Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Inflammation Research Center, VIB, B-9052 Ghent</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3">Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent</wicri:regionArea></affiliation></author><author><name sortKey="Raes, Jeroen" sort="Raes, Jeroen" uniqKey="Raes J" first="Jeroen" last="Raes">Jeroen Raes</name><affiliation wicri:level="1"><nlm:aff id="aff4">Center for the Biology of Disease, VIB, B-3000 Leuven, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Center for the Biology of Disease, VIB, B-3000 Leuven</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff5">Department Microbiology and Immunology, KU Leuven, B-3000 Leuven, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department Microbiology and Immunology, KU Leuven, B-3000 Leuven</wicri:regionArea></affiliation></author><author><name sortKey="De Vos, Martine" sort="De Vos, Martine" uniqKey="De Vos M" first="Martine" last="De Vos">Martine De Vos</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Gastroenterology, Ghent University, B-9000 Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Gastroenterology, Ghent University, B-9000 Ghent</wicri:regionArea></affiliation></author><author><name sortKey="Vandenabeele, Peter" sort="Vandenabeele, Peter" uniqKey="Vandenabeele P" first="Peter" last="Vandenabeele">Peter Vandenabeele</name><affiliation wicri:level="1"><nlm:aff id="aff2">Inflammation Research Center, VIB, B-9052 Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Inflammation Research Center, VIB, B-9052 Ghent</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3">Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff6">Methusalem Program, Ghent University, B-9000 Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Methusalem Program, Ghent University, B-9000 Ghent</wicri:regionArea></affiliation></author></analytic><series><title level="j">FEMS Microbiology Reviews</title><idno type="ISSN">0168-6445</idno><idno type="eISSN">1574-6976</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Targeted manipulation of the gut flora is increasingly being recognized as a means to improve human health. Yet, the temporal dynamics and intra- and interindividual heterogeneity of the microbiome represent experimental limitations, especially in human cross-sectional studies. Therefore, rodent models represent an invaluable tool to study the host–microbiota interface. Progress in technical and computational tools to investigate the composition and function of the microbiome has opened a new era of research and we gradually begin to understand the parameters that influence variation of host-associated microbial communities. To isolate true effects from confounding factors, it is essential to include such parameters in model intervention studies. Also, explicit journal instructions to include essential information on animal experiments are mandatory. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">FEMS Microbiol Rev</journal-id><journal-id journal-id-type="iso-abbrev">FEMS Microbiol. Rev</journal-id><journal-id journal-id-type="hwp">femsre</journal-id><journal-id journal-id-type="publisher-id">femsre</journal-id><journal-title-group><journal-title>FEMS Microbiology Reviews</journal-title></journal-title-group><issn pub-type="ppub">0168-6445</issn><issn pub-type="epub">1574-6976</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">26323480</article-id><article-id pub-id-type="pmc">4703068</article-id><article-id pub-id-type="doi">10.1093/femsre/fuv036</article-id><article-categories><subj-group subj-group-type="heading"><subject>Review Article</subject></subj-group></article-categories><title-group><article-title>Heterogeneity of the gut microbiome in mice: guidelines for optimizing experimental design</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Laukens</surname><given-names>Debby</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="corresp" rid="cor2"><sup>†</sup></xref></contrib><contrib contrib-type="author"><name><surname>Brinkman</surname><given-names>Brigitta M.</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="aff" rid="aff3"><sup>3</sup></xref><xref ref-type="corresp" rid="cor2"><sup>†</sup></xref></contrib><contrib contrib-type="author"><name><surname>Raes</surname><given-names>Jeroen</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref><xref ref-type="aff" rid="aff5"><sup>5</sup></xref></contrib><contrib contrib-type="author"><name><surname>De Vos</surname><given-names>Martine</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Vandenabeele</surname><given-names>Peter</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="aff" rid="aff3"><sup>3</sup></xref><xref ref-type="aff" rid="aff6"><sup>6</sup></xref><xref ref-type="corresp" rid="cor1">*</xref></contrib><aff id="aff1"><label>1</label>Department of Gastroenterology, Ghent University, B-9000 Ghent, Belgium</aff><aff id="aff2"><label>2</label>Inflammation Research Center, VIB, B-9052 Ghent, Belgium</aff><aff id="aff3"><label>3</label>Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium</aff><aff id="aff4"><label>4</label>Center for the Biology of Disease, VIB, B-3000 Leuven, Belgium</aff><aff id="aff5"><label>5</label>Department Microbiology and Immunology, KU Leuven, B-3000 Leuven, Belgium</aff><aff id="aff6"><label>6</label>Methusalem Program, Ghent University, B-9000 Ghent, Belgium</aff></contrib-group><contrib-group><contrib contrib-type="editor"><name><surname>Normark</surname><given-names>Birgitta Henriques</given-names></name></contrib></contrib-group><author-notes><corresp id="cor1"><label>*</label><bold>Corresponding author:</bold> Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium. Tel: +32(0)93313710; E-mail: <email>Peter.Vandenabeele@irc.vib-ugent.be</email></corresp><corresp id="cor2"><label>†</label>Equal contribution.</corresp></author-notes><pub-date pub-type="epub"><day>30</day><month>8</month><year>2015</year></pub-date><pub-date pub-type="ppub"><month>1</month><year>2016</year></pub-date><pub-date pub-type="pmc-release"><day>30</day><month>8</month><year>2015</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>40</volume><issue>1</issue><fpage>117</fpage><lpage>132</lpage><history><date date-type="accepted"><day>30</day><month>6</month><year>2015</year></date><date date-type="rev-recd"><day>05</day><month>2</month><year>2015</year></date></history><permissions><copyright-statement>© FEMS 2015.</copyright-statement><copyright-year>2015</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc-nd/4.0/"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc-nd/4.0/">http://creativecommons.org/licenses/by-nc-nd/4.0/</ext-link>), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work is properly cited. For commercial re-use, please contact <email>journals.permissions@oup.com</email></license-p></license></permissions><self-uri xlink:title="pdf" xlink:href="fuv036.pdf"></self-uri><abstract><p>Targeted manipulation of the gut flora is increasingly being recognized as a means to improve human health. Yet, the temporal dynamics and intra- and interindividual heterogeneity of the microbiome represent experimental limitations, especially in human cross-sectional studies. Therefore, rodent models represent an invaluable tool to study the host–microbiota interface. Progress in technical and computational tools to investigate the composition and function of the microbiome has opened a new era of research and we gradually begin to understand the parameters that influence variation of host-associated microbial communities. To isolate true effects from confounding factors, it is essential to include such parameters in model intervention studies. Also, explicit journal instructions to include essential information on animal experiments are mandatory. The purpose of this review is to summarize the factors that influence microbiota composition in mice and to provide guidelines to improve the reproducibility of animal experiments.</p></abstract><abstract abstract-type="precis"><p>Given the unmet need for standardizing the experimental work flow related to gut microbial research in animals, guidelines are required to isolate true effects from confounding factors.</p></abstract><abstract abstract-type="graphical"><p><fig id="fig1g" fig-type="featured" orientation="portrait" position="float"><label>Graphical Abstract Figure.</label><caption><p>Given the unmet need for standardizing the experimental work flow related to gut microbial research in animals, guidelines are required to isolate true effects from confounding factors.</p></caption><graphic xlink:href="fuv036fig1g"></graphic></fig></p></abstract><kwd-group><kwd>microbiota</kwd><kwd>confounding factors</kwd><kwd>animal facility</kwd><kwd>animal models</kwd><kwd>microbiome</kwd></kwd-group><counts><page-count count="16"></page-count></counts><custom-meta-group><custom-meta><meta-name>cover-date</meta-name><meta-value>January 2016</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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