Alterations in Ileal Mucosa Bacteria Related to Diet Complexity and Growth Performance in Young Pigs
Identifieur interne : 001241 ( Ncbi/Merge ); précédent : 001240; suivant : 001242Alterations in Ileal Mucosa Bacteria Related to Diet Complexity and Growth Performance in Young Pigs
Auteurs : Crystal L. Levesque [États-Unis] ; Seema Hooda [Canada, États-Unis] ; Kelly S. Swanson [États-Unis] ; Kees De Lange [Canada]Source :
- PLoS ONE [ 1932-6203 ] ; 2014.
Abstract
Evaluation of the prolonged impact of weaning diet on ileal mucosa bacteria and during periods of reduced and improved growth was conducted using 454 pyrosequencing.
Weaned pigs were fed HIGH or LOW complexity diets, with or without antibiotics, for 6 weeks, followed by a common grower diet. Pigs were killed at 2 (n = 4 or 5) and 8 (n = 6) weeks post-weaning (periods of reduced and improved growth, respectively). Mucosal bacteria were removed; DNA was extracted and amplified using the V1–V3 region of the 16S rRNA gene. Mucosal bacteria clustered more closely by week post-weaning than diet but 44% of bacterial species did not change from week 2 to 8. There was no effect of diet complexity or antibiotic inclusion on indices of bacterial diversity. Firmicutes made up 91 and 96% of total reads at week 2 and 8, respectively. The proportion of
Shifts in mucosal bacteria populations may be related to dietary induced changes in growth performance during reduced and improved growth but further studies are required to confirm causative relationship. Weaning diet results in species specific prolonged alterations in mucosal bacteria, particularly where high levels of in-feed antibiotics are used. A considerable portion of ileal mucosal bacteria colonize early and remain stable over time despite changes in diet.
Url:
DOI: 10.1371/journal.pone.0108472
PubMed: 25247930
PubMed Central: 4172762
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Levesque</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Animal Science, South Dakota State University, Brookings, South Dakota, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Animal Science, South Dakota State University, Brookings, South Dakota</wicri:regionArea><placeName><region type="state">Dakota du Sud</region></placeName></affiliation></author><author><name sortKey="Hooda, Seema" sort="Hooda, Seema" uniqKey="Hooda S" first="Seema" last="Hooda">Seema Hooda</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario, Canada</addr-line></nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario</wicri:regionArea><wicri:noRegion>Ontario</wicri:noRegion></affiliation><affiliation wicri:level="2"><nlm:aff id="aff3"><addr-line>Department of Animal Sciences, University of Illinois-Urbana Champaign, Urbana, Illinois, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Animal Sciences, University of Illinois-Urbana Champaign, Urbana, Illinois</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation></author><author><name sortKey="Swanson, Kelly S" sort="Swanson, Kelly S" uniqKey="Swanson K" first="Kelly S." last="Swanson">Kelly S. 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Levesque</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Animal Science, South Dakota State University, Brookings, South Dakota, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Animal Science, South Dakota State University, Brookings, South Dakota</wicri:regionArea><placeName><region type="state">Dakota du Sud</region></placeName></affiliation></author><author><name sortKey="Hooda, Seema" sort="Hooda, Seema" uniqKey="Hooda S" first="Seema" last="Hooda">Seema Hooda</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario, Canada</addr-line></nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario</wicri:regionArea><wicri:noRegion>Ontario</wicri:noRegion></affiliation><affiliation wicri:level="2"><nlm:aff id="aff3"><addr-line>Department of Animal Sciences, University of Illinois-Urbana Champaign, Urbana, Illinois, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Animal Sciences, University of Illinois-Urbana Champaign, Urbana, Illinois</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation></author><author><name sortKey="Swanson, Kelly S" sort="Swanson, Kelly S" uniqKey="Swanson K" first="Kelly S." last="Swanson">Kelly S. Swanson</name><affiliation wicri:level="2"><nlm:aff id="aff3"><addr-line>Department of Animal Sciences, University of Illinois-Urbana Champaign, Urbana, Illinois, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Animal Sciences, University of Illinois-Urbana Champaign, Urbana, Illinois</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation></author><author><name sortKey="De Lange, Kees" sort="De Lange, Kees" uniqKey="De Lange K" first="Kees" last="De Lange">Kees De Lange</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario, Canada</addr-line></nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario</wicri:regionArea><wicri:noRegion>Ontario</wicri:noRegion></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Evaluation of the prolonged impact of weaning diet on ileal mucosa bacteria and during periods of reduced and improved growth was conducted using 454 pyrosequencing.</p></sec><sec><title>Methodology/Principal Findings</title><p>Weaned pigs were fed HIGH or LOW complexity diets, with or without antibiotics, for 6 weeks, followed by a common grower diet. Pigs were killed at 2 (n = 4 or 5) and 8 (n = 6) weeks post-weaning (periods of reduced and improved growth, respectively). Mucosal bacteria were removed; DNA was extracted and amplified using the V1–V3 region of the 16S rRNA gene. Mucosal bacteria clustered more closely by week post-weaning than diet but 44% of bacterial species did not change from week 2 to 8. There was no effect of diet complexity or antibiotic inclusion on indices of bacterial diversity. Firmicutes made up 91 and 96% of total reads at week 2 and 8, respectively. The proportion of <italic>Clostridium paraputrificum</italic> increased (<italic>P</italic> = 0.003) from week 2 to 8 in pigs fed LOW but didn’t change in pigs fed HIGH; whereas <italic>Clostridium leptum</italic> decreased (<italic>P</italic> = 0.02) from week 2 to 8 in pigs fed LOW but didn’t change in pigs fed HIGH. The proportion of <italic>Sarcina</italic> genus was 3-fold higher in pigs fed A+ compared to A− at week 2 and 5-fold higher at week 8 despite the lack of in-feed antibiotics at that time.</p></sec><sec><title>Conclusions/Significance</title><p>Shifts in mucosal bacteria populations may be related to dietary induced changes in growth performance during reduced and improved growth but further studies are required to confirm causative relationship. Weaning diet results in species specific prolonged alterations in mucosal bacteria, particularly where high levels of in-feed antibiotics are used. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25247930</article-id><article-id pub-id-type="pmc">4172762</article-id><article-id pub-id-type="publisher-id">PONE-D-14-23796</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0108472</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Biology and Life Sciences</subject><subj-group><subject>Agriculture</subject><subj-group><subject>Animal Management</subject><subj-group><subject>Animal Performance</subject><subject>Animal Production</subject></subj-group></subj-group><subj-group><subject>Livestock</subject><subj-group><subject>Swine</subject></subj-group></subj-group><subj-group><subject>Agricultural Production</subject></subj-group></subj-group><subj-group><subject>Ecology</subject><subj-group><subject>Microbial Ecology</subject><subj-group><subject>Microbiome</subject></subj-group></subj-group></subj-group><subj-group><subject>Genetics</subject><subj-group><subject>Genomics</subject><subj-group><subject>Microbial Genomics</subject></subj-group></subj-group></subj-group><subj-group><subject>Microbiology</subject></subj-group><subj-group><subject>Nutrition</subject></subj-group></subj-group></article-categories><title-group><article-title>Alterations in Ileal Mucosa Bacteria Related to Diet Complexity and Growth Performance in Young Pigs</article-title><alt-title alt-title-type="running-head">Diet Complexity and Mucosal Bacteria in Pigs</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Levesque</surname><given-names>Crystal L.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Hooda</surname><given-names>Seema</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Swanson</surname><given-names>Kelly S.</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>de Lange</surname><given-names>Kees</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>Department of Animal Science, South Dakota State University, Brookings, South Dakota, United States of America</addr-line></aff><aff id="aff2"><label>2</label><addr-line>Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario, Canada</addr-line></aff><aff id="aff3"><label>3</label><addr-line>Department of Animal Sciences, University of Illinois-Urbana Champaign, Urbana, Illinois, United States of America</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Manganelli</surname><given-names>Riccardo</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>University of Padova, Medical School, Italy</addr-line></aff><author-notes><corresp id="cor1">* E-mail: <email>cdelange@uoguelph.ca</email></corresp><fn fn-type="conflict"><p><bold>Competing Interests: </bold>KDL and CLL acknowledge partial funding of the project by Ontario Pork, Swine Innovation Porc, and the Ontario Ministry of Agriculture, Food and Rural Affairs. The funding agencies were not involved in study design, data collection, analysis or interpretation, writing of the paper, or submission decisions and this does not alter the authors' adherence to PLOS ONE policies on sharing data and materials.</p></fn><fn fn-type="con"><p>Conceived and designed the experiments: CLL KDL. Performed the experiments: CLL. Analyzed the data: CLL SH. Contributed reagents/materials/analysis tools: KS. Contributed to the writing of the manuscript: CLL SH KS KDL.</p></fn></author-notes><pub-date pub-type="collection"><year>2014</year></pub-date><pub-date pub-type="epub"><day>23</day><month>9</month><year>2014</year></pub-date><volume>9</volume><issue>9</issue><elocation-id>e108472</elocation-id><history><date date-type="received"><day>28</day><month>5</month><year>2014</year></date><date date-type="accepted"><day>29</day><month>8</month><year>2014</year></date></history><permissions><copyright-year>2014</copyright-year><copyright-holder>Levesque et al</copyright-holder><license><license-p>This is an open-access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p></license></permissions><abstract><sec><title>Background</title><p>Evaluation of the prolonged impact of weaning diet on ileal mucosa bacteria and during periods of reduced and improved growth was conducted using 454 pyrosequencing.</p></sec><sec><title>Methodology/Principal Findings</title><p>Weaned pigs were fed HIGH or LOW complexity diets, with or without antibiotics, for 6 weeks, followed by a common grower diet. Pigs were killed at 2 (n = 4 or 5) and 8 (n = 6) weeks post-weaning (periods of reduced and improved growth, respectively). Mucosal bacteria were removed; DNA was extracted and amplified using the V1–V3 region of the 16S rRNA gene. Mucosal bacteria clustered more closely by week post-weaning than diet but 44% of bacterial species did not change from week 2 to 8. There was no effect of diet complexity or antibiotic inclusion on indices of bacterial diversity. Firmicutes made up 91 and 96% of total reads at week 2 and 8, respectively. The proportion of <italic>Clostridium paraputrificum</italic> increased (<italic>P</italic> = 0.003) from week 2 to 8 in pigs fed LOW but didn’t change in pigs fed HIGH; whereas <italic>Clostridium leptum</italic> decreased (<italic>P</italic> = 0.02) from week 2 to 8 in pigs fed LOW but didn’t change in pigs fed HIGH. The proportion of <italic>Sarcina</italic> genus was 3-fold higher in pigs fed A+ compared to A− at week 2 and 5-fold higher at week 8 despite the lack of in-feed antibiotics at that time.</p></sec><sec><title>Conclusions/Significance</title><p>Shifts in mucosal bacteria populations may be related to dietary induced changes in growth performance during reduced and improved growth but further studies are required to confirm causative relationship. Weaning diet results in species specific prolonged alterations in mucosal bacteria, particularly where high levels of in-feed antibiotics are used. A considerable portion of ileal mucosal bacteria colonize early and remain stable over time despite changes in diet.</p></sec></abstract><funding-group><funding-statement>Swine Innovation Porc, Ontario Ministry of Agricultural, Food and Rural Affairs, and Ontario Pork provided partial funding for this project. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement></funding-group><counts><page-count count="14"></page-count></counts><custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name><meta-value>The authors confirm that all data underlying the findings are fully available without restriction. All raw sequence data are available at the NCBI sequence read archive (<ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/Traces/sra/">http://www.ncbi.nlm.nih.gov/Traces/sra/</ext-link>) under accession numbers SAMN03003724 to SAMN03003767.</meta-value></custom-meta></custom-meta-group></article-meta><notes><title>Data Availability</title><p>The authors confirm that all data underlying the findings are fully available without restriction. All raw sequence data are available at the NCBI sequence read archive (<ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/Traces/sra/">http://www.ncbi.nlm.nih.gov/Traces/sra/</ext-link>) under accession numbers SAMN03003724 to SAMN03003767.</p></notes></front></pmc><affiliations><list><country><li>Canada</li><li>États-Unis</li></country><region><li>Dakota du Sud</li><li>Illinois</li></region></list><tree><country name="États-Unis"><region name="Dakota du Sud"><name sortKey="Levesque, Crystal L" sort="Levesque, Crystal L" uniqKey="Levesque C" first="Crystal L." last="Levesque">Crystal L. Levesque</name></region><name sortKey="Hooda, Seema" sort="Hooda, Seema" uniqKey="Hooda S" first="Seema" last="Hooda">Seema Hooda</name><name sortKey="Swanson, Kelly S" sort="Swanson, Kelly S" uniqKey="Swanson K" first="Kelly S." last="Swanson">Kelly S. Swanson</name></country><country name="Canada"><noRegion><name sortKey="Hooda, Seema" sort="Hooda, Seema" uniqKey="Hooda S" first="Seema" last="Hooda">Seema Hooda</name></noRegion><name sortKey="De Lange, Kees" sort="De Lange, Kees" uniqKey="De Lange K" first="Kees" last="De Lange">Kees De Lange</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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