Microbiome profiling of commercial pigs from farrow to finish
Abstract Balanced bacterial communities within the gastrointestinal (GI) tract of animals are a key component of gut health, resulting in optimal performance and the prevention of disease. The purpose of this study was to characterize the commercial pig’s baseline bacterial microbiome over time and...
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| Veröffentlicht in: | Journal of animal science 2018-05, Vol.96 (5), p.1778-1794 |
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| creator | De Rodas, Brenda Youmans, Bonnie P Danzeisen, Jessica L Tran, Huyen Johnson, Timothy J |
| description | Abstract
Balanced bacterial communities within the gastrointestinal (GI) tract of animals are a key component of gut health, resulting in optimal performance and the prevention of disease. The purpose of this study was to characterize the commercial pig’s baseline bacterial microbiome over time and across anatomical site. Several anatomical sites (duodenum/jejunum, ileum, cecum, and colon) were examined across multiple ages (days 0, 10, 21, 33, 62, 84, and market) for bacterial microbiome structure using 16S rRNA V4 region sequencing with Illumina MiSeq. General trends in the succession of the bacterial microbiome were observed over age, such as increasing populations of Clostridia and decreasing populations of Gammaproteobacteria (P < 0.05). However, apparent disruptions in the microbiome were also observed that did not follow these trends, specifically at sampling 24 h post-weaning where Lactobacillaceae were drastically reduced in relative abundance (P < 0.05). The introduction of solid feed between days 21 and 33 had the greatest overall impact on bacterial community structure as compared with the effects of age, changes in solid feed type, and pig movement. A core bacterial microbiome was identified across all anatomical sites consisting of the dominant operational taxonomic units (OTUs); samples were only differentiated based upon anatomical site when considering less abundant OTUs and differences in relative abundance. When considering mucosal vs. digesta samples from the cecum and ileum, several taxa were of significantly higher relative abundance in the mucosa (P < 0.05), including Anaerovibrio, Bacteroides, Desulfovibrio, Helicobacter, Oscillospira, Phascolarctobacterium, and Prevotella. Correlations between several genus-level taxa and pig weight were observed. Overall, this study provides an expanded view of the dynamic pig GI microbiome from farrow to finish. |
| doi_str_mv | 10.1093/jas/sky109 |
| format | Article |
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Balanced bacterial communities within the gastrointestinal (GI) tract of animals are a key component of gut health, resulting in optimal performance and the prevention of disease. The purpose of this study was to characterize the commercial pig’s baseline bacterial microbiome over time and across anatomical site. Several anatomical sites (duodenum/jejunum, ileum, cecum, and colon) were examined across multiple ages (days 0, 10, 21, 33, 62, 84, and market) for bacterial microbiome structure using 16S rRNA V4 region sequencing with Illumina MiSeq. General trends in the succession of the bacterial microbiome were observed over age, such as increasing populations of Clostridia and decreasing populations of Gammaproteobacteria (P < 0.05). However, apparent disruptions in the microbiome were also observed that did not follow these trends, specifically at sampling 24 h post-weaning where Lactobacillaceae were drastically reduced in relative abundance (P < 0.05). The introduction of solid feed between days 21 and 33 had the greatest overall impact on bacterial community structure as compared with the effects of age, changes in solid feed type, and pig movement. A core bacterial microbiome was identified across all anatomical sites consisting of the dominant operational taxonomic units (OTUs); samples were only differentiated based upon anatomical site when considering less abundant OTUs and differences in relative abundance. When considering mucosal vs. digesta samples from the cecum and ileum, several taxa were of significantly higher relative abundance in the mucosa (P < 0.05), including Anaerovibrio, Bacteroides, Desulfovibrio, Helicobacter, Oscillospira, Phascolarctobacterium, and Prevotella. Correlations between several genus-level taxa and pig weight were observed. Overall, this study provides an expanded view of the dynamic pig GI microbiome from farrow to finish.</description><identifier>ISSN: 0021-8812</identifier><identifier>EISSN: 1525-3163</identifier><identifier>DOI: 10.1093/jas/sky109</identifier><identifier>PMID: 29635455</identifier><language>eng</language><publisher>US: Oxford University Press</publisher><subject>Abundance ; Age factors ; Animals ; Bacteria ; Bacteria - classification ; Bacteria - genetics ; Bacteria - isolation & purification ; Cecum ; Colon ; Community structure ; Digestive system ; Duodenum ; Female ; Gastrointestinal Microbiome ; Gastrointestinal tract ; Gastrointestinal Tract - microbiology ; Hogs ; Ileum ; Intensive farming ; Jejunum ; Male ; Microbiology ; Microbiomes ; Microbiota ; Mucosa ; Populations ; Relative abundance ; RNA, Ribosomal, 16S - genetics ; rRNA 16S ; Swine ; Swine - microbiology ; Taxa ; Trends ; Weaning</subject><ispartof>Journal of animal science, 2018-05, Vol.96 (5), p.1778-1794</ispartof><rights>The Author(s) 2018. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. 2018</rights><rights>Copyright Oxford University Press, UK May 2018</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c436t-57979f7aa85fbf2a7a9e3f94e0fc772403609e1fcbb724010b2f4a119af8e27e3</citedby><cites>FETCH-LOGICAL-c436t-57979f7aa85fbf2a7a9e3f94e0fc772403609e1fcbb724010b2f4a119af8e27e3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6140882/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6140882/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,723,776,780,881,1578,27903,27904,53769,53771</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29635455$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>De Rodas, Brenda</creatorcontrib><creatorcontrib>Youmans, Bonnie P</creatorcontrib><creatorcontrib>Danzeisen, Jessica L</creatorcontrib><creatorcontrib>Tran, Huyen</creatorcontrib><creatorcontrib>Johnson, Timothy J</creatorcontrib><title>Microbiome profiling of commercial pigs from farrow to finish</title><title>Journal of animal science</title><addtitle>J Anim Sci</addtitle><description>Abstract
Balanced bacterial communities within the gastrointestinal (GI) tract of animals are a key component of gut health, resulting in optimal performance and the prevention of disease. The purpose of this study was to characterize the commercial pig’s baseline bacterial microbiome over time and across anatomical site. Several anatomical sites (duodenum/jejunum, ileum, cecum, and colon) were examined across multiple ages (days 0, 10, 21, 33, 62, 84, and market) for bacterial microbiome structure using 16S rRNA V4 region sequencing with Illumina MiSeq. General trends in the succession of the bacterial microbiome were observed over age, such as increasing populations of Clostridia and decreasing populations of Gammaproteobacteria (P < 0.05). However, apparent disruptions in the microbiome were also observed that did not follow these trends, specifically at sampling 24 h post-weaning where Lactobacillaceae were drastically reduced in relative abundance (P < 0.05). The introduction of solid feed between days 21 and 33 had the greatest overall impact on bacterial community structure as compared with the effects of age, changes in solid feed type, and pig movement. A core bacterial microbiome was identified across all anatomical sites consisting of the dominant operational taxonomic units (OTUs); samples were only differentiated based upon anatomical site when considering less abundant OTUs and differences in relative abundance. When considering mucosal vs. digesta samples from the cecum and ileum, several taxa were of significantly higher relative abundance in the mucosa (P < 0.05), including Anaerovibrio, Bacteroides, Desulfovibrio, Helicobacter, Oscillospira, Phascolarctobacterium, and Prevotella. Correlations between several genus-level taxa and pig weight were observed. Overall, this study provides an expanded view of the dynamic pig GI microbiome from farrow to finish.</description><subject>Abundance</subject><subject>Age factors</subject><subject>Animals</subject><subject>Bacteria</subject><subject>Bacteria - classification</subject><subject>Bacteria - genetics</subject><subject>Bacteria - isolation & purification</subject><subject>Cecum</subject><subject>Colon</subject><subject>Community structure</subject><subject>Digestive system</subject><subject>Duodenum</subject><subject>Female</subject><subject>Gastrointestinal Microbiome</subject><subject>Gastrointestinal tract</subject><subject>Gastrointestinal Tract - microbiology</subject><subject>Hogs</subject><subject>Ileum</subject><subject>Intensive farming</subject><subject>Jejunum</subject><subject>Male</subject><subject>Microbiology</subject><subject>Microbiomes</subject><subject>Microbiota</subject><subject>Mucosa</subject><subject>Populations</subject><subject>Relative abundance</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>rRNA 16S</subject><subject>Swine</subject><subject>Swine - microbiology</subject><subject>Taxa</subject><subject>Trends</subject><subject>Weaning</subject><issn>0021-8812</issn><issn>1525-3163</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNp9kctKxDAUhoMoznjZ-AASEEGEOrk0bbNQkMEbjLjRdUhrMpOxbWrSKvP2pnQc1IWrcw7n4z-XH4AjjC4w4nSylH7i31Yh3wJjzAiLKE7oNhgjRHCUZZiMwJ73S4QwYZztghHhCWUxY2Nw-WgKZ3NjKwUbZ7UpTT2HVsPCVpVyhZElbMzcQ-1sBbV0zn7C1kJtauMXB2BHy9Krw3XcBy-3N8_T-2j2dPcwvZ5FRUyTNmIpT7lOpcyYzjWRqeSKah4rpIs0JTGiCeIK6yLP-wqjnOhYYsylzhRJFd0HV4Nu0-WVei1U3TpZisaZSrqVsNKI353aLMTcfogExyjLSBA4Wws4-94p34rK-EKVpayV7bwgqJ-bhAcF9OQPurSdq8N5gYpxmiQM9dT5QIXvee-U3iyDkehdEcEVMbgS4OOf62_QbxsCcDoAtmv-E_oCXLuWCQ</recordid><startdate>20180504</startdate><enddate>20180504</enddate><creator>De Rodas, Brenda</creator><creator>Youmans, Bonnie P</creator><creator>Danzeisen, Jessica L</creator><creator>Tran, Huyen</creator><creator>Johnson, Timothy J</creator><general>Oxford University Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7RQ</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AF</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>M2P</scope><scope>M7P</scope><scope>M7S</scope><scope>MBDVC</scope><scope>PATMY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>Q9U</scope><scope>S0X</scope><scope>U9A</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20180504</creationdate><title>Microbiome profiling of commercial pigs from farrow to finish</title><author>De Rodas, Brenda ; Youmans, Bonnie P ; Danzeisen, Jessica L ; Tran, Huyen ; Johnson, Timothy J</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c436t-57979f7aa85fbf2a7a9e3f94e0fc772403609e1fcbb724010b2f4a119af8e27e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Abundance</topic><topic>Age factors</topic><topic>Animals</topic><topic>Bacteria</topic><topic>Bacteria - classification</topic><topic>Bacteria - genetics</topic><topic>Bacteria - isolation & purification</topic><topic>Cecum</topic><topic>Colon</topic><topic>Community structure</topic><topic>Digestive system</topic><topic>Duodenum</topic><topic>Female</topic><topic>Gastrointestinal Microbiome</topic><topic>Gastrointestinal tract</topic><topic>Gastrointestinal Tract - microbiology</topic><topic>Hogs</topic><topic>Ileum</topic><topic>Intensive farming</topic><topic>Jejunum</topic><topic>Male</topic><topic>Microbiology</topic><topic>Microbiomes</topic><topic>Microbiota</topic><topic>Mucosa</topic><topic>Populations</topic><topic>Relative abundance</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>rRNA 16S</topic><topic>Swine</topic><topic>Swine - microbiology</topic><topic>Taxa</topic><topic>Trends</topic><topic>Weaning</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>De Rodas, Brenda</creatorcontrib><creatorcontrib>Youmans, Bonnie P</creatorcontrib><creatorcontrib>Danzeisen, Jessica L</creatorcontrib><creatorcontrib>Tran, Huyen</creatorcontrib><creatorcontrib>Johnson, Timothy J</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Career & Technical Education Database</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>STEM Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection (ProQuest)</collection><collection>Natural Science Collection (ProQuest)</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Research Library</collection><collection>Science Database (ProQuest)</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Research Library (Corporate)</collection><collection>Environmental Science Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>ProQuest Central Basic</collection><collection>SIRS Editorial</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Journal of animal science</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>De Rodas, Brenda</au><au>Youmans, Bonnie P</au><au>Danzeisen, Jessica L</au><au>Tran, Huyen</au><au>Johnson, Timothy J</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Microbiome profiling of commercial pigs from farrow to finish</atitle><jtitle>Journal of animal science</jtitle><addtitle>J Anim Sci</addtitle><date>2018-05-04</date><risdate>2018</risdate><volume>96</volume><issue>5</issue><spage>1778</spage><epage>1794</epage><pages>1778-1794</pages><issn>0021-8812</issn><eissn>1525-3163</eissn><abstract>Abstract
Balanced bacterial communities within the gastrointestinal (GI) tract of animals are a key component of gut health, resulting in optimal performance and the prevention of disease. The purpose of this study was to characterize the commercial pig’s baseline bacterial microbiome over time and across anatomical site. Several anatomical sites (duodenum/jejunum, ileum, cecum, and colon) were examined across multiple ages (days 0, 10, 21, 33, 62, 84, and market) for bacterial microbiome structure using 16S rRNA V4 region sequencing with Illumina MiSeq. General trends in the succession of the bacterial microbiome were observed over age, such as increasing populations of Clostridia and decreasing populations of Gammaproteobacteria (P < 0.05). However, apparent disruptions in the microbiome were also observed that did not follow these trends, specifically at sampling 24 h post-weaning where Lactobacillaceae were drastically reduced in relative abundance (P < 0.05). The introduction of solid feed between days 21 and 33 had the greatest overall impact on bacterial community structure as compared with the effects of age, changes in solid feed type, and pig movement. A core bacterial microbiome was identified across all anatomical sites consisting of the dominant operational taxonomic units (OTUs); samples were only differentiated based upon anatomical site when considering less abundant OTUs and differences in relative abundance. When considering mucosal vs. digesta samples from the cecum and ileum, several taxa were of significantly higher relative abundance in the mucosa (P < 0.05), including Anaerovibrio, Bacteroides, Desulfovibrio, Helicobacter, Oscillospira, Phascolarctobacterium, and Prevotella. Correlations between several genus-level taxa and pig weight were observed. Overall, this study provides an expanded view of the dynamic pig GI microbiome from farrow to finish.</abstract><cop>US</cop><pub>Oxford University Press</pub><pmid>29635455</pmid><doi>10.1093/jas/sky109</doi><tpages>17</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Abundance Age factors Animals Bacteria Bacteria - classification Bacteria - genetics Bacteria - isolation & purification Cecum Colon Community structure Digestive system Duodenum Female Gastrointestinal Microbiome Gastrointestinal tract Gastrointestinal Tract - microbiology Hogs Ileum Intensive farming Jejunum Male Microbiology Microbiomes Microbiota Mucosa Populations Relative abundance RNA, Ribosomal, 16S - genetics rRNA 16S Swine Swine - microbiology Taxa Trends Weaning |
| title | Microbiome profiling of commercial pigs from farrow to finish |
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