Taxonomic and gene-centric metagenomics of the fecal microbiome of low and high feed conversion ratio (FCR) broilers
Individual weight gain in broiler growers appears to vary, which may in part be due to variation in their gut microbiota. In this paper we analyse the fecal microbiota of low and high feed conversion ratio (FCR) broilers. After shotgun sequencing of the fecal microbiome, we used the SEED database to...
Gespeichert in:
| Veröffentlicht in: | Journal of applied genetics 2014-02, Vol.55 (1), p.145-154 |
|---|---|
| Hauptverfasser: | , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 154 |
|---|---|
| container_issue | 1 |
| container_start_page | 145 |
| container_title | Journal of applied genetics |
| container_volume | 55 |
| creator | Singh, K. M Shah, T. M Reddy, Bhaskar Deshpande, S Rank, D. N Joshi, C. G |
| description | Individual weight gain in broiler growers appears to vary, which may in part be due to variation in their gut microbiota. In this paper we analyse the fecal microbiota of low and high feed conversion ratio (FCR) broilers. After shotgun sequencing of the fecal microbiome, we used the SEED database to identify the microbial diversity and metabolic potential in low and high FCR birds. The domain-level breakdown of our samples was bacteria (>95 %), eukaryotes (>2 %), archaea (>0.2 %), and viruses (>0.2 %). At the phylum level, Proteobacteria (78.83 % in low and 52.04 % in high FCR), Firmicutes (11.97 % in low and 27.53 % in high FCR) and Bacteroidetes (7.10 % in low FCR and 17.53 % in high FCR) predominated in the fecal microbial community. Poultry fecal metagenomes revealed the sequences related to 33 genera in both low and high FCR with significantly different proportion. Functional analysis revealed that genes for the metabolism of carbohydrates, amino acids and derivatives and protein metabolism were most abundant in SEED subsystem in both samples. Genes associated with stress, virulence, cell wall and cell capsule were also abundant. Indeed, genes associated with sulphur assimilation, flagellum and flagellar motility were over represented in low FCR birds. This information could help in developing strategies to improve feed efficiency and feed formulation for broiler chickens. |
| doi_str_mv | 10.1007/s13353-013-0179-4 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_cross</sourceid><recordid>TN_cdi_gale_infotracmisc_A710732405</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A710732405</galeid><sourcerecordid>A710732405</sourcerecordid><originalsourceid>FETCH-LOGICAL-c426t-ce4399ae3e6a4548a39e06dcb4e21574deb856ec0aff727fcbf5ee054dad2c213</originalsourceid><addsrcrecordid>eNp9kd1r1jAUxoMo7nX6B3ijAW_0ojNfbdrL8eJUGAz2cR3S9KRvRpuMpPPjv_d0VUGQEULgOc_vcHIeQl5zdsIZ0x8Ll7KWFePr1V2lnpCd4B2rZNvKp2THhVQV71p5RF6UcsuYbJUWz8mRUFw2WusdWa7tjxTTHBy1caAjRKgcxCWjMMNiUViLhSZPlwNQD85OFJWc-pBmWPUpfX-AD2E8oAEG6lL8BrmEFGm2S0j0_dn-8gPtcwoT6i_JM2-nAq9-v8fk5uzT9f5LdX7x-ev-9LxySjQLzqFk11mQ0FhVq9bKDlgzuF6B4LVWA_Rt3YBj1nsttHe9rwFYrQY7CCe4PCbvtr6jncCE6NOSrZtDceZUc6alUKxG18l_XHgGwH-mCB6H_hfgG4BLKCWDN3c5zDb_NJyZNRizBWMwGLMGYxQybzbm7r6fYfhL_EkCDWIzFCzFEbK5Tfc54noe7fp2g7xNxo45FHNzJRhXDLNuuHzcwXXb1fIX8Eeq7Q</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype></control><display><type>article</type><title>Taxonomic and gene-centric metagenomics of the fecal microbiome of low and high feed conversion ratio (FCR) broilers</title><source>MEDLINE</source><source>SpringerLink Journals</source><creator>Singh, K. M ; Shah, T. M ; Reddy, Bhaskar ; Deshpande, S ; Rank, D. N ; Joshi, C. G</creator><creatorcontrib>Singh, K. M ; Shah, T. M ; Reddy, Bhaskar ; Deshpande, S ; Rank, D. N ; Joshi, C. G</creatorcontrib><description>Individual weight gain in broiler growers appears to vary, which may in part be due to variation in their gut microbiota. In this paper we analyse the fecal microbiota of low and high feed conversion ratio (FCR) broilers. After shotgun sequencing of the fecal microbiome, we used the SEED database to identify the microbial diversity and metabolic potential in low and high FCR birds. The domain-level breakdown of our samples was bacteria (>95 %), eukaryotes (>2 %), archaea (>0.2 %), and viruses (>0.2 %). At the phylum level, Proteobacteria (78.83 % in low and 52.04 % in high FCR), Firmicutes (11.97 % in low and 27.53 % in high FCR) and Bacteroidetes (7.10 % in low FCR and 17.53 % in high FCR) predominated in the fecal microbial community. Poultry fecal metagenomes revealed the sequences related to 33 genera in both low and high FCR with significantly different proportion. Functional analysis revealed that genes for the metabolism of carbohydrates, amino acids and derivatives and protein metabolism were most abundant in SEED subsystem in both samples. Genes associated with stress, virulence, cell wall and cell capsule were also abundant. Indeed, genes associated with sulphur assimilation, flagellum and flagellar motility were over represented in low FCR birds. This information could help in developing strategies to improve feed efficiency and feed formulation for broiler chickens.</description><identifier>ISSN: 1234-1983</identifier><identifier>EISSN: 2190-3883</identifier><identifier>DOI: 10.1007/s13353-013-0179-4</identifier><identifier>PMID: 24136777</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer-Verlag</publisher><subject>amino acids ; Analysis ; Animal Feed ; Animal Genetics and Genomics ; Animals ; Archaea ; bacteria ; Bacteria - classification ; Bacteria - genetics ; Bacteria - isolation & purification ; Biomedical and Life Sciences ; broiler chickens ; Carbohydrate metabolism ; cell walls ; Chickens - growth & development ; Chickens - microbiology ; Costs (Law) ; DNA, Ribosomal - chemistry ; DNA, Ribosomal - genetics ; eukaryotic cells ; Feces - microbiology ; feed conversion ; feed formulation ; Female ; Firmicutes ; flagellum ; Gastrointestinal Tract - microbiology ; Genes ; growers ; High-Throughput Nucleotide Sequencing ; Human Genetics ; intestinal microorganisms ; Life Sciences ; Male ; Metagenome ; Metagenomics ; microbial communities ; Microbial Genetics and Genomics ; Microbial Genetics • Original Paper ; Microbiota ; Microbiota (Symbiotic organisms) ; Phylogeny ; Plant Genetics and Genomics ; protein metabolism ; Proteobacteria ; RNA, Ribosomal, 16S - genetics ; Sequence Analysis, DNA ; sulfur ; virulence ; viruses ; Weight Gain</subject><ispartof>Journal of applied genetics, 2014-02, Vol.55 (1), p.145-154</ispartof><rights>Institute of Plant Genetics, Polish Academy of Sciences, Poznan 2013</rights><rights>COPYRIGHT 2014 Springer</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c426t-ce4399ae3e6a4548a39e06dcb4e21574deb856ec0aff727fcbf5ee054dad2c213</citedby><cites>FETCH-LOGICAL-c426t-ce4399ae3e6a4548a39e06dcb4e21574deb856ec0aff727fcbf5ee054dad2c213</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s13353-013-0179-4$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s13353-013-0179-4$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24136777$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Singh, K. M</creatorcontrib><creatorcontrib>Shah, T. M</creatorcontrib><creatorcontrib>Reddy, Bhaskar</creatorcontrib><creatorcontrib>Deshpande, S</creatorcontrib><creatorcontrib>Rank, D. N</creatorcontrib><creatorcontrib>Joshi, C. G</creatorcontrib><title>Taxonomic and gene-centric metagenomics of the fecal microbiome of low and high feed conversion ratio (FCR) broilers</title><title>Journal of applied genetics</title><addtitle>J Appl Genetics</addtitle><addtitle>J Appl Genet</addtitle><description>Individual weight gain in broiler growers appears to vary, which may in part be due to variation in their gut microbiota. In this paper we analyse the fecal microbiota of low and high feed conversion ratio (FCR) broilers. After shotgun sequencing of the fecal microbiome, we used the SEED database to identify the microbial diversity and metabolic potential in low and high FCR birds. The domain-level breakdown of our samples was bacteria (>95 %), eukaryotes (>2 %), archaea (>0.2 %), and viruses (>0.2 %). At the phylum level, Proteobacteria (78.83 % in low and 52.04 % in high FCR), Firmicutes (11.97 % in low and 27.53 % in high FCR) and Bacteroidetes (7.10 % in low FCR and 17.53 % in high FCR) predominated in the fecal microbial community. Poultry fecal metagenomes revealed the sequences related to 33 genera in both low and high FCR with significantly different proportion. Functional analysis revealed that genes for the metabolism of carbohydrates, amino acids and derivatives and protein metabolism were most abundant in SEED subsystem in both samples. Genes associated with stress, virulence, cell wall and cell capsule were also abundant. Indeed, genes associated with sulphur assimilation, flagellum and flagellar motility were over represented in low FCR birds. This information could help in developing strategies to improve feed efficiency and feed formulation for broiler chickens.</description><subject>amino acids</subject><subject>Analysis</subject><subject>Animal Feed</subject><subject>Animal Genetics and Genomics</subject><subject>Animals</subject><subject>Archaea</subject><subject>bacteria</subject><subject>Bacteria - classification</subject><subject>Bacteria - genetics</subject><subject>Bacteria - isolation & purification</subject><subject>Biomedical and Life Sciences</subject><subject>broiler chickens</subject><subject>Carbohydrate metabolism</subject><subject>cell walls</subject><subject>Chickens - growth & development</subject><subject>Chickens - microbiology</subject><subject>Costs (Law)</subject><subject>DNA, Ribosomal - chemistry</subject><subject>DNA, Ribosomal - genetics</subject><subject>eukaryotic cells</subject><subject>Feces - microbiology</subject><subject>feed conversion</subject><subject>feed formulation</subject><subject>Female</subject><subject>Firmicutes</subject><subject>flagellum</subject><subject>Gastrointestinal Tract - microbiology</subject><subject>Genes</subject><subject>growers</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Human Genetics</subject><subject>intestinal microorganisms</subject><subject>Life Sciences</subject><subject>Male</subject><subject>Metagenome</subject><subject>Metagenomics</subject><subject>microbial communities</subject><subject>Microbial Genetics and Genomics</subject><subject>Microbial Genetics • Original Paper</subject><subject>Microbiota</subject><subject>Microbiota (Symbiotic organisms)</subject><subject>Phylogeny</subject><subject>Plant Genetics and Genomics</subject><subject>protein metabolism</subject><subject>Proteobacteria</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>Sequence Analysis, DNA</subject><subject>sulfur</subject><subject>virulence</subject><subject>viruses</subject><subject>Weight Gain</subject><issn>1234-1983</issn><issn>2190-3883</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kd1r1jAUxoMo7nX6B3ijAW_0ojNfbdrL8eJUGAz2cR3S9KRvRpuMpPPjv_d0VUGQEULgOc_vcHIeQl5zdsIZ0x8Ll7KWFePr1V2lnpCd4B2rZNvKp2THhVQV71p5RF6UcsuYbJUWz8mRUFw2WusdWa7tjxTTHBy1caAjRKgcxCWjMMNiUViLhSZPlwNQD85OFJWc-pBmWPUpfX-AD2E8oAEG6lL8BrmEFGm2S0j0_dn-8gPtcwoT6i_JM2-nAq9-v8fk5uzT9f5LdX7x-ev-9LxySjQLzqFk11mQ0FhVq9bKDlgzuF6B4LVWA_Rt3YBj1nsttHe9rwFYrQY7CCe4PCbvtr6jncCE6NOSrZtDceZUc6alUKxG18l_XHgGwH-mCB6H_hfgG4BLKCWDN3c5zDb_NJyZNRizBWMwGLMGYxQybzbm7r6fYfhL_EkCDWIzFCzFEbK5Tfc54noe7fp2g7xNxo45FHNzJRhXDLNuuHzcwXXb1fIX8Eeq7Q</recordid><startdate>20140201</startdate><enddate>20140201</enddate><creator>Singh, K. M</creator><creator>Shah, T. M</creator><creator>Reddy, Bhaskar</creator><creator>Deshpande, S</creator><creator>Rank, D. N</creator><creator>Joshi, C. G</creator><general>Springer-Verlag</general><general>Springer Berlin Heidelberg</general><general>Springer</general><scope>FBQ</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope></search><sort><creationdate>20140201</creationdate><title>Taxonomic and gene-centric metagenomics of the fecal microbiome of low and high feed conversion ratio (FCR) broilers</title><author>Singh, K. M ; Shah, T. M ; Reddy, Bhaskar ; Deshpande, S ; Rank, D. N ; Joshi, C. G</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c426t-ce4399ae3e6a4548a39e06dcb4e21574deb856ec0aff727fcbf5ee054dad2c213</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>amino acids</topic><topic>Analysis</topic><topic>Animal Feed</topic><topic>Animal Genetics and Genomics</topic><topic>Animals</topic><topic>Archaea</topic><topic>bacteria</topic><topic>Bacteria - classification</topic><topic>Bacteria - genetics</topic><topic>Bacteria - isolation & purification</topic><topic>Biomedical and Life Sciences</topic><topic>broiler chickens</topic><topic>Carbohydrate metabolism</topic><topic>cell walls</topic><topic>Chickens - growth & development</topic><topic>Chickens - microbiology</topic><topic>Costs (Law)</topic><topic>DNA, Ribosomal - chemistry</topic><topic>DNA, Ribosomal - genetics</topic><topic>eukaryotic cells</topic><topic>Feces - microbiology</topic><topic>feed conversion</topic><topic>feed formulation</topic><topic>Female</topic><topic>Firmicutes</topic><topic>flagellum</topic><topic>Gastrointestinal Tract - microbiology</topic><topic>Genes</topic><topic>growers</topic><topic>High-Throughput Nucleotide Sequencing</topic><topic>Human Genetics</topic><topic>intestinal microorganisms</topic><topic>Life Sciences</topic><topic>Male</topic><topic>Metagenome</topic><topic>Metagenomics</topic><topic>microbial communities</topic><topic>Microbial Genetics and Genomics</topic><topic>Microbial Genetics • Original Paper</topic><topic>Microbiota</topic><topic>Microbiota (Symbiotic organisms)</topic><topic>Phylogeny</topic><topic>Plant Genetics and Genomics</topic><topic>protein metabolism</topic><topic>Proteobacteria</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>Sequence Analysis, DNA</topic><topic>sulfur</topic><topic>virulence</topic><topic>viruses</topic><topic>Weight Gain</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Singh, K. M</creatorcontrib><creatorcontrib>Shah, T. M</creatorcontrib><creatorcontrib>Reddy, Bhaskar</creatorcontrib><creatorcontrib>Deshpande, S</creatorcontrib><creatorcontrib>Rank, D. N</creatorcontrib><creatorcontrib>Joshi, C. G</creatorcontrib><collection>AGRIS</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><jtitle>Journal of applied genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Singh, K. M</au><au>Shah, T. M</au><au>Reddy, Bhaskar</au><au>Deshpande, S</au><au>Rank, D. N</au><au>Joshi, C. G</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Taxonomic and gene-centric metagenomics of the fecal microbiome of low and high feed conversion ratio (FCR) broilers</atitle><jtitle>Journal of applied genetics</jtitle><stitle>J Appl Genetics</stitle><addtitle>J Appl Genet</addtitle><date>2014-02-01</date><risdate>2014</risdate><volume>55</volume><issue>1</issue><spage>145</spage><epage>154</epage><pages>145-154</pages><issn>1234-1983</issn><eissn>2190-3883</eissn><abstract>Individual weight gain in broiler growers appears to vary, which may in part be due to variation in their gut microbiota. In this paper we analyse the fecal microbiota of low and high feed conversion ratio (FCR) broilers. After shotgun sequencing of the fecal microbiome, we used the SEED database to identify the microbial diversity and metabolic potential in low and high FCR birds. The domain-level breakdown of our samples was bacteria (>95 %), eukaryotes (>2 %), archaea (>0.2 %), and viruses (>0.2 %). At the phylum level, Proteobacteria (78.83 % in low and 52.04 % in high FCR), Firmicutes (11.97 % in low and 27.53 % in high FCR) and Bacteroidetes (7.10 % in low FCR and 17.53 % in high FCR) predominated in the fecal microbial community. Poultry fecal metagenomes revealed the sequences related to 33 genera in both low and high FCR with significantly different proportion. Functional analysis revealed that genes for the metabolism of carbohydrates, amino acids and derivatives and protein metabolism were most abundant in SEED subsystem in both samples. Genes associated with stress, virulence, cell wall and cell capsule were also abundant. Indeed, genes associated with sulphur assimilation, flagellum and flagellar motility were over represented in low FCR birds. This information could help in developing strategies to improve feed efficiency and feed formulation for broiler chickens.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer-Verlag</pub><pmid>24136777</pmid><doi>10.1007/s13353-013-0179-4</doi><tpages>10</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1234-1983 |
| ispartof | Journal of applied genetics, 2014-02, Vol.55 (1), p.145-154 |
| issn | 1234-1983 2190-3883 |
| language | eng |
| recordid | cdi_gale_infotracmisc_A710732405 |
| source | MEDLINE; SpringerLink Journals |
| subjects | amino acids Analysis Animal Feed Animal Genetics and Genomics Animals Archaea bacteria Bacteria - classification Bacteria - genetics Bacteria - isolation & purification Biomedical and Life Sciences broiler chickens Carbohydrate metabolism cell walls Chickens - growth & development Chickens - microbiology Costs (Law) DNA, Ribosomal - chemistry DNA, Ribosomal - genetics eukaryotic cells Feces - microbiology feed conversion feed formulation Female Firmicutes flagellum Gastrointestinal Tract - microbiology Genes growers High-Throughput Nucleotide Sequencing Human Genetics intestinal microorganisms Life Sciences Male Metagenome Metagenomics microbial communities Microbial Genetics and Genomics Microbial Genetics • Original Paper Microbiota Microbiota (Symbiotic organisms) Phylogeny Plant Genetics and Genomics protein metabolism Proteobacteria RNA, Ribosomal, 16S - genetics Sequence Analysis, DNA sulfur virulence viruses Weight Gain |
| title | Taxonomic and gene-centric metagenomics of the fecal microbiome of low and high feed conversion ratio (FCR) broilers |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-28T13%3A01%3A36IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Taxonomic%20and%20gene-centric%20metagenomics%20of%20the%20fecal%20microbiome%20of%20low%20and%20high%20feed%20conversion%20ratio%20(FCR)%20broilers&rft.jtitle=Journal%20of%20applied%20genetics&rft.au=Singh,%20K.%20M&rft.date=2014-02-01&rft.volume=55&rft.issue=1&rft.spage=145&rft.epage=154&rft.pages=145-154&rft.issn=1234-1983&rft.eissn=2190-3883&rft_id=info:doi/10.1007/s13353-013-0179-4&rft_dat=%3Cgale_cross%3EA710732405%3C/gale_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_id=info:pmid/24136777&rft_galeid=A710732405&rfr_iscdi=true |