Culture-independent identification of gut bacteria correlated with the onset of diabetes in a rat model
Bacteria associated with the onset of type 1 diabetes in a rat model system were identified. In two experiments, stool samples were collected at three time points after birth from bio-breeding diabetes-prone (BB-DP) and bio-breeding diabetes-resistant (BB-DR) rats. DNA was isolated from these sample...
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| Veröffentlicht in: | The ISME Journal 2009-05, Vol.3 (5), p.536-548 |
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| creator | Roesch, Luiz FW Lorca, Graciela L Casella, George Giongo, Adriana Naranjo, Andres Pionzio, Arianna M Li, Nan Mai, Volker Wasserfall, Clive H Schatz, Desmond Atkinson, Mark A Neu, Josef Triplett, Eric W |
| description | Bacteria associated with the onset of type 1 diabetes in a rat model system were identified. In two experiments, stool samples were collected at three time points after birth from bio-breeding diabetes-prone (BB-DP) and bio-breeding diabetes-resistant (BB-DR) rats. DNA was isolated from these samples and the 16S rRNA gene was amplified using universal primer sets. In the first experiment, bands specific to BB-DP and BB-DR genotypes were identified by automated ribosomal intergenic spacer analysis at the time of diabetes onset in BB-DP.
Lactobacillus
and
Bacteroides
strains were identified in the BB-DR- and BB-DP-specific bands, respectively. Sanger sequencing showed that the BB-DP and BB-DR bacterial communities differed significantly but too few reads were available to identify significant differences at the genus or species levels. A second experiment confirmed these results using higher throughput pyrosequencing and quantitative PCR of 16S rRNA with more rats per genotype. An average of 4541 and 3381 16S rRNA bacterial reads were obtained from each of the 10 BB-DR and 10 BB-DP samples collected at time of diabetes onset. Nine genera were more abundant in BB-DP whereas another nine genera were more abundant in BB-DR. Thirteen and eleven species were more abundant in BB-DP and BB-DR, respectively. An average of 23% and 10% of all reads could be classified at the genus and species levels, respectively. Quantitative PCR verified the higher abundance of
Lactobacillus
and
Bifidobacterium
in the BB-DR samples. Whether these changes are caused by diabetes or are involved in the development of the disease is unknown. |
| doi_str_mv | 10.1038/ismej.2009.5 |
| format | Article |
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Lactobacillus
and
Bacteroides
strains were identified in the BB-DR- and BB-DP-specific bands, respectively. Sanger sequencing showed that the BB-DP and BB-DR bacterial communities differed significantly but too few reads were available to identify significant differences at the genus or species levels. A second experiment confirmed these results using higher throughput pyrosequencing and quantitative PCR of 16S rRNA with more rats per genotype. An average of 4541 and 3381 16S rRNA bacterial reads were obtained from each of the 10 BB-DR and 10 BB-DP samples collected at time of diabetes onset. Nine genera were more abundant in BB-DP whereas another nine genera were more abundant in BB-DR. Thirteen and eleven species were more abundant in BB-DP and BB-DR, respectively. An average of 23% and 10% of all reads could be classified at the genus and species levels, respectively. Quantitative PCR verified the higher abundance of
Lactobacillus
and
Bifidobacterium
in the BB-DR samples. Whether these changes are caused by diabetes or are involved in the development of the disease is unknown.</description><identifier>ISSN: 1751-7362</identifier><identifier>EISSN: 1751-7370</identifier><identifier>DOI: 10.1038/ismej.2009.5</identifier><identifier>PMID: 19225551</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>Animals ; Bacteria ; Bacteria - classification ; Bacteria - isolation & purification ; Bacteroides ; Bifidobacterium ; Biodiversity ; Biomedical and Life Sciences ; Cluster Analysis ; Deoxyribonucleic acid ; Diabetes Mellitus ; DNA ; DNA, Bacterial - chemistry ; DNA, Bacterial - genetics ; DNA, Ribosomal - chemistry ; DNA, Ribosomal - genetics ; DNA, Ribosomal Spacer - chemistry ; DNA, Ribosomal Spacer - genetics ; Ecology ; Evolutionary Biology ; Gastrointestinal Tract - microbiology ; Genes, rRNA ; Genotypes ; Lactobacillus ; Life Sciences ; Microbial Ecology ; Microbial Genetics and Genomics ; Microbiology ; Molecular Sequence Data ; original-article ; Phylogeny ; Rats ; RNA, Bacterial - genetics ; RNA, Ribosomal, 16S - genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid</subject><ispartof>The ISME Journal, 2009-05, Vol.3 (5), p.536-548</ispartof><rights>International Society for Microbial Ecology 2009</rights><rights>Copyright Nature Publishing Group May 2009</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c547t-b4f1933a7503c7c03a6c5090825dde98c8768842c3b77b70c7e767d1c1f4fa733</citedby><cites>FETCH-LOGICAL-c547t-b4f1933a7503c7c03a6c5090825dde98c8768842c3b77b70c7e767d1c1f4fa733</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,315,782,786,887,27931,27932</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19225551$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Roesch, Luiz FW</creatorcontrib><creatorcontrib>Lorca, Graciela L</creatorcontrib><creatorcontrib>Casella, George</creatorcontrib><creatorcontrib>Giongo, Adriana</creatorcontrib><creatorcontrib>Naranjo, Andres</creatorcontrib><creatorcontrib>Pionzio, Arianna M</creatorcontrib><creatorcontrib>Li, Nan</creatorcontrib><creatorcontrib>Mai, Volker</creatorcontrib><creatorcontrib>Wasserfall, Clive H</creatorcontrib><creatorcontrib>Schatz, Desmond</creatorcontrib><creatorcontrib>Atkinson, Mark A</creatorcontrib><creatorcontrib>Neu, Josef</creatorcontrib><creatorcontrib>Triplett, Eric W</creatorcontrib><title>Culture-independent identification of gut bacteria correlated with the onset of diabetes in a rat model</title><title>The ISME Journal</title><addtitle>ISME J</addtitle><addtitle>ISME J</addtitle><description>Bacteria associated with the onset of type 1 diabetes in a rat model system were identified. In two experiments, stool samples were collected at three time points after birth from bio-breeding diabetes-prone (BB-DP) and bio-breeding diabetes-resistant (BB-DR) rats. DNA was isolated from these samples and the 16S rRNA gene was amplified using universal primer sets. In the first experiment, bands specific to BB-DP and BB-DR genotypes were identified by automated ribosomal intergenic spacer analysis at the time of diabetes onset in BB-DP.
Lactobacillus
and
Bacteroides
strains were identified in the BB-DR- and BB-DP-specific bands, respectively. Sanger sequencing showed that the BB-DP and BB-DR bacterial communities differed significantly but too few reads were available to identify significant differences at the genus or species levels. A second experiment confirmed these results using higher throughput pyrosequencing and quantitative PCR of 16S rRNA with more rats per genotype. An average of 4541 and 3381 16S rRNA bacterial reads were obtained from each of the 10 BB-DR and 10 BB-DP samples collected at time of diabetes onset. Nine genera were more abundant in BB-DP whereas another nine genera were more abundant in BB-DR. Thirteen and eleven species were more abundant in BB-DP and BB-DR, respectively. An average of 23% and 10% of all reads could be classified at the genus and species levels, respectively. Quantitative PCR verified the higher abundance of
Lactobacillus
and
Bifidobacterium
in the BB-DR samples. Whether these changes are caused by diabetes or are involved in the development of the disease is unknown.</description><subject>Animals</subject><subject>Bacteria</subject><subject>Bacteria - classification</subject><subject>Bacteria - isolation & purification</subject><subject>Bacteroides</subject><subject>Bifidobacterium</subject><subject>Biodiversity</subject><subject>Biomedical and Life Sciences</subject><subject>Cluster Analysis</subject><subject>Deoxyribonucleic acid</subject><subject>Diabetes Mellitus</subject><subject>DNA</subject><subject>DNA, Bacterial - chemistry</subject><subject>DNA, Bacterial - genetics</subject><subject>DNA, Ribosomal - chemistry</subject><subject>DNA, Ribosomal - genetics</subject><subject>DNA, Ribosomal Spacer - chemistry</subject><subject>DNA, Ribosomal Spacer - genetics</subject><subject>Ecology</subject><subject>Evolutionary Biology</subject><subject>Gastrointestinal Tract - microbiology</subject><subject>Genes, rRNA</subject><subject>Genotypes</subject><subject>Lactobacillus</subject><subject>Life Sciences</subject><subject>Microbial Ecology</subject><subject>Microbial Genetics and Genomics</subject><subject>Microbiology</subject><subject>Molecular Sequence Data</subject><subject>original-article</subject><subject>Phylogeny</subject><subject>Rats</subject><subject>RNA, Bacterial - genetics</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>Sequence Analysis, DNA</subject><subject>Sequence Homology, Nucleic Acid</subject><issn>1751-7362</issn><issn>1751-7370</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqFks1rFDEYh4NYbK3ePEtA6MlZ8zGZJBdBlvoBhV7qOWQy7-xmmUnWJFPxv3emu6xVhF7eBN6HJ3nzC0JvKFlRwtUHn0fYrRgheiWeoQsqBa0kl-T5ad-wc_Qy5x0hQjaNfIHOqWZMCEEv0GY9DWVKUPnQwR7mEgr2S_W9d7b4GHDs8WYquLWuQPIWu5gSDLZAh3_6ssVlCziGDGUhO29bKJCxD9jiZAseYwfDK3TW2yHD6-N6ib5_vr5bf61ubr98W3-6qZyoZanauqeacysF4U46wm3jBNFEMdF1oJVTslGqZo63UraSOAmykR11tK97Kzm_RB8P3v3UjtC5eZBkB7NPfrTpl4nWm787wW_NJt4bpiXjRM-Cq6MgxR8T5GJGnx0Mgw0Qp2waSWtNG_okyIhQRKlmBt_9A-7ilML8CoYSpmdEi0X3_kC5FHNO0J_uTIlZgjYPQZslaCNm_O3jOf_Ax2RnoDoAeW6FDaTHp_5XiA98sMt_OAkfoIUR_DfUz8CD</recordid><startdate>20090501</startdate><enddate>20090501</enddate><creator>Roesch, Luiz FW</creator><creator>Lorca, Graciela L</creator><creator>Casella, George</creator><creator>Giongo, Adriana</creator><creator>Naranjo, Andres</creator><creator>Pionzio, Arianna M</creator><creator>Li, Nan</creator><creator>Mai, Volker</creator><creator>Wasserfall, Clive H</creator><creator>Schatz, Desmond</creator><creator>Atkinson, Mark A</creator><creator>Neu, Josef</creator><creator>Triplett, Eric W</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</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>7QL</scope><scope>7SN</scope><scope>7ST</scope><scope>7T7</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PATMY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PYCSY</scope><scope>SOI</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20090501</creationdate><title>Culture-independent identification of gut bacteria correlated with the onset of diabetes in a rat model</title><author>Roesch, Luiz FW ; Lorca, Graciela L ; Casella, George ; Giongo, Adriana ; Naranjo, Andres ; Pionzio, Arianna M ; Li, Nan ; Mai, Volker ; Wasserfall, Clive H ; Schatz, Desmond ; Atkinson, Mark A ; Neu, Josef ; Triplett, Eric W</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c547t-b4f1933a7503c7c03a6c5090825dde98c8768842c3b77b70c7e767d1c1f4fa733</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>Animals</topic><topic>Bacteria</topic><topic>Bacteria - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>The ISME Journal</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Roesch, Luiz FW</au><au>Lorca, Graciela L</au><au>Casella, George</au><au>Giongo, Adriana</au><au>Naranjo, Andres</au><au>Pionzio, Arianna M</au><au>Li, Nan</au><au>Mai, Volker</au><au>Wasserfall, Clive H</au><au>Schatz, Desmond</au><au>Atkinson, Mark A</au><au>Neu, Josef</au><au>Triplett, Eric W</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Culture-independent identification of gut bacteria correlated with the onset of diabetes in a rat model</atitle><jtitle>The ISME Journal</jtitle><stitle>ISME J</stitle><addtitle>ISME J</addtitle><date>2009-05-01</date><risdate>2009</risdate><volume>3</volume><issue>5</issue><spage>536</spage><epage>548</epage><pages>536-548</pages><issn>1751-7362</issn><eissn>1751-7370</eissn><abstract>Bacteria associated with the onset of type 1 diabetes in a rat model system were identified. In two experiments, stool samples were collected at three time points after birth from bio-breeding diabetes-prone (BB-DP) and bio-breeding diabetes-resistant (BB-DR) rats. DNA was isolated from these samples and the 16S rRNA gene was amplified using universal primer sets. In the first experiment, bands specific to BB-DP and BB-DR genotypes were identified by automated ribosomal intergenic spacer analysis at the time of diabetes onset in BB-DP.
Lactobacillus
and
Bacteroides
strains were identified in the BB-DR- and BB-DP-specific bands, respectively. Sanger sequencing showed that the BB-DP and BB-DR bacterial communities differed significantly but too few reads were available to identify significant differences at the genus or species levels. A second experiment confirmed these results using higher throughput pyrosequencing and quantitative PCR of 16S rRNA with more rats per genotype. An average of 4541 and 3381 16S rRNA bacterial reads were obtained from each of the 10 BB-DR and 10 BB-DP samples collected at time of diabetes onset. Nine genera were more abundant in BB-DP whereas another nine genera were more abundant in BB-DR. Thirteen and eleven species were more abundant in BB-DP and BB-DR, respectively. An average of 23% and 10% of all reads could be classified at the genus and species levels, respectively. Quantitative PCR verified the higher abundance of
Lactobacillus
and
Bifidobacterium
in the BB-DR samples. Whether these changes are caused by diabetes or are involved in the development of the disease is unknown.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>19225551</pmid><doi>10.1038/ismej.2009.5</doi><tpages>13</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | The ISME Journal, 2009-05, Vol.3 (5), p.536-548 |
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| source | MEDLINE; Access via Oxford University Press (Open Access Collection); Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Oxford University Press Journals All Titles (1996-Current) |
| subjects | Animals Bacteria Bacteria - classification Bacteria - isolation & purification Bacteroides Bifidobacterium Biodiversity Biomedical and Life Sciences Cluster Analysis Deoxyribonucleic acid Diabetes Mellitus DNA DNA, Bacterial - chemistry DNA, Bacterial - genetics DNA, Ribosomal - chemistry DNA, Ribosomal - genetics DNA, Ribosomal Spacer - chemistry DNA, Ribosomal Spacer - genetics Ecology Evolutionary Biology Gastrointestinal Tract - microbiology Genes, rRNA Genotypes Lactobacillus Life Sciences Microbial Ecology Microbial Genetics and Genomics Microbiology Molecular Sequence Data original-article Phylogeny Rats RNA, Bacterial - genetics RNA, Ribosomal, 16S - genetics Sequence Analysis, DNA Sequence Homology, Nucleic Acid |
| title | Culture-independent identification of gut bacteria correlated with the onset of diabetes in a rat model |
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