Application of rpoB sequence similarity analysis, REP-PCR and BOX-PCR for the differentiation of species within the genus Geobacillus
To investigate the applicability of rpoB gene, which encodes the β subunit of RNA polymerase, to be used as an alternative to 16S rRNA for sequence similarity analysis in the thermophilic genus Geobacillus. Rapid and reproducible repetitive extragenic palindromic fingerprinting techniques (REP- and...
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| Veröffentlicht in: | Letters in applied microbiology 2008-03, Vol.46 (3), p.395-401 |
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| container_title | Letters in applied microbiology |
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| creator | Meintanis, C Chalkou, K.I Kormas, K. Ar Lymperopoulou, D.S Katsifas, E.A Hatzinikolaou, D.G Karagouni, A.D |
| description | To investigate the applicability of rpoB gene, which encodes the β subunit of RNA polymerase, to be used as an alternative to 16S rRNA for sequence similarity analysis in the thermophilic genus Geobacillus. Rapid and reproducible repetitive extragenic palindromic fingerprinting techniques (REP- and BOX-polymerase chain reaction) were also used. rpoB DNA (458 bp) were amplified from 21 Geobacillus- and Bacillus type strains, producing different BOX- and REP-PCR profiles, in addition to 11 thermophilic isolates of Geobacillus and Bacillus species from a Santorini volcano habitat. The sequences and the phylogenetic tree of rpoB were compared with those obtained from 16S rRNA gene analysis. The results demonstrated between 90-100% (16S rRNA) and 74-100% (rpoB) similarity among examined bacteria. BOX- and REP-PCR can be applied for molecular typing within Geobacillus genus. rpoB sequence similarity analysis permits a more accurate discrimination of the species within the Geobacillus genus than the more commonly used 16S rRNA. The obtained results suggested that rpoB sequence similarity analysis is a powerful tool for discrimination between species within the ecologically and industrially important strains of Geobacillus genus. |
| doi_str_mv | 10.1111/j.1472-765X.2008.02328.x |
| format | Article |
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Ar ; Lymperopoulou, D.S ; Katsifas, E.A ; Hatzinikolaou, D.G ; Karagouni, A.D</creator><creatorcontrib>Meintanis, C ; Chalkou, K.I ; Kormas, K. Ar ; Lymperopoulou, D.S ; Katsifas, E.A ; Hatzinikolaou, D.G ; Karagouni, A.D</creatorcontrib><description>To investigate the applicability of rpoB gene, which encodes the β subunit of RNA polymerase, to be used as an alternative to 16S rRNA for sequence similarity analysis in the thermophilic genus Geobacillus. Rapid and reproducible repetitive extragenic palindromic fingerprinting techniques (REP- and BOX-polymerase chain reaction) were also used. rpoB DNA (458 bp) were amplified from 21 Geobacillus- and Bacillus type strains, producing different BOX- and REP-PCR profiles, in addition to 11 thermophilic isolates of Geobacillus and Bacillus species from a Santorini volcano habitat. The sequences and the phylogenetic tree of rpoB were compared with those obtained from 16S rRNA gene analysis. The results demonstrated between 90-100% (16S rRNA) and 74-100% (rpoB) similarity among examined bacteria. BOX- and REP-PCR can be applied for molecular typing within Geobacillus genus. rpoB sequence similarity analysis permits a more accurate discrimination of the species within the Geobacillus genus than the more commonly used 16S rRNA. The obtained results suggested that rpoB sequence similarity analysis is a powerful tool for discrimination between species within the ecologically and industrially important strains of Geobacillus genus.</description><identifier>ISSN: 0266-8254</identifier><identifier>EISSN: 1472-765X</identifier><identifier>DOI: 10.1111/j.1472-765X.2008.02328.x</identifier><identifier>PMID: 18266638</identifier><identifier>CODEN: LAMIE7</identifier><language>eng</language><publisher>Oxford, UK: Oxford, UK : Blackwell Publishing Ltd</publisher><subject>16S rRNA ; Bacillaceae - classification ; Bacillaceae - enzymology ; Bacillaceae - genetics ; Bacterial Typing Techniques ; Biological and medical sciences ; DNA, Bacterial - analysis ; DNA-Directed RNA Polymerases - chemistry ; DNA-Directed RNA Polymerases - genetics ; Fundamental and applied biological sciences. Psychology ; Geobacillus ; Hot Temperature ; Microbiology ; Molecular Sequence Data ; PCR ; Phylogeny ; phyologeny ; Polymerase Chain Reaction - methods ; RNA, Ribosomal, 16S - genetics ; rpoB ; Sequence Analysis, DNA ; Species Specificity</subject><ispartof>Letters in applied microbiology, 2008-03, Vol.46 (3), p.395-401</ispartof><rights>2008 The Authors</rights><rights>2008 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4878-58034917d19a3c71074655e0fae7cd59bf1a400704bd30c34d84262b6147d1933</citedby><cites>FETCH-LOGICAL-c4878-58034917d19a3c71074655e0fae7cd59bf1a400704bd30c34d84262b6147d1933</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fj.1472-765X.2008.02328.x$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fj.1472-765X.2008.02328.x$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1417,27924,27925,45574,45575</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=20123230$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18266638$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Meintanis, C</creatorcontrib><creatorcontrib>Chalkou, K.I</creatorcontrib><creatorcontrib>Kormas, K. Ar</creatorcontrib><creatorcontrib>Lymperopoulou, D.S</creatorcontrib><creatorcontrib>Katsifas, E.A</creatorcontrib><creatorcontrib>Hatzinikolaou, D.G</creatorcontrib><creatorcontrib>Karagouni, A.D</creatorcontrib><title>Application of rpoB sequence similarity analysis, REP-PCR and BOX-PCR for the differentiation of species within the genus Geobacillus</title><title>Letters in applied microbiology</title><addtitle>Lett Appl Microbiol</addtitle><description>To investigate the applicability of rpoB gene, which encodes the β subunit of RNA polymerase, to be used as an alternative to 16S rRNA for sequence similarity analysis in the thermophilic genus Geobacillus. Rapid and reproducible repetitive extragenic palindromic fingerprinting techniques (REP- and BOX-polymerase chain reaction) were also used. rpoB DNA (458 bp) were amplified from 21 Geobacillus- and Bacillus type strains, producing different BOX- and REP-PCR profiles, in addition to 11 thermophilic isolates of Geobacillus and Bacillus species from a Santorini volcano habitat. The sequences and the phylogenetic tree of rpoB were compared with those obtained from 16S rRNA gene analysis. The results demonstrated between 90-100% (16S rRNA) and 74-100% (rpoB) similarity among examined bacteria. BOX- and REP-PCR can be applied for molecular typing within Geobacillus genus. rpoB sequence similarity analysis permits a more accurate discrimination of the species within the Geobacillus genus than the more commonly used 16S rRNA. The obtained results suggested that rpoB sequence similarity analysis is a powerful tool for discrimination between species within the ecologically and industrially important strains of Geobacillus genus.</description><subject>16S rRNA</subject><subject>Bacillaceae - classification</subject><subject>Bacillaceae - enzymology</subject><subject>Bacillaceae - genetics</subject><subject>Bacterial Typing Techniques</subject><subject>Biological and medical sciences</subject><subject>DNA, Bacterial - analysis</subject><subject>DNA-Directed RNA Polymerases - chemistry</subject><subject>DNA-Directed RNA Polymerases - genetics</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Geobacillus</subject><subject>Hot Temperature</subject><subject>Microbiology</subject><subject>Molecular Sequence Data</subject><subject>PCR</subject><subject>Phylogeny</subject><subject>phyologeny</subject><subject>Polymerase Chain Reaction - methods</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>rpoB</subject><subject>Sequence Analysis, DNA</subject><subject>Species Specificity</subject><issn>0266-8254</issn><issn>1472-765X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2008</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkc1u3CAUhVHVqpmmeYWWTbuqXX5sgxddTEb5k6ZKlCZSdghjSBgxxgFbyTxA3zt4ZjTdlg2I-51z4VwAIEY5TuvnKscFIxmryoecIMRzRCjh-es7MDsU3oMZIlWVcVIWR-BTjCuUSEzqj-AI81SpKJ-Bv_O-d1bJwfoOegND709h1M-j7pSG0a6tk8EOGyg76TbRxh_w9uwmu1ncppsWnl4_bM_GBzg8adhaY3TQ3WAPjrHXyuoIX-zwZLst9ai7McIL7RuprHNj_Aw-GOmiPtnvx-D-_OxucZktry-uFvNlpgrOeFZyRIsasxbXkiqGESuqstTISM1UW9aNwbJAiKGiaSlStGh5QSrSVCmUpKH0GHzf-fbBpy_GQaxtVNo52Wk_RsEQJRVmLIF8B6rgYwzaiD7YtQwbgZGYRiBWYkpaTEmLaQRiOwLxmqRf9j3GZq3bf8J95gn4tgdkVNKZIDtl44EjCCcnihL3a8e9WKc3__0AsZz_nk5J_3WnN9IL-RhSj_s_yZ0muKxLTugbpiiq4A</recordid><startdate>200803</startdate><enddate>200803</enddate><creator>Meintanis, C</creator><creator>Chalkou, K.I</creator><creator>Kormas, K. Ar</creator><creator>Lymperopoulou, D.S</creator><creator>Katsifas, E.A</creator><creator>Hatzinikolaou, D.G</creator><creator>Karagouni, A.D</creator><general>Oxford, UK : Blackwell Publishing Ltd</general><general>Blackwell Publishing Ltd</general><general>Blackwell Science</general><scope>FBQ</scope><scope>IQODW</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><scope>7X8</scope></search><sort><creationdate>200803</creationdate><title>Application of rpoB sequence similarity analysis, REP-PCR and BOX-PCR for the differentiation of species within the genus Geobacillus</title><author>Meintanis, C ; Chalkou, K.I ; Kormas, K. Ar ; Lymperopoulou, D.S ; Katsifas, E.A ; Hatzinikolaou, D.G ; Karagouni, A.D</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4878-58034917d19a3c71074655e0fae7cd59bf1a400704bd30c34d84262b6147d1933</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2008</creationdate><topic>16S rRNA</topic><topic>Bacillaceae - classification</topic><topic>Bacillaceae - enzymology</topic><topic>Bacillaceae - genetics</topic><topic>Bacterial Typing Techniques</topic><topic>Biological and medical sciences</topic><topic>DNA, Bacterial - analysis</topic><topic>DNA-Directed RNA Polymerases - chemistry</topic><topic>DNA-Directed RNA Polymerases - genetics</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Geobacillus</topic><topic>Hot Temperature</topic><topic>Microbiology</topic><topic>Molecular Sequence Data</topic><topic>PCR</topic><topic>Phylogeny</topic><topic>phyologeny</topic><topic>Polymerase Chain Reaction - methods</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>rpoB</topic><topic>Sequence Analysis, DNA</topic><topic>Species Specificity</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Meintanis, C</creatorcontrib><creatorcontrib>Chalkou, K.I</creatorcontrib><creatorcontrib>Kormas, K. Ar</creatorcontrib><creatorcontrib>Lymperopoulou, D.S</creatorcontrib><creatorcontrib>Katsifas, E.A</creatorcontrib><creatorcontrib>Hatzinikolaou, D.G</creatorcontrib><creatorcontrib>Karagouni, A.D</creatorcontrib><collection>AGRIS</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Letters in applied microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Meintanis, C</au><au>Chalkou, K.I</au><au>Kormas, K. Ar</au><au>Lymperopoulou, D.S</au><au>Katsifas, E.A</au><au>Hatzinikolaou, D.G</au><au>Karagouni, A.D</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Application of rpoB sequence similarity analysis, REP-PCR and BOX-PCR for the differentiation of species within the genus Geobacillus</atitle><jtitle>Letters in applied microbiology</jtitle><addtitle>Lett Appl Microbiol</addtitle><date>2008-03</date><risdate>2008</risdate><volume>46</volume><issue>3</issue><spage>395</spage><epage>401</epage><pages>395-401</pages><issn>0266-8254</issn><eissn>1472-765X</eissn><coden>LAMIE7</coden><abstract>To investigate the applicability of rpoB gene, which encodes the β subunit of RNA polymerase, to be used as an alternative to 16S rRNA for sequence similarity analysis in the thermophilic genus Geobacillus. Rapid and reproducible repetitive extragenic palindromic fingerprinting techniques (REP- and BOX-polymerase chain reaction) were also used. rpoB DNA (458 bp) were amplified from 21 Geobacillus- and Bacillus type strains, producing different BOX- and REP-PCR profiles, in addition to 11 thermophilic isolates of Geobacillus and Bacillus species from a Santorini volcano habitat. The sequences and the phylogenetic tree of rpoB were compared with those obtained from 16S rRNA gene analysis. The results demonstrated between 90-100% (16S rRNA) and 74-100% (rpoB) similarity among examined bacteria. BOX- and REP-PCR can be applied for molecular typing within Geobacillus genus. rpoB sequence similarity analysis permits a more accurate discrimination of the species within the Geobacillus genus than the more commonly used 16S rRNA. The obtained results suggested that rpoB sequence similarity analysis is a powerful tool for discrimination between species within the ecologically and industrially important strains of Geobacillus genus.</abstract><cop>Oxford, UK</cop><pub>Oxford, UK : Blackwell Publishing Ltd</pub><pmid>18266638</pmid><doi>10.1111/j.1472-765X.2008.02328.x</doi><tpages>7</tpages></addata></record> |
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| ispartof | Letters in applied microbiology, 2008-03, Vol.46 (3), p.395-401 |
| issn | 0266-8254 1472-765X |
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| source | MEDLINE; Access via Wiley Online Library; Oxford University Press Journals All Titles (1996-Current); EZB-FREE-00999 freely available EZB journals; Alma/SFX Local Collection |
| subjects | 16S rRNA Bacillaceae - classification Bacillaceae - enzymology Bacillaceae - genetics Bacterial Typing Techniques Biological and medical sciences DNA, Bacterial - analysis DNA-Directed RNA Polymerases - chemistry DNA-Directed RNA Polymerases - genetics Fundamental and applied biological sciences. Psychology Geobacillus Hot Temperature Microbiology Molecular Sequence Data PCR Phylogeny phyologeny Polymerase Chain Reaction - methods RNA, Ribosomal, 16S - genetics rpoB Sequence Analysis, DNA Species Specificity |
| title | Application of rpoB sequence similarity analysis, REP-PCR and BOX-PCR for the differentiation of species within the genus Geobacillus |
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