Simultaneous enumeration of different bacteria using reverse sample genome probing technique

Quantitative reverse sample genome probing (RSGP) with λDNA as an internal standard was used to enumerate the total numbers of Rhizobium sp. CCRC 13560, Rhizobium meliloti CCRC 13516 and Bradyrhizobium sp. CCRC 13585. K λ / Kx ratios varied between the three species but also in response to the amoun...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Journal of microbiological methods 2005-04, Vol.61 (1), p.87-94
Hauptverfasser: Lee, S.L., Chao, W.L.
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page 94
container_issue 1
container_start_page 87
container_title Journal of microbiological methods
container_volume 61
creator Lee, S.L.
Chao, W.L.
description Quantitative reverse sample genome probing (RSGP) with λDNA as an internal standard was used to enumerate the total numbers of Rhizobium sp. CCRC 13560, Rhizobium meliloti CCRC 13516 and Bradyrhizobium sp. CCRC 13585. K λ / Kx ratios varied between the three species but also in response to the amounts of λDNA or genomic DNA used in the labeling mixture or fixed upon the membrane. Comparative enumerations of pure cultures revealed higher counts using genomic probing as compared with growth-based colony forming units (CFU; 3.4±1.7-fold higher for R. meliloti, 6.4±7.8-fold higher for Rhizobium sp. and 0.34±0.17-fold higher for Bradyrhizobium sp.). In mixed cultures, the estimated cell numbers using genomic probing were 126±172-, 85±83- and 4.0±3.4-fold higher (same respective order) than the growth-based assay. By replacing the k λ / k x ratio with k′ λ / k′ x (slope from signal intensity of differently diluted λDNA/slope from signal intensity of differently diluted target DNA× f x / f λ ), significant improvement in the accuracy of the estimation was achieved. The calculated cell numbers via the genomic probe technique were 0.99±0.13-, 1.25±0.23- and 0.18±0.11-fold higher than the respective CFUs in pure cultures of R. meliloti, Rhizobium sp. and Bradyrhizobium sp. In samples containing mixed populations, the estimated numbers from genomic probing were 1.25±0.51-, 45.9±14.8- and 0.27±0.07-fold higher than the CFU-derived cell count (same respective order).
doi_str_mv 10.1016/j.mimet.2004.11.008
format Article
fullrecord <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_67385150</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><els_id>S0167701204003288</els_id><sourcerecordid>17837086</sourcerecordid><originalsourceid>FETCH-LOGICAL-c418t-abf99711656adb6eb6c8ac02c83cd2fc21f57788b54e37627348b0b7427c0d183</originalsourceid><addsrcrecordid>eNqFkE2LFDEQhoMo7uzqLxAkF711m-qPJH3wIMvqCgse1JsQknRlzdBJj0l6wX9vxhnYm57qUM9bHw8hr4C1wIC_27fBByxtx9jQArSMySdkB1J0jezH6SnZVUo0gkF3QS5z3jMGYz_I5-QCRi44TNOO_Pjqw7YUHXHdMsW4BUy6-DXS1dHZO4cJY6FG24LJa7plH-9pwgdMGWnW4bAgvce4BqSHtJpjt6D9Gf2vDV-QZ04vGV-e6xX5_vHm2_Vtc_fl0-frD3eNHUCWRhs3TQKAj1zPhqPhVmrLOit7O3fOduBGIaQ044C94J2oTxhmxNAJy2aQ_RV5e5pbL6hrc1HBZ4vLcnpLcdHLEUb2XxCE7AWTvIL9CbRpzTmhU4fkg06_FTB1tK_26q99dbSvAFS1X1Ovz-M3E3B-zJx1V-DNGdDZ6sUlHa3PjxwfxCDEkXt_4rBae_CYVLYeo8XZJ7RFzav_5yF_APCVpT8</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>17837086</pqid></control><display><type>article</type><title>Simultaneous enumeration of different bacteria using reverse sample genome probing technique</title><source>MEDLINE</source><source>Elsevier ScienceDirect Journals Complete</source><creator>Lee, S.L. ; Chao, W.L.</creator><creatorcontrib>Lee, S.L. ; Chao, W.L.</creatorcontrib><description>Quantitative reverse sample genome probing (RSGP) with λDNA as an internal standard was used to enumerate the total numbers of Rhizobium sp. CCRC 13560, Rhizobium meliloti CCRC 13516 and Bradyrhizobium sp. CCRC 13585. K λ / Kx ratios varied between the three species but also in response to the amounts of λDNA or genomic DNA used in the labeling mixture or fixed upon the membrane. Comparative enumerations of pure cultures revealed higher counts using genomic probing as compared with growth-based colony forming units (CFU; 3.4±1.7-fold higher for R. meliloti, 6.4±7.8-fold higher for Rhizobium sp. and 0.34±0.17-fold higher for Bradyrhizobium sp.). In mixed cultures, the estimated cell numbers using genomic probing were 126±172-, 85±83- and 4.0±3.4-fold higher (same respective order) than the growth-based assay. By replacing the k λ / k x ratio with k′ λ / k′ x (slope from signal intensity of differently diluted λDNA/slope from signal intensity of differently diluted target DNA× f x / f λ ), significant improvement in the accuracy of the estimation was achieved. The calculated cell numbers via the genomic probe technique were 0.99±0.13-, 1.25±0.23- and 0.18±0.11-fold higher than the respective CFUs in pure cultures of R. meliloti, Rhizobium sp. and Bradyrhizobium sp. In samples containing mixed populations, the estimated numbers from genomic probing were 1.25±0.51-, 45.9±14.8- and 0.27±0.07-fold higher than the CFU-derived cell count (same respective order).</description><identifier>ISSN: 0167-7012</identifier><identifier>EISSN: 1872-8359</identifier><identifier>DOI: 10.1016/j.mimet.2004.11.008</identifier><identifier>PMID: 15676199</identifier><identifier>CODEN: JMIMDQ</identifier><language>eng</language><publisher>Shannon: Elsevier B.V</publisher><subject>Bacteriology ; Biological and medical sciences ; Bradyrhizobium ; Bradyrhizobium - genetics ; Bradyrhizobium - growth &amp; development ; Bradyrhizobium - isolation &amp; purification ; Colony Count, Microbial ; DNA, Bacterial - genetics ; Enumaration ; Environmental Microbiology ; Fundamental and applied biological sciences. Psychology ; Genome, Bacterial ; Microbiology ; Miscellaneous ; Nucleic Acid Hybridization - methods ; Reverse sample genome probing ; Rhizobium meliloti ; Sinorhizobium meliloti - genetics ; Sinorhizobium meliloti - growth &amp; development ; Sinorhizobium meliloti - isolation &amp; purification</subject><ispartof>Journal of microbiological methods, 2005-04, Vol.61 (1), p.87-94</ispartof><rights>2004 Elsevier B.V.</rights><rights>2005 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c418t-abf99711656adb6eb6c8ac02c83cd2fc21f57788b54e37627348b0b7427c0d183</citedby><cites>FETCH-LOGICAL-c418t-abf99711656adb6eb6c8ac02c83cd2fc21f57788b54e37627348b0b7427c0d183</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0167701204003288$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,776,780,3537,27901,27902,65534</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&amp;idt=16474779$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/15676199$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lee, S.L.</creatorcontrib><creatorcontrib>Chao, W.L.</creatorcontrib><title>Simultaneous enumeration of different bacteria using reverse sample genome probing technique</title><title>Journal of microbiological methods</title><addtitle>J Microbiol Methods</addtitle><description>Quantitative reverse sample genome probing (RSGP) with λDNA as an internal standard was used to enumerate the total numbers of Rhizobium sp. CCRC 13560, Rhizobium meliloti CCRC 13516 and Bradyrhizobium sp. CCRC 13585. K λ / Kx ratios varied between the three species but also in response to the amounts of λDNA or genomic DNA used in the labeling mixture or fixed upon the membrane. Comparative enumerations of pure cultures revealed higher counts using genomic probing as compared with growth-based colony forming units (CFU; 3.4±1.7-fold higher for R. meliloti, 6.4±7.8-fold higher for Rhizobium sp. and 0.34±0.17-fold higher for Bradyrhizobium sp.). In mixed cultures, the estimated cell numbers using genomic probing were 126±172-, 85±83- and 4.0±3.4-fold higher (same respective order) than the growth-based assay. By replacing the k λ / k x ratio with k′ λ / k′ x (slope from signal intensity of differently diluted λDNA/slope from signal intensity of differently diluted target DNA× f x / f λ ), significant improvement in the accuracy of the estimation was achieved. The calculated cell numbers via the genomic probe technique were 0.99±0.13-, 1.25±0.23- and 0.18±0.11-fold higher than the respective CFUs in pure cultures of R. meliloti, Rhizobium sp. and Bradyrhizobium sp. In samples containing mixed populations, the estimated numbers from genomic probing were 1.25±0.51-, 45.9±14.8- and 0.27±0.07-fold higher than the CFU-derived cell count (same respective order).</description><subject>Bacteriology</subject><subject>Biological and medical sciences</subject><subject>Bradyrhizobium</subject><subject>Bradyrhizobium - genetics</subject><subject>Bradyrhizobium - growth &amp; development</subject><subject>Bradyrhizobium - isolation &amp; purification</subject><subject>Colony Count, Microbial</subject><subject>DNA, Bacterial - genetics</subject><subject>Enumaration</subject><subject>Environmental Microbiology</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genome, Bacterial</subject><subject>Microbiology</subject><subject>Miscellaneous</subject><subject>Nucleic Acid Hybridization - methods</subject><subject>Reverse sample genome probing</subject><subject>Rhizobium meliloti</subject><subject>Sinorhizobium meliloti - genetics</subject><subject>Sinorhizobium meliloti - growth &amp; development</subject><subject>Sinorhizobium meliloti - isolation &amp; purification</subject><issn>0167-7012</issn><issn>1872-8359</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkE2LFDEQhoMo7uzqLxAkF711m-qPJH3wIMvqCgse1JsQknRlzdBJj0l6wX9vxhnYm57qUM9bHw8hr4C1wIC_27fBByxtx9jQArSMySdkB1J0jezH6SnZVUo0gkF3QS5z3jMGYz_I5-QCRi44TNOO_Pjqw7YUHXHdMsW4BUy6-DXS1dHZO4cJY6FG24LJa7plH-9pwgdMGWnW4bAgvce4BqSHtJpjt6D9Gf2vDV-QZ04vGV-e6xX5_vHm2_Vtc_fl0-frD3eNHUCWRhs3TQKAj1zPhqPhVmrLOit7O3fOduBGIaQ044C94J2oTxhmxNAJy2aQ_RV5e5pbL6hrc1HBZ4vLcnpLcdHLEUb2XxCE7AWTvIL9CbRpzTmhU4fkg06_FTB1tK_26q99dbSvAFS1X1Ovz-M3E3B-zJx1V-DNGdDZ6sUlHa3PjxwfxCDEkXt_4rBae_CYVLYeo8XZJ7RFzav_5yF_APCVpT8</recordid><startdate>20050401</startdate><enddate>20050401</enddate><creator>Lee, S.L.</creator><creator>Chao, W.L.</creator><general>Elsevier B.V</general><general>Elsevier Science</general><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>7QL</scope><scope>7T7</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>P64</scope><scope>7X8</scope></search><sort><creationdate>20050401</creationdate><title>Simultaneous enumeration of different bacteria using reverse sample genome probing technique</title><author>Lee, S.L. ; Chao, W.L.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c418t-abf99711656adb6eb6c8ac02c83cd2fc21f57788b54e37627348b0b7427c0d183</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2005</creationdate><topic>Bacteriology</topic><topic>Biological and medical sciences</topic><topic>Bradyrhizobium</topic><topic>Bradyrhizobium - genetics</topic><topic>Bradyrhizobium - growth &amp; development</topic><topic>Bradyrhizobium - isolation &amp; purification</topic><topic>Colony Count, Microbial</topic><topic>DNA, Bacterial - genetics</topic><topic>Enumaration</topic><topic>Environmental Microbiology</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genome, Bacterial</topic><topic>Microbiology</topic><topic>Miscellaneous</topic><topic>Nucleic Acid Hybridization - methods</topic><topic>Reverse sample genome probing</topic><topic>Rhizobium meliloti</topic><topic>Sinorhizobium meliloti - genetics</topic><topic>Sinorhizobium meliloti - growth &amp; development</topic><topic>Sinorhizobium meliloti - isolation &amp; purification</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lee, S.L.</creatorcontrib><creatorcontrib>Chao, W.L.</creatorcontrib><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>Bacteriology Abstracts (Microbiology B)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of microbiological methods</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lee, S.L.</au><au>Chao, W.L.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Simultaneous enumeration of different bacteria using reverse sample genome probing technique</atitle><jtitle>Journal of microbiological methods</jtitle><addtitle>J Microbiol Methods</addtitle><date>2005-04-01</date><risdate>2005</risdate><volume>61</volume><issue>1</issue><spage>87</spage><epage>94</epage><pages>87-94</pages><issn>0167-7012</issn><eissn>1872-8359</eissn><coden>JMIMDQ</coden><abstract>Quantitative reverse sample genome probing (RSGP) with λDNA as an internal standard was used to enumerate the total numbers of Rhizobium sp. CCRC 13560, Rhizobium meliloti CCRC 13516 and Bradyrhizobium sp. CCRC 13585. K λ / Kx ratios varied between the three species but also in response to the amounts of λDNA or genomic DNA used in the labeling mixture or fixed upon the membrane. Comparative enumerations of pure cultures revealed higher counts using genomic probing as compared with growth-based colony forming units (CFU; 3.4±1.7-fold higher for R. meliloti, 6.4±7.8-fold higher for Rhizobium sp. and 0.34±0.17-fold higher for Bradyrhizobium sp.). In mixed cultures, the estimated cell numbers using genomic probing were 126±172-, 85±83- and 4.0±3.4-fold higher (same respective order) than the growth-based assay. By replacing the k λ / k x ratio with k′ λ / k′ x (slope from signal intensity of differently diluted λDNA/slope from signal intensity of differently diluted target DNA× f x / f λ ), significant improvement in the accuracy of the estimation was achieved. The calculated cell numbers via the genomic probe technique were 0.99±0.13-, 1.25±0.23- and 0.18±0.11-fold higher than the respective CFUs in pure cultures of R. meliloti, Rhizobium sp. and Bradyrhizobium sp. In samples containing mixed populations, the estimated numbers from genomic probing were 1.25±0.51-, 45.9±14.8- and 0.27±0.07-fold higher than the CFU-derived cell count (same respective order).</abstract><cop>Shannon</cop><pub>Elsevier B.V</pub><pmid>15676199</pmid><doi>10.1016/j.mimet.2004.11.008</doi><tpages>8</tpages></addata></record>
fulltext fulltext
identifier ISSN: 0167-7012
ispartof Journal of microbiological methods, 2005-04, Vol.61 (1), p.87-94
issn 0167-7012
1872-8359
language eng
recordid cdi_proquest_miscellaneous_67385150
source MEDLINE; Elsevier ScienceDirect Journals Complete
subjects Bacteriology
Biological and medical sciences
Bradyrhizobium
Bradyrhizobium - genetics
Bradyrhizobium - growth & development
Bradyrhizobium - isolation & purification
Colony Count, Microbial
DNA, Bacterial - genetics
Enumaration
Environmental Microbiology
Fundamental and applied biological sciences. Psychology
Genome, Bacterial
Microbiology
Miscellaneous
Nucleic Acid Hybridization - methods
Reverse sample genome probing
Rhizobium meliloti
Sinorhizobium meliloti - genetics
Sinorhizobium meliloti - growth & development
Sinorhizobium meliloti - isolation & purification
title Simultaneous enumeration of different bacteria using reverse sample genome probing technique
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-17T17%3A22%3A36IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Simultaneous%20enumeration%20of%20different%20bacteria%20using%20reverse%20sample%20genome%20probing%20technique&rft.jtitle=Journal%20of%20microbiological%20methods&rft.au=Lee,%20S.L.&rft.date=2005-04-01&rft.volume=61&rft.issue=1&rft.spage=87&rft.epage=94&rft.pages=87-94&rft.issn=0167-7012&rft.eissn=1872-8359&rft.coden=JMIMDQ&rft_id=info:doi/10.1016/j.mimet.2004.11.008&rft_dat=%3Cproquest_cross%3E17837086%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=17837086&rft_id=info:pmid/15676199&rft_els_id=S0167701204003288&rfr_iscdi=true