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...
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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 |
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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 & 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</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>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=16474779$$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 & development</subject><subject>Bradyrhizobium - isolation & 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 & development</subject><subject>Sinorhizobium meliloti - isolation & 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 & development</topic><topic>Bradyrhizobium - isolation & 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 & development</topic><topic>Sinorhizobium meliloti - isolation & 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> |
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language | eng |
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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 |
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