@article{RN16,
   author = {Acinas, S. G. and Ferrera, I. and Sarmento, H. and Diez-Vives, C. and Forn, I. and Ruiz-Gonzalez, C. and Cornejo-Castillo, F. M. and Salazar, G. and Gasol, J. M.},
   title = {Validation of a new catalysed reporter deposition-fluorescence in situ hybridization probe for the accurate quantification of marine Bacteroidetes populations},
   journal = {Environ Microbiol},
   volume = {17},
   number = {10},
   pages = {3557-69},
   note = {Acinas, Silvia G
Ferrera, Isabel
Sarmento, Hugo
Diez-Vives, Cristina
Forn, Irene
Ruiz-Gonzalez, Clara
Cornejo-Castillo, Francisco M
Salazar, Guillem
Gasol, Josep M
eng
Comparative Study
Research Support, Non-U.S. Gov't
Validation Study
England
Environ Microbiol. 2015 Oct;17(10):3557-69. doi: 10.1111/1462-2920.12517. Epub 2014 Jul 7.},
   abstract = {Catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH) is a powerful approach to quantify bacterial taxa. In this study, we compare the performance of the widely used Bacteroidetes CF319a probe with the new CF968 probe. In silico analyses and tests with isolates demonstrate that CF319a hybridizes with non-Bacteroidetes sequences from the Rhodobacteraceae and Alteromonadaceae families. We test the probes' accuracy in 37 globally distributed marine samples and over two consecutive years at the Blanes Bay Microbial Observatory (NW Mediterranean). We also compared the CARD-FISH data with the Bacteroidetes 16S rRNA gene sequences retrieved from 27 marine metagenomes from the TARA Oceans expedition. We find no significant differences in abundances between both approaches, although CF319a targeted some unspecific sequences and both probes displayed different abundances of specific Bacteroidetes phylotypes. Our results demonstrate that quantitative estimations by using both probes are significantly different in certain oceanographic regions (Mediterranean Sea, Red Sea and Arabian Sea) and that CF968 shows seasonality within marine Bacteroidetes, notably large differences between summer and winter that is overlooked by CF319a. We propose CF968 as an alternative to CF319a for targeting the whole Bacteroidetes phylum since it has better coverage, greater specificity and overall better quantifies marine Bacteroidetes.},
   keywords = {Alteromonadaceae/genetics
Bacteroidetes/*classification/genetics
DNA Probes/*genetics
DNA, Bacterial/*genetics
In Situ Hybridization, Fluorescence/*methods
Mediterranean Sea
RNA, Ribosomal, 16S/genetics
Rhodobacteraceae/genetics
Seasons
Seawater/microbiology
Sequence Analysis, DNA},
   ISSN = {1462-2920 (Electronic)
1462-2912 (Linking)},
   DOI = {10.1111/1462-2920.12517},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/24890225},
   year = {2015},
   type = {Journal Article}
}

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M."],"bibdata":{"bibtype":"article","type":"Journal Article","author":[{"propositions":[],"lastnames":["Acinas"],"firstnames":["S.","G."],"suffixes":[]},{"propositions":[],"lastnames":["Ferrera"],"firstnames":["I."],"suffixes":[]},{"propositions":[],"lastnames":["Sarmento"],"firstnames":["H."],"suffixes":[]},{"propositions":[],"lastnames":["Diez-Vives"],"firstnames":["C."],"suffixes":[]},{"propositions":[],"lastnames":["Forn"],"firstnames":["I."],"suffixes":[]},{"propositions":[],"lastnames":["Ruiz-Gonzalez"],"firstnames":["C."],"suffixes":[]},{"propositions":[],"lastnames":["Cornejo-Castillo"],"firstnames":["F.","M."],"suffixes":[]},{"propositions":[],"lastnames":["Salazar"],"firstnames":["G."],"suffixes":[]},{"propositions":[],"lastnames":["Gasol"],"firstnames":["J.","M."],"suffixes":[]}],"title":"Validation of a new catalysed reporter deposition-fluorescence in situ hybridization probe for the accurate quantification of marine Bacteroidetes populations","journal":"Environ Microbiol","volume":"17","number":"10","pages":"3557-69","note":"Acinas, Silvia G Ferrera, Isabel Sarmento, Hugo Diez-Vives, Cristina Forn, Irene Ruiz-Gonzalez, Clara Cornejo-Castillo, Francisco M Salazar, Guillem Gasol, Josep M eng Comparative Study Research Support, Non-U.S. Gov't Validation Study England Environ Microbiol. 2015 Oct;17(10):3557-69. doi: 10.1111/1462-2920.12517. Epub 2014 Jul 7.","abstract":"Catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH) is a powerful approach to quantify bacterial taxa. In this study, we compare the performance of the widely used Bacteroidetes CF319a probe with the new CF968 probe. In silico analyses and tests with isolates demonstrate that CF319a hybridizes with non-Bacteroidetes sequences from the Rhodobacteraceae and Alteromonadaceae families. We test the probes' accuracy in 37 globally distributed marine samples and over two consecutive years at the Blanes Bay Microbial Observatory (NW Mediterranean). We also compared the CARD-FISH data with the Bacteroidetes 16S rRNA gene sequences retrieved from 27 marine metagenomes from the TARA Oceans expedition. We find no significant differences in abundances between both approaches, although CF319a targeted some unspecific sequences and both probes displayed different abundances of specific Bacteroidetes phylotypes. Our results demonstrate that quantitative estimations by using both probes are significantly different in certain oceanographic regions (Mediterranean Sea, Red Sea and Arabian Sea) and that CF968 shows seasonality within marine Bacteroidetes, notably large differences between summer and winter that is overlooked by CF319a. We propose CF968 as an alternative to CF319a for targeting the whole Bacteroidetes phylum since it has better coverage, greater specificity and overall better quantifies marine Bacteroidetes.","keywords":"Alteromonadaceae/genetics Bacteroidetes/*classification/genetics DNA Probes/*genetics DNA, Bacterial/*genetics In Situ Hybridization, Fluorescence/*methods Mediterranean Sea RNA, Ribosomal, 16S/genetics Rhodobacteraceae/genetics Seasons Seawater/microbiology Sequence Analysis, DNA","issn":"1462-2920 (Electronic) 1462-2912 (Linking)","doi":"10.1111/1462-2920.12517","url":"https://www.ncbi.nlm.nih.gov/pubmed/24890225","year":"2015","bibtex":"@article{RN16,\r\n author = {Acinas, S. G. and Ferrera, I. and Sarmento, H. and Diez-Vives, C. and Forn, I. and Ruiz-Gonzalez, C. and Cornejo-Castillo, F. M. and Salazar, G. and Gasol, J. M.},\r\n title = {Validation of a new catalysed reporter deposition-fluorescence in situ hybridization probe for the accurate quantification of marine Bacteroidetes populations},\r\n journal = {Environ Microbiol},\r\n volume = {17},\r\n number = {10},\r\n pages = {3557-69},\r\n note = {Acinas, Silvia G\r\nFerrera, Isabel\r\nSarmento, Hugo\r\nDiez-Vives, Cristina\r\nForn, Irene\r\nRuiz-Gonzalez, Clara\r\nCornejo-Castillo, Francisco M\r\nSalazar, Guillem\r\nGasol, Josep M\r\neng\r\nComparative Study\r\nResearch Support, Non-U.S. Gov't\r\nValidation Study\r\nEngland\r\nEnviron Microbiol. 2015 Oct;17(10):3557-69. doi: 10.1111/1462-2920.12517. Epub 2014 Jul 7.},\r\n abstract = {Catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH) is a powerful approach to quantify bacterial taxa. In this study, we compare the performance of the widely used Bacteroidetes CF319a probe with the new CF968 probe. In silico analyses and tests with isolates demonstrate that CF319a hybridizes with non-Bacteroidetes sequences from the Rhodobacteraceae and Alteromonadaceae families. We test the probes' accuracy in 37 globally distributed marine samples and over two consecutive years at the Blanes Bay Microbial Observatory (NW Mediterranean). We also compared the CARD-FISH data with the Bacteroidetes 16S rRNA gene sequences retrieved from 27 marine metagenomes from the TARA Oceans expedition. We find no significant differences in abundances between both approaches, although CF319a targeted some unspecific sequences and both probes displayed different abundances of specific Bacteroidetes phylotypes. Our results demonstrate that quantitative estimations by using both probes are significantly different in certain oceanographic regions (Mediterranean Sea, Red Sea and Arabian Sea) and that CF968 shows seasonality within marine Bacteroidetes, notably large differences between summer and winter that is overlooked by CF319a. 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