Advantages and limitations of genomics in prokaryotic taxonomy
Taxonomic classification is an important field of microbiology, as it enables scientists to identify prokaryotes worldwide. Although the current classification system is still based on the one designed by Carolus Linnaeus, the currently available genomic content of several thousands of sequenced pro...
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| Veröffentlicht in: | Clinical microbiology and infection 2013-09, Vol.19 (9), p.790-795 |
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| creator | Sentausa, E. Fournier, P.-E. |
| description | Taxonomic classification is an important field of microbiology, as it enables scientists to identify prokaryotes worldwide. Although the current classification system is still based on the one designed by Carolus Linnaeus, the currently available genomic content of several thousands of sequenced prokaryotic genomes represents a unique source of taxonomic information that should not be ignored. In addition, the development of faster, cheaper and improved sequencing methods has made genomics a tool that has a place in the workflow of a routine microbiology laboratory. Thus, genomics has reached a stage where it may be used in prokaryotic taxonomic classification, with criteria such as the genome index of average nucleotide identity being an alternative to DNA–DNA hybridization. However, several hurdles remain, including the lack of genomic sequences of many prokaryotic taxonomic representatives, and consensus procedures to describe new prokaryotic taxa that do not, as yet, accommodate genomic data. We herein review the advantages and disadvantages of using genomics in prokaryotic taxonomy. |
| doi_str_mv | 10.1111/1469-0691.12181 |
| format | Article |
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We herein review the advantages and disadvantages of using genomics in prokaryotic taxonomy.</description><subject>Advantages</subject><subject>Average nucleotide identity</subject><subject>Bacteria - classification</subject><subject>Bacteria - genetics</subject><subject>Bacteria - isolation & purification</subject><subject>Bacterial Typing Techniques</subject><subject>Classification</subject><subject>DNA–DNA hybridization</subject><subject>genome-based phylogeny</subject><subject>Genomics</subject><subject>Genomics - methods</subject><subject>Phylogeny</subject><subject>prokaryotic taxonomy</subject><subject>Sequence Analysis, DNA</subject><subject>Species Specificity</subject><subject>Taxonomy</subject><issn>1198-743X</issn><issn>1469-0691</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkEtLxDAURoMoPkbX7qTgxk01N89mI8jgC0bcKLgLmTQdom0zNh11_r0Z57EQxGwSknM_vhyEjgGfQ1oXwITKsVBwDgQK2EL7m5vtdAZV5JLRlz10EOMrxphQynbRHqFM4TSxjy6vyg_T9mbiYmbaMqt943vT-9DGLFTZxLWh8TZmvs2mXXgz3Tz03ma9-QrpZX6IdipTR3e02gfo-eb6aXiXjx5v74dXo9wyQSBnohScYSmIBWnsuFK4lFLCmFVFUQgJ3NoCE2W4EYILyqngpZOWcyAKqKUDdLbMTSXeZy72uvHRuro2rQuzqIERITmWVCT09Bf6GmZdm9pp4EQJQQpJE3WxpGwXYuxcpaedb9L3NGC9UKsXIvVCpP5RmyZOVrmzcePKDb92mQC-BD597eb_5enh6GEdrJZzLgn88K7T0XrXWlf6ztlel8H_WeobXl-SvQ</recordid><startdate>201309</startdate><enddate>201309</enddate><creator>Sentausa, E.</creator><creator>Fournier, P.-E.</creator><general>Elsevier Ltd</general><general>Elsevier Limited</general><scope>6I.</scope><scope>AAFTH</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>7U9</scope><scope>C1K</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>7X8</scope></search><sort><creationdate>201309</creationdate><title>Advantages and limitations of genomics in prokaryotic taxonomy</title><author>Sentausa, E. ; Fournier, P.-E.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4621-46d6540762c17acbf90d7771b4f8886715cc8029a5a665635365de7c5512913c3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Advantages</topic><topic>Average nucleotide identity</topic><topic>Bacteria - classification</topic><topic>Bacteria - genetics</topic><topic>Bacteria - isolation & purification</topic><topic>Bacterial Typing Techniques</topic><topic>Classification</topic><topic>DNA–DNA hybridization</topic><topic>genome-based phylogeny</topic><topic>Genomics</topic><topic>Genomics - methods</topic><topic>Phylogeny</topic><topic>prokaryotic taxonomy</topic><topic>Sequence Analysis, DNA</topic><topic>Species Specificity</topic><topic>Taxonomy</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Sentausa, E.</creatorcontrib><creatorcontrib>Fournier, P.-E.</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</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>Virology and AIDS Abstracts</collection><collection>Environmental Sciences and Pollution Management</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>MEDLINE - Academic</collection><jtitle>Clinical microbiology and infection</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sentausa, E.</au><au>Fournier, P.-E.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Advantages and limitations of genomics in prokaryotic taxonomy</atitle><jtitle>Clinical microbiology and infection</jtitle><addtitle>Clin Microbiol Infect</addtitle><date>2013-09</date><risdate>2013</risdate><volume>19</volume><issue>9</issue><spage>790</spage><epage>795</epage><pages>790-795</pages><issn>1198-743X</issn><eissn>1469-0691</eissn><abstract>Taxonomic classification is an important field of microbiology, as it enables scientists to identify prokaryotes worldwide. 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| ispartof | Clinical microbiology and infection, 2013-09, Vol.19 (9), p.790-795 |
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| source | MEDLINE; EZB-FREE-00999 freely available EZB journals; Wiley Online Library All Journals; Alma/SFX Local Collection |
| subjects | Advantages Average nucleotide identity Bacteria - classification Bacteria - genetics Bacteria - isolation & purification Bacterial Typing Techniques Classification DNA–DNA hybridization genome-based phylogeny Genomics Genomics - methods Phylogeny prokaryotic taxonomy Sequence Analysis, DNA Species Specificity Taxonomy |
| title | Advantages and limitations of genomics in prokaryotic taxonomy |
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