The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses.

16S ribosomal RNA currently represents the most important target of study in bacterial ecology. Its use for the description of bacterial diversity is, however, limited by the presence of variable copy numbers in bacterial genomes and sequence variation within closely related taxa or within a genome....

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Autores principales:	Tomáš Větrovský, Petr Baldrian
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e8aa325137db4123b2b798779036a0fb
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spelling	oai:doaj.org-article:e8aa325137db4123b2b798779036a0fb2021-11-18T07:55:43ZThe variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses.1932-620310.1371/journal.pone.0057923https://doaj.org/article/e8aa325137db4123b2b798779036a0fb2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23460914/?tool=EBIhttps://doaj.org/toc/1932-620316S ribosomal RNA currently represents the most important target of study in bacterial ecology. Its use for the description of bacterial diversity is, however, limited by the presence of variable copy numbers in bacterial genomes and sequence variation within closely related taxa or within a genome. Here we use the information from sequenced bacterial genomes to explore the variability of 16S rRNA sequences and copy numbers at various taxonomic levels and apply it to estimate bacterial genome and DNA abundances. In total, 7,081 16S rRNA sequences were in silico extracted from 1,690 available bacterial genomes (1-15 per genome). While there are several phyla containing low 16S rRNA copy numbers, in certain taxa, e.g., the Firmicutes and Gammaproteobacteria, the variation is large. Genome sizes are more conserved at all tested taxonomic levels than 16S rRNA copy numbers. Only a minority of bacterial genomes harbors identical 16S rRNA gene copies, and sequence diversity increases with increasing copy numbers. While certain taxa harbor dissimilar 16S rRNA genes, others contain sequences common to multiple species. Sequence identity clusters (often termed operational taxonomic units) thus provide an imperfect representation of bacterial taxa of a certain phylogenetic rank. We have demonstrated that the information on 16S rRNA copy numbers and genome sizes of genome-sequenced bacteria may be used as an estimate for the closest related taxon in an environmental dataset to calculate alternative estimates of the relative abundance of individual bacterial taxa in environmental samples. Using an example from forest soil, this procedure would increase the abundance estimates of Acidobacteria and decrease these of Firmicutes. Using the currently available information, alternative estimates of bacterial community composition may be obtained in this way if the variation of 16S rRNA copy numbers among bacteria is considered.Tomáš VětrovskýPetr BaldrianPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 2, p e57923 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Tomáš Větrovský Petr Baldrian The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses.
description	16S ribosomal RNA currently represents the most important target of study in bacterial ecology. Its use for the description of bacterial diversity is, however, limited by the presence of variable copy numbers in bacterial genomes and sequence variation within closely related taxa or within a genome. Here we use the information from sequenced bacterial genomes to explore the variability of 16S rRNA sequences and copy numbers at various taxonomic levels and apply it to estimate bacterial genome and DNA abundances. In total, 7,081 16S rRNA sequences were in silico extracted from 1,690 available bacterial genomes (1-15 per genome). While there are several phyla containing low 16S rRNA copy numbers, in certain taxa, e.g., the Firmicutes and Gammaproteobacteria, the variation is large. Genome sizes are more conserved at all tested taxonomic levels than 16S rRNA copy numbers. Only a minority of bacterial genomes harbors identical 16S rRNA gene copies, and sequence diversity increases with increasing copy numbers. While certain taxa harbor dissimilar 16S rRNA genes, others contain sequences common to multiple species. Sequence identity clusters (often termed operational taxonomic units) thus provide an imperfect representation of bacterial taxa of a certain phylogenetic rank. We have demonstrated that the information on 16S rRNA copy numbers and genome sizes of genome-sequenced bacteria may be used as an estimate for the closest related taxon in an environmental dataset to calculate alternative estimates of the relative abundance of individual bacterial taxa in environmental samples. Using an example from forest soil, this procedure would increase the abundance estimates of Acidobacteria and decrease these of Firmicutes. Using the currently available information, alternative estimates of bacterial community composition may be obtained in this way if the variation of 16S rRNA copy numbers among bacteria is considered.
format	article
author	Tomáš Větrovský Petr Baldrian
author_facet	Tomáš Větrovský Petr Baldrian
author_sort	Tomáš Větrovský
title	The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses.
title_short	The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses.
title_full	The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses.
title_fullStr	The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses.
title_full_unstemmed	The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses.
title_sort	variability of the 16s rrna gene in bacterial genomes and its consequences for bacterial community analyses.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/e8aa325137db4123b2b798779036a0fb
work_keys_str_mv	AT tomasvetrovsky thevariabilityofthe16srrnageneinbacterialgenomesanditsconsequencesforbacterialcommunityanalyses AT petrbaldrian thevariabilityofthe16srrnageneinbacterialgenomesanditsconsequencesforbacterialcommunityanalyses AT tomasvetrovsky variabilityofthe16srrnageneinbacterialgenomesanditsconsequencesforbacterialcommunityanalyses AT petrbaldrian variabilityofthe16srrnageneinbacterialgenomesanditsconsequencesforbacterialcommunityanalyses
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The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses.

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