title: Diversity of 16S rRNA genes within individual prokaryotic genomes.
abstract: Analysis of intragenomic variation of 16S rRNA genes is a unique approach to examining the concept of ribosomal constraints on rRNA genes; the degree of variation is an important parameter to consider for estimation of the diversity of a complex microbiome in the recently initiated Human Microbiome Project (http://nihroadmap.nih.gov/hmp). The current GenBank database has a collection of 883 prokaryotic genomes representing 568 unique species, of which 425 species contained 2 to 15 copies of 16S rRNA genes per genome (2.22 +/- 0.81). Sequence diversity among the 16S rRNA genes in a genome was found in 235 species (from 0.06% to 20.38%; 0.55% +/- 1.46%). Compared with the 16S rRNA-based threshold for operational definition of species (1 to 1.3% diversity), the diversity was borderline (between 1% and 1.3%) in 10 species and >1.3% in 14 species. The diversified 16S rRNA genes in Haloarcula marismortui (diversity, 5.63%) and Thermoanaerobacter tengcongensis (6.70%) were highly conserved at the 2 degrees structure level, while the diversified gene in B. afzelii (20.38%) appears to be a pseudogene. The diversified genes in the remaining 21 species were also conserved, except for a truncated 16S rRNA gene in "Candidatus Protochlamydia amoebophila." Thus, this survey of intragenomic diversity of 16S rRNA genes provides strong evidence supporting the theory of ribosomal constraint. Taxonomic classification using the 16S rRNA-based operational threshold could misclassify a number of species into more than one species, leading to an overestimation of the diversity of a complex microbiome. This phenomenon is especially seen in 7 bacterial species associated with the human microbiome or diseases.
authors.affiliation: New York University College of Arts and Science, New York, New York 10012, USA.
authors.forename: Anna Y
authors.initials: AY
authors.lastname: Pei
authors.forename: William E
authors.initials: WE
authors.lastname: Oberdorf
authors.forename: Carlos W
authors.initials: CW
authors.lastname: Nossa
authors.forename: Ankush
authors.initials: A
authors.lastname: Agarwal
authors.forename: Pooja
authors.initials: P
authors.lastname: Chokshi
authors.forename: Erika A
authors.initials: EA
authors.lastname: Gerz
authors.forename: Zhida
authors.initials: Z
authors.lastname: Jin
authors.forename: Peng
authors.initials: P
authors.lastname: Lee
authors.forename: Liying
authors.initials: L
authors.lastname: Yang
authors.forename: Michael
authors.initials: M
authors.lastname: Poles
authors.forename: Stuart M
authors.initials: SM
authors.lastname: Brown
authors.forename: Steven
authors.initials: S
authors.lastname: Sotero
authors.forename: Todd
authors.initials: T
authors.lastname: Desantis
authors.forename: Eoin
authors.initials: E
authors.lastname: Brodie
authors.forename: Karen
authors.initials: K
authors.lastname: Nelson
authors.forename: Zhiheng
authors.initials: Z
authors.lastname: Pei
mesh_terms: D020459:Genes, rRNA / Q000235:genetics*; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D011110:Polymorphism, Genetic; D012336:RNA, Ribosomal, 16S / Q000235:genetics*
chemical_list: D012336:RNA, Ribosomal, 16S