Intragenomic and intraspecific heterogeneity in rrs may surpass interspecific variability in a natural population of Veillonella

Abstract

As well as intraspecific heterogeneity, intragenomic heterogeneity between 16S rRNA gene copies has been described for a range of bacteria. Due to the wide use of 16S rRNA gene sequence analysis for taxonomy, identification and metagenomics, evaluating the extent of these heterogeneities in natural populations is an essential prerequisite. We investigated inter-and intragenomic 16S rRNA gene heterogeneity of the variable region V3 in a population of 149 clinical isolates of Veillonella spp. of human origin and in 13 type or reference Veillonella strains using PCR-temporal temperature gel electrophoresis (TTGE). 16S rRNA gene diversity was high in the studied population, as 45 different banding patterns were observed. Intragenomic heterogeneity was demonstrated for 110 (74 %) isolates and 8 (61.5 %) type or reference strains displaying two or three different gene copies. Polymorphic nucleotide positions accounted for 0.5-2.5 % of the sequence and were scattered in helices H16 and H17 of the rRNA molecule. Some of them changed the secondary structure of H17. Phylotaxonomic structure of the population based on the single-copy housekeeping gene rpoB was compared with TTGE patterns. The intragenomic V3 heterogeneity, as well as recombination events between strains or isolates of different rpoB clades, impaired the 16S rRNA-based identification for some Veillonella species. Such approaches should be conducted in other bacterial populations to optimize the interpretation of 16S rRNA gene sequences in taxonomy and/or diversity studies.

Increased level of intragenomic 16S rRNA gene heterogeneity in commensal strains closely related to Haemophilus influenzae

“…1). Similar problems with classifications based on 16S rRNA gene sequences have been documented for the genera Nocardia (Conville & Witebsky, 2007), Veillonella (Marchandin et al, 2003;Michon et al, 2010) and Streptococcus (Kilian et al, 2008).…”

“…document multiple-copy gene heterogeneity, but gradient gel-based methods also have drawbacks (Hestekin & Barron, 2006;Michon et al, 2010). Although single polymorphic positions in our material may have escaped detection, the disclosure of polymorphisms in the present report is robustly verified by the use of several experimental designs.…”

Human Coinfection with Bartonella henselae and Two Hemotropic Mycoplasma Variants Resembling Mycoplasma ovis

“…The detection of multiple different 16S rRNA gene sequences in this patient and the Hungarian sheep flock might also be explained by the existence of multiple copies of the 16S rRNA gene within a single strain of M. ovis, each having a variable genetic composition, as reported for other bacteria (16). The only hemotropic mycoplasma species for which 16S rRNA gene copy number has been ascertained is Mycoplasma haemofelis, which has a single copy of the 16S rRNA gene (2).…”

Dental Caries from a Molecular Microbiological Perspective

“…Systematic errors associated with the detection of 'high G+C organisms', including the Actinomyces and Bifidobacteriaceae , have been demonstrated such that these significant taxa are not accurately determined yet readily detected using culture techniques [Munson et al, 2004;Beighton et al, 2008;Frank et al, 2008;Preza et al, 2008]. Other issues relate to the inability of even full 16S rRNA sequences to differentiate between species, and this is of particular concern when investigating the microbiota associated with the caries process, as not all Streptococcus , Lactobacillus , Veillonellae and Actinomyces can be differentiated using 16S rRNA sequencing [Naser et al, 2007;Bishop et al, 2009;Henssge et al, 2009;Michon et al, 2010]. The use of shorter sequences compounds this problem, making the identification of many clones possible only to the genus level.…”