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.

Four previously unknown, gram-negative, anaerobic coccal strains were isolated from the tongue biofilm of healthy human adults (ages 22-29 years). The isolates displayed all phenotypic characteristics of the genus Veillonella. Comparative analysis of the 16S rRNA, dnaK and rpoB gene sequences indicated that the four strains were phylogenetically homogeneous and comprised a distinct novel lineage within the genus Veillonella. The production of major cellular fatty acids (C13 : 0 and C17 : 1�s8) was consistent with that of other members of the genus Veillonella. Based on these observations, strains B16(T), A16, B4 and Y6 represent a novel species, for which the name Veillonella tobetsuensis sp. nov. is proposed, with the type strain B16(T) (= JCM 17976(T) = ATCC BAA-2400(T)).

The genes encoding methylmalonyl-CoA decarboxylase from Veillonella parvula were cloned on plasmids using oligonucleotides derived from N-terminal amino acid sequences as specific probes. The entire DNA sequence of the methylmalonyl-CoA decarboxylase genes together with upstream and downstream regions was determined. The genes encoding subunits alpha (mmdA), delta (mmdD), epsilon (mmdE), gamma (mmdC), and beta (mmdB) of the decarboxylase were clustered on the chromosome in the given order. The previously unnoted epsilon-chain (M(r) 5,888) was clearly shown to be a subunit of the decarboxylase by correspondence of the N-terminal amino acid sequence with that deduced from the DNA sequence of mmdE. The alpha-subunit was 60% identical with the carboxyltransferase domain of rat liver propionyl-CoA carboxylase, the beta-subunit showed 61% sequence identity with the beta-subunit of oxaloacetate decarboxylase from Klebsiella pneumoniae, and the biotin-containing gamma-subunit was 29-39% identical with biotin-domains of other biotin enzymes. The delta-subunit of methylmalonyl-CoA decarboxylase and the gamma-subunit of oxaloacetate decarboxylase did not show significant sequence homology. The gross structure of both proteins, however, was similar, consisting of a hydrophobic membrane anchor near the N terminus, a proline/alanine linker, and a remarkable accumulation of charged amino acids in the C-terminal part. The sequence of the small epsilon-subunit could be aligned to the C-terminal region of the delta-subunit downstream of the proline/alanine linker, where the two subunits were 47% identical. Of considerable interest for the mechanism of Na+ transport are the long stretches of complete sequence identity between the hydrophobic beta-subunits of methylmalonyl-CoA decarboxylase and oxaloacetate decarboxylase and the presence of two conserved aspartic acid residues within putative membrane-spanning helices.