The importance of Veillonella spp. in human infections is uncertain, and they are generally considered to be of low virulence. Veillonella form biofilms, often with Streptococcus spp., and species of these genera have been found to be more abundant in the oral microflora of people with poor oral health [5]. Studies have shown that during formation selleck kinase inhibitor of early dental plaque, the fraction of Veillonella spp. changes in mixed-microbial colonies with streptococci [6]. Thus, Veillonella spp. may play a role in caries formation as they utilize the lactic acid produced by the organisms conducive to caries [7]. Veillonella are also among the most common anaerobic species reported from pulmonary samples and are frequently recovered from cystic fibrosis cases [8].

The organisms are also abundant in the human gut flora, where their numbers were found to be higher in children with type I diabetes compared to healthy controls [9]. Currently, 12 species of Veillonella have been characterized [10,11] including V. parvula, V. atypica and V. dispar, which are found in the human oral cavity. The Negativicutes are the only diderm (literally ‘two skins’) members of the phylum Firmicutes as they possess an inner and an outer membrane. Their placement within the Firmicutes has been widely accepted, and has been confirmed by 16S rRNA analysis [12]. However, their genomes have not been analyzed in detail to confirm their taxonomic position. This work presents a broad analysis of the Negativicutes with focus on the Veillonella spp. using comparative microbial genomics.

A total of 24 genomes from the Negativicutes were compared to 121 genomes covering most of the taxonomic span of sequenced bacterial genomes. We investigated how the Negativicutes genomes compared to other bacterial genomes using three different and complementary approaches: 1) phylogenetic trees to visualize the relative distance of the Negativicutes genomes to other genomes; 2) amino acid composition, nucleotide tetramer frequency and metabolism analysis using 2-D clustering and heatmaps to compare genomes; and 3) proteomic comparison across the Negativicutes genomes. Materials and Methods Genome sequences used for analysis The set of 145 genomes included in this study (24 Negativicutes genomes and 121 other prokaryotic genomes covering 26 phyla) are listed in Table 1.

Table Cilengitide 1 Genomes used in this study 16S rRNA tree For this analysis, 16S rRNA sequences were predicted from the whole genome sequences of the selected organisms, using the RNAmmer algorithm [13]. These sequences were aligned using the MAFFT program, with the iterative refinement algorithm using maximum iteration (1000) and default parameters for gap penalties [14]. A distance tree was constructed using MEGA5 [15] with the Neighbor-joining algorithm [16] and 1,000 bootstrap re-samplings. The taxa in the resulting tree were collapsed to phyla, except for the Negativicutes.