The lanes of Veillonella in Figure 5 are dominated by light colors, indicative of medium metabolic potential; that is, in contrast to some genomes where most of the pathways are present (dark red for Proteobacteria for example) or missing (dark green for http://www.selleckchem.com/products/XL184.html other Negativicutes), the Veillonella genomes have partial pathways (based on knowledge primarily from aerobic genomes). There is no reason to believe that the Veillonella genomes should have less metabolic potential than other Negativicutes. Indeed, it is likely that the differences in metabolic potential of Veillonella are truly reflective of alternative capabilities for these bacteria. Figure 5 Heatmap of metabolism potential, based on Kyoto Encyclopedia of Genes and Genomes ontology (KEGG).
The green color in the heatmap indicates weak metabolic potential, while red signals strong potential. The arrows to the right indicate the scores for lipopolysaccharide … It was further investigated how conserved the predicted proteomes are within the Negativicutes. As a quantitative measure for homology, shared protein-coding genes were identified by pairwise BLASTP comparison and expressed as a percentage of the combined proteomes. The results are shown in a matrix (Figure 6). In addition to the proteomes of the 24 Negativicutes, the comparison includes Clostridium botulinum, Cl. cellulolyticum and Desulfotomaculum reducens, as these Firmicutes were shown to share characteristics with Negativicutes in previous analyses (cf. Figures 1 and and3).3). The proteome of E. coli K12 is included as an example of a Gram-negative intestinal bacterium.
The BLAST matrix was constructed using reciprocal best BLAST hits to determine the presence of shared protein family between two genomes. Inspection of Figure 6 shows that the genus Veillonella is relatively homogeneous; any two members of this genus share between 67% and 90% homology (1,357 to 1,682 protein families), irrespective of the species. The genus Selenomonas is more heterogeneous, with pairwise homology varying from 42% to 82% between any two species (980 to 1659 protein families). The three proteomes of Dialister spp., covering two species, share between 40% and 84% homology. The highest homologous fraction identified between two members of different genera within the Negativicutes is 43% (Mitsuokella multacida compared to Selenomonas sputigena, whereas the lowest homology is 15% (Dialister spp.
compared to Thermosinus carboxydivorans). Negativicutes share between 9% and 33% homology with the analyzed Firmicutes, whereas Cilengitide slightly lower homology is detected with E. coli (between 7% and 24%). Figure 6 Proteome comparison represented by a BLAST matrix, based on 24 Negativicutes genomes with reciprocal best hits. The genomes of Clostridium botulinum, Cl. cellulolyticum, Desulfotomaculum reducens and E. coli are added for comparison. Inter-genus comparisons …