Construction of BLAST matrix and proteome comparison Reciprocal BLAST was performed selleck chem inhibitor between each genome pair. The program blastall version 2.2.25 was used for BLAST implementation using default settings (BLASTp, E-value set to 1��10?5 for non-homologs and 1��10?8 for homologs, without filtering). A hit was considered significant at a BLAST cutoff of 95% identity and 95% coverage (of the longest gene in comparison). The number of hits was then given as a percentage of the genes in the column representing the corresponding genome. The diagonal designates internal homologs, computed by blasting each genome with itself. To avoid including identical genes, the second highest scoring hits were used. Furthermore, we also performed homology reduction of the diagonal hits, using an implementation of the Hobohm algorithm [26].

Results Twenty-four Negativicutes genomes were compared to 121 other prokaryotic genomes covering 22 Bacterial and 4 Archaeal phyla. When available, at least two genomes were included for every phylum. The first analysis presented here is based on 16S rRNA alignments. A single 16S rRNA gene was extracted from each of the genomes and an alignment was produced spanning the maximum length of the gene. A phylogenetic tree was constructed based on this alignment, as shown in Figure 1. With the exception of the Negativicutes, branches of the tree were collapsed in those cases where the analyzed species within a phylum clustered together.

With the exception of some Firmicutes, the analyzed genomes cluster according to their phylum, although the Deferribacteres phylum is mixed with the Proteobacteria phyla, and two members of Proteobacteria are not positioned with other members of their phylum (Lawsonia intracellularis and Magnetococcus). That most phyla could be collapsed is consistent with the weight of 16S rRNA similarities in currently accepted taxonomic descriptions of prokaryotes. The Firmicutes, however, show less consistency. Although most of the analyzed Firmicutes cluster together, two species are separated from the Firmicutes branch (Eubacterium cylindroides and Thermoanaerobacter sp., both members of Clostridia). The Negativicutes are positioned within the Firmicutes cluster, and this part of the tree is expanded in the figure for clarity. As can be seen, phylogeny of the 16S rRNA gene provides good resolution between the different genera of the analyzed Negativicutes.

Batimastat All Veillonella spp. are clustered within one branch of the Negativicutes. The Acidaminococcaceae (to which Phascolarctobacterium spp. also belong) are placed within the cluster of the Veillonellaceae, in accordance with their current classification [27]. The Acidaminococcaceae used to be recognized as a separate family within the Negativicutes, just like the Veillonellaceae, and during preparation of this contribution these two families were presented as such in the Taxonomy database at NCBI.