The relevant part of the heatmap based

The relevant part of the heatmap based selleck Nutlin-3a on amino acid frequency is shown in Figure 4. All Veillonella genomes cluster together within the Negativicutes, with the exception of two of the three Dialister genomes, which are found most closely related to Clostridium species (See supplemental information for a version of this figure showing all the genomes). The major Negativicutes cluster also contains a Geobacillus (which is a Gram-positive Firmicutes) and a methanogenic Archaean. Interestingly, the closest relatives to this cluster are not Clostridia, as the previous phylogenetic trees suggest, but a number of Proteobacteria. It is striking that the amino acid frequency analysis detects similarities to Proteobacteria, with which the Negativicutes have their two membranes in common.

Figure 4 A zoomed heatmap of the amino acid frequency found in the deduced proteomes of all 145 genomes. A fragment of the heatmap is shown, presenting the cluster in which all but two Negativicutes are found. The remaining two, both Dialister microaerophilus … The metabolic properties encoded by the genomes were analyzed next, based on KEGG comparisons [24]. The results are again visualized in a heatmap (Figure 5). We hypothesized that this analysis could identify similarities based on niche adaptation. For simplicity, only a selected number of phyla are shown: apart from the Firmicutes, genomes are included that represent Bacteroidetes and Proteobacteria (both of which contain members frequently found in the oral or gut microbiome), while Cyanobacteria are included as representatives of a phylum that occupy an environmental niche.

Since the genomes are compared based on predicted proteomes, their annotation was standardized in order to reduce artificial variation caused by gene annotation differences. As can be seen in Figure 5, the Veillonella genomes all cluster together at the right-hand side of the plot, within a larger cluster containing most of the other Negativicutes and some Firmicutes. The three Dialister species are placed outside the Negativicutes cluster. The other Firmicutes that are found combined with the Negativicutes, based on their metabolic potential, are Clostridium cellulolyticum, Eubacterium rectale, Lactococcus lactis, Streptococcus pneumoniae and Turicibacter sanguinis. These are all common members of the oral or intestine microbiome.

As expected, the metabolic pathway for lipopolysaccharide biosynthesis is shared between the Negativicutes and other Gram-negative species, as indicated by the arrows in Figure 5. Interestingly, the Cyanobacteria form a small cluster within, not outside the tree, together with a Haliangium and a Sorangium species as their closest neighbors (both are social Myxococcales Anacetrapib belonging to the Deltaproteobacteria).

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