Pan-genomics of Ochrobactrum species from clinical and environmental origins reveals distinct populations and possible links

Pathogenicity and Its Implications in Taxonomy: The Brucella and Ochrobactrum Case

“…The gentle slope of the pangenome/core genome ratio curve for the Brucella members on a logarithmic scale shows that the genus’s increase in genetic diversity per sequenced genome added is low ( Figure 2 ). Accordingly, the estimated core genome size for the genus is ~1000 genes with a pangenome size close to ~11,000 genes, a figure that agrees with several studies [ 20 , 22 , 23 , 24 , 25 , 26 , 27 ]. Therefore, the dispersion of the Brucella species in trees constructed using different phylogenetic strategies displays good correspondence.…”

“…In the Ochrobactrum genus, the genetic repertoire is much more extensive than the gene content of the individual strains and species, and a significant number of genes per additional sequenced genome are continuously added, as shown by the pronounced pangenome/core genome curve slope ( Figure 2 ). As expected, the estimated core genome for the Ochrobactrum genus corresponds just to ~75 genes, while the complete pangenome is, up to now, close to 74,000 genes, that is, ~1000 times larger than the core genome [ 22 ]. Therefore, predicting the actual size and content of the Ochrobactrum pangenome is, in practical terms, unfeasible because the number of genes is constantly climbing due to numerous recombination and shuffling events.…”

“…Some of these differences are associated with the presence of variable numbers of plasmids or chromides in the Ochrobactrum species [ 20 ], while in Brucella, the genome size and absence of plasmids is a constant trait ( Table 1 and Figure 2 ), all characteristics of great relevance (see below). Similarly unnoticed is the biological meaning of the ~170 Brucella proteins whose genes are not found in the Ochrobactrum genomes, 40% clustering into 15 genomic sections, and the ~249 genes in 13 genomic regions unique to Brucella [ 22 , 23 ]; also critical are the idiosyncratic insertion sequences (e.g., IS711) and genomic islands with a different evolutionary history, including those encoding one Type IV secretion system and the genes involved in synthesizing the lipopolysaccharide (LPS) O-chain. It is worth noting that both are involved in virulence and the intracellular lifestyle of Brucella organisms [ 23 , 35 , 46 , 49 , 50 ], while the two Type IV secretion systems found in Ochrobactrum seem devoted to plasmid conjugation with a different evolutionary history [ 68 ].…”

“…None of the Ochrobactrum phages described have activity against Brucella species [ 29 ]. In addition, the Ochrobactrum organisms contain from 4 to 12 rRNA operons and a broad spectrum of metabolic alternatives [ 22 , 37 ]. Consequently, Ochrobactrum organisms display the characteristic wide-open pangenome of soil bacteria subjected to continuous scattering and genomic diversification [ 22 , 23 ].…”

“…In addition, the Ochrobactrum organisms contain from 4 to 12 rRNA operons and a broad spectrum of metabolic alternatives [ 22 , 37 ]. Consequently, Ochrobactrum organisms display the characteristic wide-open pangenome of soil bacteria subjected to continuous scattering and genomic diversification [ 22 , 23 ]. In the Ochrobactrum genus, the genetic repertoire is much more extensive than the gene content of the individual strains and species, and a significant number of genes per additional sequenced genome are continuously added, as shown by the pronounced pangenome/core genome curve slope ( Figure 2 ).…”