Taxonomic Organization of the Family Brucellaceae Based on a Phylogenomic Approach

Abstract

Deciphering the evolutionary history of pathogenic bacteria and their near neighbors may help to understand the genetic or ecological bases which led to their pathogenic behavior. The Brucellaceae family comprises zoonotic pathogenic species belonging to the genus Brucella as well as the environmental genus Ochrobactrum for which some species are considered as opportunistic pathogens. Here, we used a phylogenomic approach including a set of 145 Brucellaceae genomes representative of the family diversity and more than 40 genomes of the order Rhizobiales to infer the taxonomic relationships between the family's species. Our results clarified some unresolved phylogenetic ambiguities, conducting to the exclusion of Mycoplana spp. out of the family Brucellaceae and the positioning of all Brucella spp. as a single genomic species within the current Ochrobactrum species diversity. Additional analyses also revealed that Ochrobactrum spp. separate into two clades, one comprising mostly environmental species while the other one includes the species considered as pathogens (Brucella spp.) or opportunistic pathogens (mainly O. anthropi, O. intermedium, and O. pseudintermedium). Finally, we show that O. intermedium is undergoing a beginning of genome reduction suggestive of an ongoing ecological niche specialization, and that some lineages of O. intermedium and O. anthropi may shift toward an adaption to the human host.

Application of Whole Genome Sequencing and Pan-Family Multi-Locus Sequence Analysis to Characterize Relationships Within the Family Brucellaceae

“…The current work supports previous findings, based on single-gene, multi-locus and whole genome analyses, which indicated that the genus Ochrobactrum represents a polyphyletic grouping (Kämpfer et al, 2013;Aujoulat et al, 2014;Leclercq et al, 2019). Our study provides the most comprehensive analysis to date of the composition of these groupings, and their relationships to other members of the family.…”

“…Very recently, Leclercq et al (2019) used WGS data to investigate relationships within the family Brucellaceae, as well as its position within the wider Rhizobiales. These authors confirmed the genus Brucella to be a monophyletic grouping within the genus Ochrobactrum, and that Ochrobactrum spp.…”

“…divide into two distinct clades. However, Leclercq et al (2019) did not incorporate type strains reflecting the full taxonomic diversity of either Ochrobactrum or Brucella. Additionally, the remaining genera within the Brucellaceae were either under-represented (Pseudochrobactrum and Mycoplana) or absent (Paenochrobactrum and Daeguia).…”

Brucella Genomics: Macro and Micro Evolution

“…From the lifestyle perspective, this Class includes free-living, commensals, endosymbionts, opportunistic, and intracellular pathogenic bacteria [ 2 , 3 , 4 ] and therefore is an excellent model for studying the evolution of parasitic bacteria. The genus Brucella belongs to one of the Class families, the Brucellaceae family, which includes the genera Pseudochrobactrum, Falsochrobactrum, Ochrobactrum , and Brucella [ 5 ]. The average genome size of Brucella organisms is 3.3 Mb, divided into two circular chromosomes of different sizes: 2.1 Mb and 1.2 Mb [ 6 ].…”

“…Multi-locus sequence type (MLST) and multiple loci variable number of tandem repeats (VNTR) analysis (MLVA) are now used to infer genetic diversity in Brucella by sequencing multiple genetic loci. They allow geographic clustering of the isolates, tracking sources of infection and their global dispersion [ 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 ]. Although the MLST classification has some practical application, sensu stricto a genetic variability is a continuous event that cannot be restricted to types, but rather to phylogenetic relations.…”