TABLE 1.

Concerns arising from the Ochrobactrum/Brucella cladistics presented in reference 1

Concern	Comment
Phylogeny based on evolutionary abstraction	The authors extol the utility of alignment supermatrices of core genomes for inferring trees of closely related species, but they infer a tree based on BLASTp distance neighbor joining with minimum evolution refinement for all alphaproteobacteria and then, with this tree, revise the closely related Brucella/Ochrobactrum, whose core genomes are easily alignable.
Phylogenetics without context	The omission and addition of sequences commonly change tree topologies. Leaving out samples that are not type strains will likely necessitate further revisions to correct misleading topologies or to account for yet-to-be type strain placements.
The proposed “Brucella” is polyphyletic at conception	All brucellae (core and not core) are consistently recovered as monophyletic; however, Ochrobactrum is commonly rendered polyphyletic by Brucella but also Pseudochrobactrum, Falsochrobactrum, and Paenochrobactrum, as shown in the authors’ own rRNA tree and the works they cite.
Omission of alternative taxonomy fixes	Renaming the Ochrobactrum thiophenivorans clade to another genus resolves the polyphyly presented by the authors, keeping Brucella and the Ochrobactrum anthropi/intermedium clade monophyletic. This resolution is supported by Leclercq et al. (19) and the GTDB (https://gtdb.ecogenomic.org) and leaves the type species of Ochrobactrum (Ochrobactrum anthropi) and Brucella (Brucella melitensis) within their respective genera.