Phylogenomic analysis and characterization of carbon monoxide utilization genes in the family Phyllobacteriaceae with reclassification of Aminobacter carboxidus (Meyer et al. 1993, Hrdt et al. 2020) as Aminobacter lissarensis comb. nov. (McDonald et al. 2005)

The monotypic carboxydophilic genus Carbophilus has recently been transferred to the genus Aminobacter within the family Phyllobacteriaceae, and Carbophilus carboxidus was renamed Aminobacter carboxidus (comb. nov.) [Hrdt et al. 2020]. Due to the poor resolution of the 16S rRNA gene-based phylogeny, an extensive phylogenomic analysis of the family Phyllobacteriaceae was conducted, with particular focus on the genus Aminobacter. Whole genome-based analyses of Phyllobacteriaceae type strains provided evidenced that the genus Aminobacter forms a monophyletic cluster, clearly demarcated from all other members of the family. Close relatedness between A. carboxidus DSM 1086(T) and A. lissarensis DSM 17454(T) was inferred from core proteome phylogeny, shared gene content, and multilocus sequence analyses. ANI and GGDC provided genetic similarity values above the species demarcating threshold for these two type strains. Metabolic profiling and cell morphology analysis corroborated the phenotypic identity between A. carboxidus DSM 1086(T) and A. lissarensis DSM 17454(T). Search for the presence of carbon monoxide dehydrogenase (CODH) genes in Phyllobacteriaceae genomes revealed that the form II CODH is widespread in the family, whereas form I CODH was detected in few Mesorhizobium type strains, and in both A. carboxidus DSM 1086(T) and A. lissarensis DSM 17454(T). Results of phylogenomic, chemotaxonomic, and morphological investigations, combined with the presence of similarly arranged CODH genes, indicate that A. carboxidus DSM 1086(T) and A. lissarensis DSM 17454(T) are distinct strains of the same species. Hence A. carboxidus is a later subjective heterotypic synonym of A. lissarensis. (C) 2021 Elsevier GmbH. All rights reserved.

Automated summary

The study revealed that two strains of Aminobacter, A. carboxidus DSM 1086(T) and A. lissarensis DSM 17454(T), exhibit close relatedness based on core proteome phylogeny, shared gene content, and multilocus sequence analyses, indicating that they are distinct strains of the same species.