Reclassification of Catabacter hongkongensis as Christensenella hongkongensis comb. nov. based on whole genome analysis

Abstract

The genera Catabacter (family 'Catabacteraceae') and Christensenella (family Christensenellaceae) are close relatives within the phylum Firmicutes. Members of these genera are strictly anaerobic, non-spore-forming and short straight rods with diverse phenotypes. Phylogenetic analysis of 16S rRNA genes suggest that Catabacter splits Christensenella into a polyphyletic clade. In an effort to ensure that family/genus names represent monophyletic clades, we performed a whole-genome based analysis of the genomes available for the cultured representatives of these genera: four species of Christensenella and two strains of Catabacter hongkongensis. A concatenated alignment of 135 shared protein sequences of single-copy core genes present in the included strains indicates that C. hongkongensis is indeed nested within the Christensenella clade. Based on their evolutionary relationship, we propose the transfer of Catabacter hongkongensis to the genus Christensenella as Christensenella hongkongensis comb. nov.

Keywords: Catabacter; Christensenella; reclassification; whole genome phylogeny.

Fig. 1.

Heatmap of ANI values amongst the genomes of Catabacter hongkongensis strains and Christensenella species in this study. Type strains are marked with an asterisk.

Fig. 2.

Phylogenetic tree showing the relationship of Catabacter hongkongensis to Christensenella species based on 16S rRNA gene sequence analysis. GenBank accession numbers are provided in parentheses. The gene ID number of JGI IMG Integrated Microbial Genomes and Microbiomes is provided for the16S rRNA sequence of Catabacter honkongensis ABBA15K. Type strains are marked with an asterisk. Bootstrap values are expressed as a percentage for 100 iterations. Clostridium and Eubacterium are used for the outgroup. The tree is rooted by Eubacterium limosum . Scale bar indicates 0.1 nucleotide substitutions per site.

Fig. 3.

Phylogeny tree reconstructed by the approximately maximum-likelihood method showing the position of Catabacter relative to Christensenella based on 135 concatenated. core protein sequences with 51 813 aligned amino acid sites. All the nodes are strongly supported with SH-like support values of 1. Type strains are marked with asterisk. Clostridium and Eubacterium are used for the outgroup. The tree is rooted by Eubacterium limosum ATCC 8486. Scale bar indicates 0.1 amino acid substitutions per site.