Taxonomic Re-Classification and Expansion of the Phylum Chloroflexota Based on over 5000 Genomes and Metagenome-Assembled Genomes

Abstract

The phylum <i>Chloroflexota</i> (formerly Chloroflexi) encompasses metabolically diverse bacteria that often have high prevalence in terrestrial and aquatic habitats, some even with biotechnological application. However, there is substantial disagreement in public databases which lineage should be considered a member of the phylum and at what taxonomic level. Here, we addressed these issues through extensive phylogenomic analyses. The analyses were based on a collection of >5000 Chloroflexota genomes and metagenome-assembled genomes (MAGs) from public databases, novel environmental sites, as well as newly generated MAGs from publicly available sequence reads via an improved binning approach incorporating covariance information. Based on calculated relative evolutionary divergence, we propose that <i>Candidatus</i> Dormibacterota should be listed as a class (i.e., <i>Ca</i>. Dormibacteria) within <i>Chloroflexota</i> together with the classes <i>Anaerolineae</i>, <i>Chloroflexia</i>, <i>Dehalococcoidia</i>, <i>Ktedonobacteria</i>, <i>Ca</i>. Limnocylindria, <i>Thermomicrobia</i>, and two other classes containing only uncultured members. All other <i>Chloroflexota</i> lineages previously listed at the class rank appear to be rather orders or families in the <i>Anaerolineae</i> and <i>Dehalococcoidia</i>, which contain the vast majority of genomes and exhibited the strongest phylogenetic radiation within the phylum. Furthermore, the study suggests that a common ecophysiological capability of members of the phylum is to successfully cope with low energy fluxes.