AUTHOR=Suresh G. , Lodha Tushar D. , Indu B. , Sasikala Ch. , Ramana Ch. V. 

TITLE=Taxogenomics Resolves Conflict in the Genus Rhodobacter: A Two and Half Decades Pending Thought to Reclassify the Genus Rhodobacter

JOURNAL=Frontiers in Microbiology

VOLUME=10

YEAR=2019

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2019.02480

DOI=10.3389/fmicb.2019.02480

ISSN=1664-302X

ABSTRACT=<p>The genus <italic>Rhodobacter</italic> is taxonomically well studied, and some members are model organisms. However, this genus is comprised of a heterogeneous group of members. 16S rRNA gene-based phylogeny of the genus <italic>Rhodobacter</italic> indicates a motley assemblage of anoxygenic phototrophic bacteria (genus <italic>Rhodobacter</italic>) with interspersing members of other genera (chemotrophs) making the genus polyphyletic. Taxogenomics was performed to resolve the taxonomic conflicts of the genus <italic>Rhodobacter</italic> using twelve type strains. The phylogenomic analysis showed that <italic>Rhodobacter</italic> spp. can be grouped into four monophyletic clusters with interspersing chemotrophs. Genomic indices (ANI and <italic>d</italic>DDH) confirmed that all the current species are well defined, except <italic>Rhodobacter megalophilus</italic>. The average amino acid identity values between the monophyletic clusters of <italic>Rhodobacter</italic> members, as well as with the chemotrophic genera, are less than 80% whereas the percentage of conserved proteins values were below 70%, which has been observed among several genera related to <italic>Rhodobacter</italic>. The pan-genome analysis has shown that there are only 1239 core genes shared between the 12 species of the genus <italic>Rhodobacter</italic>. The polyphasic taxonomic analysis supports the phylogenomic and genomic studies in distinguishing the four <italic>Rhodobacter</italic> clusters. Each cluster is comprised of one to seven species according to the current <italic>Rhodobacter</italic> taxonomy. Therefore, to address this taxonomic discrepancy we propose to reclassify the members of the genus <italic>Rhodobacter</italic> into three new genera, <italic>Luteovulum</italic> gen. nov., <italic>Phaeovulum</italic> gen. nov. and <italic>Fuscovulum</italic> gen. nov., and provide an emended description of the genus <italic>Rhodobacter sensu stricto</italic>. Also, we propose reclassification of <italic>Rhodobacter megalophilus</italic> as a sub-species of <italic>Rhodobacter sphaeroides</italic>.</p>