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Phylogenomic evaluation of members above the species level within the phylum F irmicutes based on conserved proteins
Author(s) -
Zhang Weiwei,
Lu Zhitang
Publication year - 2015
Publication title -
environmental microbiology reports
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.229
H-Index - 69
ISSN - 1758-2229
DOI - 10.1111/1758-2229.12241
Subject(s) - phylum , phylogenetic tree , firmicutes , biology , phylogenetics , clostridiales , evolutionary biology , ribosomal rna , 16s ribosomal rna , zoology , genetics , gene
Summary Currently, numerous taxonomic units above species level of the phylum F irmicutes are ambiguously placed in the phylogeny determined by 16S rRNA gene. Here, we evaluated the use of 16S rRNA gene compared with 81 conserved proteins ( CPs ) or 41 ribosomal proteins ( RPs ) as phylogenetic markers and applied this to the analysis of the phylum F irmicutes . Results show that the phylogenetic trees constructed are in good agreement with each other; however, the protein‐based trees are able to resolve the relationships between several branches where so far only ambiguous classifications are possible. Thus, the phylogeny deduced based on concatenated proteins provides significant basis for re‐classifying members in this phylum. It indicates that the genera C oprothermobacter and T hermodesulfobium represent two new phyla; the families P aenibacillaceae and A licyclobacillaceae should be elevated to order level; and the families B acillaceae and T hermodesulfobiaceae should be separated to 2 and 3 families respectively. We also suggest that four novel families should be proposed in the orders C lostridiales and B acillales , and 11 genera should be moved to other existing families different from the current classification status. Moreover, notably, RPs are a well‐suited subset of CP s that could be applied to F irmicutes phylogenetic analysis instead of the 16S rRNA gene.