Genome-based taxonomic framework for the class Negativicutes: division of the class Negativicutes into the orders Selenomonadales emend., Acidaminococcales ord. nov. and Veillonellales ord. nov.
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abstract
The classNegativicutesis currently divided into one order and two families on the basis of 16S rRNA gene sequence phylogenies. We report here comprehensive comparative genomic analyses of the sequenced members of the classNegativicutesto demarcate its different evolutionary groups in molecular terms, independently of phylogenetic trees. Our comparative genomic analyses have identified 14 conserved signature indels (CSIs) and 48 conserved signature proteins (CSPs) that either are specific for the entire class or differentiate four main groups within the class. Two CSIs and nine CSPs are shared uniquely by all or most members of the classNegativicutes, distinguishing this class from all other sequenced members of the phylumFirmicutes. Four other CSIs and six CSPs were specific characteristics of the familyAcidaminococcaceae, two CSIs and four CSPs were uniquely present in the familyVeillonellaceae, six CSIs and eight CSPs were found only inSelenomonasand related genera, and 17 CSPs were identified uniquely inSporomusaand related genera. Four additional CSPs support a pairing of the groups containing the generaSelenomonasandSporomusa. We also report detailed phylogenetic analyses for theNegativicutesbased on core protein sequences and 16S rRNA gene sequences, which strongly support the four main groups identified by CSIs and by CSPs. Based on the results from different lines of investigation, we propose a division of the classNegativicutesinto an emended orderSelenomonadalescontaining the new familiesSelenomonadaceaefam. nov. andSporomusaceaefam. nov. and two new orders,Acidaminococcalesord. nov. andVeillonellalesord. nov., respectively containing the familiesAcidaminococcaceaeandVeillonellaceae.
