The class Negativicutes is 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 class Negativicutes to 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 class Negativicutes, distinguishing this class from all other sequenced members of the phylum Firmicutes. Four other CSIs and six CSPs were specific characteristics of the family Acidaminococcaceae, two CSIs and four CSPs were uniquely present in the family Veillonellaceae, six CSIs and eight CSPs were found only in Selenomonas and related genera, and 17 CSPs were identified uniquely in Sporomusa and related genera. Four additional CSPs support a pairing of the groups containing the genera Selenomonas and Sporomusa. We also report detailed phylogenetic analyses for the Negativicutes based 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 class Negativicutes into an emended order Selenomonadales containing the new families Selenomonadaceae fam. nov. and Sporomusaceae fam. nov. and two new orders, Acidaminococcales ord. nov. and Veillonellales ord. nov., respectively containing the families Acidaminococcaceae and Veillonellaceae.
The oxytrichid species Pleurotricha curdsi ( Shi et al., 2002 ) Gupta et al., 2003 , isolated from a tributary of the Yangtze River in the Mudong district of Chongqing, southern China, was reinvestigated with emphasis on its morphology, morphogenesis and small-subunit (SSU) rDNA-based phylogeny. Compared with three previously described populations, the Mudong population of P. curdsi is characterized by its large body size, 170–295 × 65–110 μm in vivo, and by having a variable number of right marginal rows, either two or three. Likewise, the number of right marginal rows anlagen (RMA) is also variable, i.e. usually two, but sometimes several small extra anlagen that give rise to the formation of the third row, are present to the left of the RMAs. We posit that the Mudong population is an intermediate form between the three previously described populations. Phylogenetic analyses based on the SSU rDNA sequence data show that all populations of P. curdsi cluster with the type species of the genus, Pleurotricha lanceolata, in a clade nested within the Oxytrichidae.