Revised Road Map to the Phylum Firmicutes

Abstract

The phylum Firmicutes contains three classes, “ Bacilli ”, “ Clostridia ” and “ Erysipelotrichia ”. The Mollicutes were removed from the phylum given the general low support by alternative markers and its unique phenotypic properties, in particular the lack of rigid cell walls. The family Erysipelotrichaceae , which includes wall‐forming Gram‐positive organisms previously classified with the Mollicutes , was retained in the Firmicutes as a novel class, “ Erysipelotrichia ”, and order, “ Erysipelotrichales ”. While the bipartition of the classes “ Clostridia ” and “ Bacilli ” is corroborated by the new analyses, some of the taxa previously assigned to the “ Clostridia ” tend to root outside the Firmicutes and may represent separate phyla. These include taxa previously classified within the “ Thermoanaerobacterales ” and Syntrophomonadaceae , which may contain a number of phylogenetic clades that are distinct at the phylum level. However, given the absence of corroboration by other phylogenetic markers for many of these assignments and a clear consensus on the definition of a phylum, these taxa were retained within the Firmicutes for the present.

Phylogenomic evaluation of members above the species level within the phylum Firmicutes based on conserved proteins

“…The classes Bacilli and Clostridia , two major components of the phylum Firmicutes , appeared to be multiphyletic in the trees constructed based on 16S rRNA gene and proteins, which was congruence with previous researches (Wolf et al ., ; Ludwig et al ., ). The class Bacilli currently contains two orders, Bacillales and Lactobacillales .…”

“…Moreover, two unclassified genera ( Gemella and Exiguobacterium ) in the order Bacillales were also included in our analysis. The genus Gemella has been previously classified within the family Staphylococcaceae , and then transferred to Family XI Incertae sedis within Bacillales , based on 16S rRNA phylogeny and several biochemical properties (Ludwig et al ., ). Contrary to the previous reports, the genus Gemella was clustered together with the members of the class Erysipelotrichia in 16S rRNA gene‐based trees constructed in this study.…”

“…, the genus Exiguobacterium was distinguished from any of the described families, which was in agreement with the 16S rRNA gene‐based tree (Fig. ) and the current taxonomy (Ludwig et al ., ). Thus, a new family status should be proposed for the genus Exiguobacterium .…”

“…This order composed of six families, half of which were paraphyletic. As reported, the phylogenetic position of the genera in the family Carnobacteriaceae appeared to be ambiguous in the 16S rRNA gene tree (Ludwig et al ., ). The phylogenies based on CPs and RPs may provide new information for the reassignments of these taxa.…”

“…The division Firmicutes encompassed all of Gram‐positive bacteria when the phylum was first described by Gibbons and Murray (Gibbons and Murray, ). But only Gram‐positive bacteria with a low DNA mol% G + C are included in this phylum in the current classification system (Ludwig et al ., ). To date, the phylum contains five classes, namely Bacilli , Clostridia , Erysipelotrichia , Negativicutes and Thermolithobacteria .…”