Non-contiguous finished genome sequence and description of Nosocomiicoccus massiliensis sp. nov.

Abstract

Nosocomiicoccus massiliensis strain NP2T sp. nov. is the type strain of a new species within the genus Nosocomiicoccus. This strain, whose genome is described here, was isolated from the fecal flora of an AIDS-infected patient living in Marseille, France. N. massiliensis is a Gram-positive aerobic coccus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,645,244 bp long genome (one chromosome but no plasmid) contains 1,738 protein-coding and 45 RNA genes, including 3 rRNA genes.

Phylogenomic analyses of the Staphylococcaceae family suggest the reclassification of five species within the genus Staphylococcus as heterotypic synonyms, the promotion of five subspecies to novel species, the taxonomic reassignment of five Staphylococcus species to Mammaliicoccus gen. nov., and the formal assignment of Nosocomiicoccus to the family Staphylococcaceae

“…The description is the same as given by Alves et al [5] with the following amendments. Member of the family Staphylococcaceae based on 16S rRNA gene sequence homology [4][5][6][7]. This taxonomic assignment is also consistent with phylogenies based on whole genome sequences as well as OGRIs such as AAI, ANI, and dDDH.…”

“…1), but never explicitly confined into the family Staphylococcaceae [4,5]. However, it has been considered a member of this family in subsequent works [6,7]. When compared to other members of the Staphylococcaceae, Nosocomiicoccus exhibits similar AAI, ANI, and dDDH values ( Figs S1-S3).…”

“…The genus Nosocomiicoccus was originally circumscribed as a member of the Bacillaceae due to high 16S rRNA gene sequence similarity with members of the genera Jeotgalicoccus , Salinicococcus , and Staphylococcus (), but never explicitly confined into the family Staphylococcaceae [4, 5]. However, it has been considered a member of this family in subsequent works [6, 7]. When compared to other members of the Staphylococcaceae, Nosocomiicoccus exhibits similar AAI, ANI, and dDDH values (Figs S1–S3).…”

“…Another genus, Jeotgalicoccus, contains 10 validly published species that are halotolerant or moderately halophilic, capable of facultative anaerobic growth, and commonly associated with fermented foods [6]. The genus Nosocomiicoccus is comprised of two species, N. ampullae and N. massiliensis, both of which were isolated from clinical samples [5,7]. The genera Aliicoccus, Abyssicoccus, Auricoccus and Corticicoccus are each comprised of a single species that was isolated from a hypersaline lake, marine sediment, the skin of human ear and the bark of Populus species respectively [9,10,12,13].…”

“…ampullae and N. massiliensis , both of which were isolated from clinical samples [5, 7]. The genera Aliicoccus , Abyssicoccus , Auricoccus and Corticicoccus are each comprised of a single species that was isolated from a hypersaline lake, marine sediment, the skin of human ear and the bark of Populus species respectively [9, 10, 12, 13].…”