Peptoniphilus nemausensis sp. nov. a new Gram-positive anaerobic coccus isolated from human clinical samples, an emendated description of the genus Peptoniphilus and an evaluation of the taxonomic status of Peptoniphilus species with not validly published names

Fabien Aujoulat (1, 2) , Christelle Mazuet (3) , Alexis Criscuolo (4) , Michel Popoff (5) , Cécilia Enault (6) , Laure Diancourt (3) , Estelle Jumas-Bilak , Jean-Philippe Lavigne (7, 6) , Hélène Marchandin (1, 6)

1 HSM - Hydrosciences Montpellier
2 CHRU Montpellier - Centre Hospitalier Régional Universitaire [Montpellier]
3 CNR - Centre National de Référence des Bactéries Anaérobies et Botulisme - National Reference Center Anaerobic Bacteria and Botulism
4 Département de Biologie Computationnelle - Department of Computational Biology
5 Toxines bactériennes - Bacterial Toxins
6 CHU Nîmes - Centre Hospitalier Universitaire de Nîmes
7 VBMI - Virulence bactérienne et maladies infectieuses

A Gram-positive, anaerobic coccus isolated from a human surgical site infection was previously shown to belong to an unknown species of the genus Peptoniphilus initially proposed as ‘Peptoniphilus nemausus’ sp. nov., based on both 16S rRNA gene sequence identity of 97.9% with the most closely related species Peptoniphilus coxii and an individualized phylogenetic branching within the genus Peptoniphilus. A polyphasic characterization of the novel species is proposed herein. Whole genome sequence analysis showed an average nucleotide identity value of 84.75% and digital DNA-DNA hybridization value of 28.9% against P. coxii type strain. The strain displayed unique features among members of the genus Peptoniphilus, as it was able to hydrolyze aesculin, and produced acetate as the major metabolic end-product without associated production of butyrate. Growth was observed under microaerophilic conditions. From all these data, the isolate is confirmed as belonging to a new Peptoniphilus species, for which the name Peptoniphilus nemausensis sp. nov. is proposed. The type strain is 1804121828T (= LMG 31466T = CECT 9935T). A database survey using a highly polymorphic partial sequence of the 16S rRNA gene of P. nemausensis revealed P. nemausensis to be a particularly rare skin-associated species in humans. An emendated description of the Peptoniphilus genus is proposed based on a review of the characteristics of the 12 new species with validly published names since the genus description in 2001 and of P. nemausensis. Finally, the relationships between members of the genus Peptoniphilus were explored based on whole genome sequence analysis in order to clarify the taxonomic status of not yet validly published species showing that three pairs of species should be considered as synonyms: Peptoniphilus timonensis and ‘Peptoniphilus phoceensis’, Peptoniphilus lacydonensis and ‘Peptoniphilus rhinitidis’, Peptoniphilus tyrrelliae and Peptoniphilus senegalensis.

Mots clés: Clinical isolate; Diversity; Human skin; Peptoniphilus; Polyphasic taxonomy

Domaines: Biotechnologie; Microbiologie et Parasitologie

Fabien Aujoulat, Christelle Mazuet, Alexis Criscuolo, Michel Popoff, Cécilia Enault, et al.. Peptoniphilus nemausensis sp. nov. a new Gram-positive anaerobic coccus isolated from human clinical samples, an emendated description of the genus Peptoniphilus and an evaluation of the taxonomic status of Peptoniphilus species with not validly published names. Systematic and Applied Microbiology, 2021, 44 (5), pp.126235. ⟨10.1016/j.syapm.2021.126235⟩. ⟨pasteur-03311410⟩