Abstract
We report the main characteristics of ‘Khoudiadiopia massiliensis’ gen. nov., sp. nov., strain Marseille-P2746T (= CSUR P2746), a new member of the Peptoniphilaceae family isolated from a vaginal swab of a patient suffering from bacterial vaginosis.
Keywords: Culturomics, human microbiome, Khoudiadiopia massiliensis, taxono-genomics, vaginal microbiota
The study of the vaginal microbiota diversity from patients with bacterial vaginosis is part of the ongoing microbial culturomics revolution in our laboratory [1]. A new member from the new family Peptoniphilaceae was isolated during this study that could not be identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry screening on a Microflex spectrometer (Bruker Daltonics, Leipzig, Germany), from a vaginal sample of a 26-year-old French woman suffering from bacterial vaginosis in the hospital Nord in Marseille (France). The patient gave her informed and signed consent and the study was authorized by the local ethics committee of the IFR48 (Marseille, France) under agreement 09-022. Strain Marseille-P2746T was first cultivated in April 2016 after 48 h of incubation in an anaerobic atmosphere at 37°C on Schaedler agar and Trypticase soy agar (BD Diagnostics, Le Pont de Claix, France), after 4 days of pre-incubation in a blood culture bottle enriched with rumen and sheep blood. Colonies were bright grey. Bacterial cells were Gram-positive, non-motile and non-spore-forming with a mean diameter of 0.55 μm. Strain Marseille-P2746T is a strictly anaerobic coccus and exhibits oxidase activity but no catalase activity. Using the universal primer pair FD1 and rp2 as previously described [2], and a 3130-XL sequencer (Applied Biosciences, Saint Aubin, France), the 16S rRNA gene was sequenced. Strain Marseille-P2746T exhibited an 89.28% 16S rRNA gene sequence identity with Murdochiella asaccharolytica strain WAL 1855CT (GenBank Accession number EU483153), the phylogenetically closest species with a validly published name (Fig. 1). This value was lower than the 95% 16S rRNA gene sequence threshold proposed by Stackebrandt and Ebers [3] to define a new genus without carrying out DNA–DNA hybridization and classifies it as a new genus within the Peptoniphilaceae family (phylum Firmicutes), first created in 2014 [4]. Murdochiella asaccharolytica is an obligate anaerobic species isolated from a sacro-pilonidal cyst aspirate from an immunocompetent patient. It is also Gram-stain-positive, non-motile, non-spore-forming, and also shows a negative catalase activity [5].
Fig. 1.
Phylogenetic tree highlighting the phylogenetic position of ‘Khoudiadiopia massiliensis’ gen. nov. strain Marseille-P2746TT relative to other close species. GenBank accession numbers are indicated in parentheses. Sequences were aligned using ClustalW, and the tree was constructed with the Neighbour-joining method and 500 bootstrap replicates using the MEGA6 software. Numbers at the nodes are percentages of bootstrap values > 95%. The scale bar indicates a 2% nucleotide sequence divergence.
Strain Marseille-P2746T has >10% 16S rRNA gene sequence divergence with its closest phylogenetic neighbour [6], so we propose the creation of a new genus named ‘Khoudiadiopia’ gen. nov. (khou.dia.dio'pia, N.L. fem. n. khoudiadiopia from the contraction of the first and last names of the Senegalese microbiologist Khoudia Diop). Strain Marseille-P2746T is the type strain of ‘Khoudiadiopia massiliensis’ gen. nov., sp. nov., the type species of the new genus ‘Khoudiadiopia’ gen. nov.
Nucleotide sequence accession number
The 16S rRNA gene sequence was deposited in EMBL-EBI under Accession number LT598561.
Deposit in a culture collection
‘Khoudiadiopia massiliensis’ gen. nov., sp. nov. was deposited in the ‘Collection de Souches de l’Unité des Rickettsies' (CSUR, WDCM 875) under number CSUR P2746.
Acknowledgement
This research is funded by the Méditerranée-Infection Foundation.
Transparency declaration
No conflicts of interest declared.
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