Abstract
We present here the main characteristics of ‘Phocea massiliensis’ strain Marseille-P2769T (CSUR P2769), which is a new genus isolated from the stool of a 45-year-old patient.
Keywords: Culturomics, Genomics, Human-gut, ‘Phocea massiliensis’, taxonomy
In March 2016, as a part of our culturomics studies [1], we isolated from the stool sample of a 45-year-old patient hospitalized for the treatment of a melanoma, a bacterial strain that could not be identified by our systematic matrix-assisted laser desorption–ionization time-of-flight mass spectrometry (MALDI-TOF-MS) screening on a MicroFlex spectrometer (Bruker Daltonics, Bremen, Germany) [2]. This study was approved by the local committee of the IFR48 (Marseille, France) under agreement number 09-022 and the consent of the patient was obtained. The initial growth was observed after the stool sample had been pre-incubated in a blood bottle culture (Becton-Dickinson, Pont de Claix, France), with the addition of 5% sheep rumen for 5 days. Several colonies appeared after 3 days of cultivation on 5% sheep blood agar (bioMérieux, Marcy l'Etoile, France) in anaerobic conditions generated by AnaeroGen™ (bioMérieux). Agar-grown colonies ranged from 1 to 2 mm in diameter and were beige and circular. Bacterial cells were Gram-negative bacilli, strictly anaerobic, motile and non-spore-forming (0.4–0.5 × 2.5–3 μm). Strain Marseille-P2769 was catalase and oxidase negative. As previously described, we sequenced the complete 16S rRNA gene using a 3130-XL sequencer (Applied Biosciences, Saint Aubin, France) with the universal primers FD1 and RP2 (Eurogentec, Angers, France) [3]. Strain Marseille-P2769 exhibited a 92% sequence identity with Anaerotruncus colihominis strain JM4-15T (GenBank accession number KR364734), the phylogenetically closest species with standing in nomenclature. Indeed, with a similarity <95%, strain Marseille-P2769 was putatively classified as a member of a new genus within the family Ruminococcaceae in the Firmicutes phylum [4].
Anaerotruncus colihominis was isolated from human faeces and was described in 2004 [5]. It was obligatory anaerobic, Gram-positive, non-spore-forming and cells were rods (0.5–2.5 μm). Catalase was not produced.
Strain Marseille-P2769 exhibited a 16S rRNA sequence divergence >5% with its phylogenetically closest species with standing in nomenclature [6], so we propose the creation of the new genus ‘Phocea’ gen. nov., (pho.ce.en′sis. L. fem. adj. phoceensis referring to Phocea, the Greek name of the city which founded Marseille, where the strain was isolated). Strain Marseille-P2769T is the type strain of the new species ‘Phocea massiliensis’ gen. nov., sp. nov (see Fig. 1).
Fig. 1.
Phylogenetic tree showing the position of ‘Phocea massiliensis’ strain Marseille-P2769T relative to other phylogenetically close members of the family Ruminococcaceae. GenBank accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences were obtained using the maximum-likelihood method within the MEGA software. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 500 times to generate a majority consensus tree. Only values >70% were displayed. The scale bar indicates a 2% nucleotide sequence divergence.
MALDI-TOF-MS spectrum accession number
The MALDI-TOF-MS spectrum of ‘Phocea massiliensis’ is available at http://www.mediterranee-infection.com/article.php?laref=256&titre=urms-database.
Nucleotide sequence accession number
The 16S rRNA gene sequence of strain Marseille-P2769 was deposited in GenBank under accession number LT558849.
Deposit in a culture collection
Strain Marseille-P2769 was deposited in the Collection de Souches de l'Unité des Rickettsies (CSUR, WDCM 875) under number P2769.
Conflict of Interest
The authors have no conflicts of interest to declare.
Acknowledgements
This research was funded by Méditerranée-Infection Foundation.
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