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New Microbes New Infect. 2017 May; 17: 33–35.
Published online 2016 November 18. doi:  10.1016/j.nmni.2016.11.015
PMCID: PMC5328708

‘Metaprevotella massiliensis’ gen. nov., sp. nov., isolated from human ileum

Abstract

We report here the main characteristics of ‘Metaprevotella massiliensis’ strain Marseille-P-3114T (CSURP3114) that was isolated from a human ileum sample.

Keywords: Culturomics, human gut, Metaprevotella massiliensis, microbiota, taxonogenomics

In 2016, as a part of culturomics study [1] targeted at the study of the modifications of the human microbiome along the whole gastrointestinal tract, we isolated from the ileum of a 25–year-old patient with Crohn disease a bacterial strain that escaped identification by our systematic matrix-assisted desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) screening on a Microflex spectrometer (Bruker Daltonics, Bremen, Germany) [2]. The patient provided signed informed consent, and the study was validated by the ethics committee of the Institut Fédératif de Recherche IFR48 under number 09-022.

Strain Marseille P-3114T growth was obtained on 5% sheep’s blood–enriched Columbia agar medium (bioMérieux, Marcy l’Etoile, France) in an anaerobic atmosphere (anaeroGEN, Oxoid, Dardilly, France) after a 30-day enrichment of the fresh ileal sample in an anaerobic haemoculture bottle (Becton Dickinson, Pont de Claix, France) added with 5 mL of sterile sheep’s blood (bioMérieux) and 5 mL of 0.2 μm filtered (Thermo Fisher Scientific, Villebon-sur-Yvette, France) rumen at 37°C.

After 96 hours’ anaerobic incubation on 5% sheep’s blood–enriched agar (bioMérieux) at 37°C, colonies were circular, convex with entire edges and translucent. Mean diameter was 0.5 to 2 mm. After 3 weeks’ incubation under the same conditions, dark pigment production was observed. Bacterial cells were Gram-negative rods 0.3 to 0.5 μm wide by 1 to 2 μm long. Strain Marseille-P-3114T tested catalase and oxidase negative. Different temperatures (20, 28, 37, 45 and 55°C) and atmospheres (anaerobic, microaerophilic and aerobic conditions) were tested on 5% sheep’s blood–enriched Columbia agar (bioMérieux). Growth was achieved only under anaerobic atmosphere at 37°C. Sporulation test (20 minutes at 80°C) was negative.

The 16S rRNA gene was sequenced using fD1-rP2 primers as previously described [3], using a 3130-XL sequencer (Applied Biosciences, Saint Aubin, France). Strain Marseille-P-3114T exhibited a 89.39% sequence identity with Prevotella buccae strain ATCC 33574T (GenBank accession no. L16477), the phylogenetically closest species with standing in nomenclature (Fig. 1), which putatively classified strain Marseille-P-3114T as a member of a new genus within the family Prevotellaceae in the phylum Bacteroidetes. The Family Prevotellaceae was proposed by Krieg in 2012 and was validated the same year [4]; it actually comprises four genera with validly published names: Prevotella, Alloprevotella, Hallella and Paraprevotella [5]. The genus Prevotella was created in 1990 to accommodate those Bacteroides that were only moderately saccharolytic and were not able to properly grow in bile-enriched medium [6], and today it contains 49 species with a standing in nomenclature. Species belonging to this genus are Gram-negative, anaerobic, non-spore-forming, nonmotile rods, and their common habitats are mammals, although one species has been retrieved from environmental source (Prevotella oryzae, isolated from rice field soil) [7]. They are generally considered to be a commensal species, but under particular circumstances, they are able to induce a wide range of diseases such as bacteraemia, disseminated abscesses, meningitis and endocarditis [8].

Fig. 1
Phylogenetic tree showing position of ‘Metaprevotella massiliensis’ strain Marseille-P-3114T relative to other phylogenetically close neighbours. Sequences were aligned using CLUSTALW, and phylogenetic inferences were obtained using maximum-likelihood ...

On the basis of the 16S rRNA sequence divergence of strain Marseille-P3114T with the phylogenetically closest species with standing in nomenclature [9], we propose here the creation of the new genus Metaprevotella (Me.ta.pre.vo.tel′la, Gr. adv. meta, ‘besides’; N.L. ‘beyond’; N.L. fem. n. Prevotella, a bacterial generic name; N.L. fem. n. Metaprevotella ‘organism related to the genus Prevotella but different’) for which the strain Marseille-P-3114T (= CSURP3114 = DSM 103534) is the type strain. Strain Marseille-P3114T is the type strain of Metaprevotella massiliensis gen. nov., sp. nov. (mas.si.li.en′sis, L. fem. adj. massiliensis, for Massilia, the Roman name of Marseille).

The MALDI-TOF MS spectrum of ‘Metaprevotella massiliensis’ strain Marseille-P3114T is available online (http://www.mediterranee-infection.com/article.php?laref=256&titre=urms-database).

Nucleotide sequence accession number

The 16s r RNA gene sequence was deposited in GenBank under accession number LT598559.

Deposit in a culture collection

Strain Marseille-P3114T was deposited in the Collection de Souches de l’Unité des Rickettsies (CSUR, WDCM 875) under number P3114 and in the Deutsche Sammlung von Mikroorganismen und Zellkulturen under number DSM103534.

Acknowledgement

This study was funded by the Fondation Méditerranée Infection.

Conflict of Interest

None declared.

References

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