'Halomonas massiliensis' sp. nov., a new halotolerant bacterium isolated from the human gut.

We report here the main characteristics of 'Halomonas massiliensis' strain Marseille-P2426(T) (CSUR P2426), a new species of the Halomonas genus that was isolated from the stool sample of a healthy 24-year-old Senegalese man.

A new bacterium named strain Marseille-P2426, was isolated from a stool sample of a healthy Senegalese man in May 2016. This isolate is part of a wider culturomics study aiming to cultivate bacterial diversity colonizing the human gut [1]. The study was approved by the Institut Fédératif de Recherche 48 (Faculty of Medicine, Marseille, France), under agreement number 09-022 and the patient gave an informed consent. No identification was obtained for the strain Marseille-P2426 using 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]. The strain Marseille-P2426 was cultured in a homemade liquid medium [3] incubated for 2 days in an aerobic atmosphere at 37°C. Optimal growth for the strain Marseille-P2426 was obtained at 37°C at pH 7; strain Marseille-P2426 is halotolerant and tolerates NaCl concentration up to 20%. Strain Marseille-P2426 is a Gram-negative bacterium, motile non-spore-forming and does not exhibit catalase or oxidase activities. The growing colonies on our homemade culture medium were orange, circular, entire, smooth, convex, with a diameter of 1.0–2.0 mm. Individual cells have a slightly curved form with a flagellum and exhibited 2 μm in length and 0.6 μm in diameter under electron microscopy. We sequenced the complete 16S rRNA gene using universal primers FD1 and RP2 (Eurogentec, Angers, France) as previously described [4], using a 3130-XL sequencer (Applied Biosciences, Saint Aubin, France). Strain Marseille-P2426 exhibited a 16S rRNA gene sequence identity of 97.5% with Halomonas alkaliantarctica strain CRSST (GenBank Accession number, NR_114902), the phylogenetically closest species with standing in nomenclature (Fig. 1), which classifies it as a member of a new species within the Halomonas genus in the family Halomonadaceae [5]. So far, the genus Halomonas includes more than 80 species with validly published names [6]. Halomonas species are described as halotolerant or halophilic, Gram-negative, aerobic and rod-shaped bacteria [7]. Strain Marseille-P2426 exhibited a 16S rRNA sequence divergence >1.3% with Halomonas alkaliantarctica, the closest related species with standing in nomenclature [8], which classifies it as a new representative of the Halomonas genus isolated from human gut. Based on the information reported here, we propose the creation of ‘Halomonas massiliensis’ sp. nov., (mas.si.li.en'sis. L. masc. adj. massiliensis of Massilia, the old Roman name for Marseille, where the strain was isolated) and the strain Marseille-P2426T is the type strain.

Fig. 1

Phylogenetic tree highlighting the position of ‘Halomonas massiliensis’ strain Marseille-P2426T (in red) relative to other phylogenetically closest members of the Halomonas genus. Numbers at the nodes are percentages of bootstrap values obtained by repeating 500 times the analysis to generate a majority consensus tree. Only values > 95% were displayed. The scale bar represents a 2% nucleotide sequence divergence.

MALDI-TOF-MS spectrum accession number

The MALDI-TOF-MS spectrum of “H. 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 the strain Marseille-P2426T was deposited in GenBank under Accession number LT223576.

Deposit in a culture collection

Strain Marseille-P2426T was deposited in the Collection de Souches de l’Unité des Rickettsies (CSUR, WDCM 875) under number P2426.

Conflict of Interest

None declared.