Detailed description of Senegalia massiliensis strain SIT17T, a bacterium isolated from the human gut

Strain SIT17T was isolated from the stool of a healthy 13-month-old Senegalese boy. It is a Gram-positive, anaerobic, rod-shaped, non-spore-forming and mobile bacterium. It exhibited 92.74% 16S rRNA gene sequence similarity with the Brassicibacter thermophilus strain Cel2f, the phylogenetically most closely related species. Its genome is about 2.87 Mb long with 27.39 mol% G + C content. We provide more details of Senegalia massiliensis strain SIT17T (= CSURP2130 = DSM 103071), the creation of which was previously announced.


Introduction
Recently, the culturomics concept developed in our laboratory has allowed us to change the paradigm of the human gut microbiota [1]. Indeed, by this method, >50% of the microorganisms present in the human gut microbiota are known [2]. To improve culture and bacterial identification, culturomics is associated with a new process named taxonogenomics to provide exhaustive information and to better characterize bacterial species [3][4][5]. Combining phenotypic characteristics and genomic analysis and comparison, this polyphasic approach exceeds the limits of conventional methods long used for the description of new species [6][7][8].
Here, we present the classification and features of Senegalia massiliensis strain SIT17 T , including a description of the complete genome sequencing and annotation.
Isolation and growth conditions Strain SIT17 T was first isolated in 2015 from the stool of a healthy 13-month-old Senegalese boy [9]. The sample was collected in Senegal and was then frozen at -80°C. Subsequently, it was transported in dry ice to Marseille, where the bacterial culture was started. The initial growth of bacterial cells was obtained on Columbia agar with 5% sheep's blood after 2 days of anaerobic incubation at 37°C. The identification of strain SIT17 T using matrix assisted laser desorption/ionization time-of-flight mass spectrometry was unsuccessful. The process was performed on a Microflex LT spectrometer (Bruker, Daltonics, Bremen, Germany) as previously described [10][11]. The spectra obtained were imported and analysed using the BIOTYPER 3.0 software against the Bruker database, which is permanently improved with the local MEPHI database (Fig. 1).

Strain identification and phylogenetic analysis
In order to identify the strain SIT17 T , the 16S rRNA gene was amplified using the fD1 and rP2 primer pair (Eurogentec, Angers, France) and sequenced using the Big Dye® Terminator v1.1 Cycle Sequencing Kit and 3500xLGenetic Analyzer capillary sequencer (Thermofisher, Saint-Aubin, France), as previously reported [12]. The 16S rRNA nucleotide sequences were assembled and corrected using CODONCODE ALIGNER software (http://www.codoncode.com). The PCR-amplified genes coding for 16S rRNA of Senegalia massiliensis yielded 92.74% similarity level with Brassicibacter thermophilus strain Cel2f (GenBank accession no: NR137216) [13], the phylogenetically closest species with standing in nomenclature (Fig. 2). This value was lower than 95%, which is the recommended threshold for delineating a new bacterial genus based on 16S rRNA gene sequence without DNA-DNA hybridization [14][15]. Classification and general features are summarized in Table 1.

Genomic properties and comparison
The genome of strain SIT17 T is 2 866 883 bp long with 27.39 mol% G + C content and it contains 2933 coding genes (Fig. 4) Table 4. Results from pairwise genome comparison obtained from analysis of the digital DNA-DNA hybridization using GGDC software [18] are shown in Table 5. ORTHOANI values among the closely related species ranged from 64.37%, between A. metalliredigens and Clostridiisalibacter paucivorans, to 70.05 % between Caldisalinibacter kiritimatiensis and S. massiliensis. When S. massiliensis was compared with these closely related species, values ranged from 65.93% with A. metalliredigens to 70.05% with Caldisalinibacter kiritimatiensis (Fig. 5).

Ethics and consent
The child's parents provided signed informed consent and the study was approved by the ethics committee of the Institut Fédératif de Recherche IFR48 under number 09-022.