Genome Sequence of Enorma sp. Strain Marseille-P9525T, a Member of a Human Gut Microbiome.

Strain Marseille-P9525T was isolated from the gut microbiota of a 28-year-old woman and exhibits a 2.23-Mb (G+C content, 66.8%) draft genome sequence containing 1,902 protein-coding genes, 49 tRNAs, and 3 rRNAs. The 16S rRNA sequencing and in silico DNA-DNA hybridization indicated that strain Marseille-P9525T represents a new species to be described.

ANNOUNCEMENT

Enorma massiliensis was the first species of the genus Enorma recently described within the family Coriobacteriaceae (1). The genus Enorma contains three species, namely, E. massiliensis, Enorma timonensis, and Enorma phocaeensis, which are all Gram-positive, obligatory anaerobic, and nonmotile bacteria isolated from human fecal microbiota under an anaerobic atmosphere (1–3). A culture-based study (4) of the stools from a 28-year-old healthy woman living in Burkina Faso yielded the isolation and culture of strain Marseille-P9525T (CSUR P9525). Here, we report the genome sequence of strain Marseille-P9525T and describe its genomic content.

Strain Marseille-P9525T was subcultured on Colombia agar incorporating 5% sheep blood (bioMérieux, Marcy l’Etoile, France) at 37°C under anaerobic conditions (AnaeroGen Compact; Oxoid, Thermo Scientific, Dardilly, France). DNA was extracted in 50 μl using the EZ1 BioRobot and EZ1 DNA tissue kit (Qiagen, Courtaboeuf, France) and was quantified using a Qubit assay with a high-sensitivity kit (Life Technologies, Carlsbad, CA, USA) to 0.2 ng/liter. DNA was then sequenced using MiSeq technology (Illumina, Inc., San Diego, CA, USA) with paired-end applications. The DNA was fragmented and amplified by limited PCR (12 cycles), introducing dual-index barcodes and sequencing adapters. After purification on AMPure XP beads (Beckman Coulter, Inc., Fullerton, CA, USA), libraries were normalized and pooled for MiSeq paired-end sequencing. An automated cluster generation of 12 runs with dual-indexed 2 × 251-bp reads was performed for 40 hours. A total of 7,810,996 paired-end reads with a 35 to 251-bp sequence length were quality checked using FastQC, trimmed using Trimmomatic version 0.36.6 (5), and assembled using SPAdes software version 3.5.0 (6). To run SPAdes, we used the pipeline option “–careful” in order to reduce the number of mismatches and short indels. Default parameters for k values, i.e., k-mer values of 127, 99, 77, 55, 33, and 21, were applied, and default parameters were used for all software, unless otherwise noted. Finally, the Marseille-P9525T draft genome was assembled into 48 contigs and 48 scaffolds, with a total size of 2,234,108 bp and a G+C content of 66.8%, giving an unclosed molecule. Automatic annotation was performed with Prokka version 1.12 (7). The genome (one chromosome but no plasmid) presents one repeat region and is predicted to carry 1,951 genes, including 1,902 protein-coding genes and 49 tRNA genes. Strain Marseille-P9525T exhibits 98.3% 16S rRNA gene sequence identity with E. phocaeensis strain Marseille-P3242 (GenBank accession number NR_147403), 96.76% identity with E. timonensis (NR_144707), 95.30% with E. massiliensis (NR_125606), 94.03% with Collinsella tanakaei (NR_112899), and 93.96% with Collinsella ihuae (LN881598).

The 2.23-Mb draft genome sequence of strain Marseille-P9525T is smaller than those of E. phocaeensis, E. massiliensis, E. timonensis, C. tanakaei, and C. ihuae (2.38 Mb, 2.37 Mb, 2.33 Mb, 2.49 Mb, and 2.84 Mb, respectively). Based on the 16S rRNA gene sequence proximity, genomes were selected and incorporated into an in silico genomic comparison. Genomic similarities estimated using OrthoANI version 0.93.1 (https://www.ezbiocloud.net/tools/orthoani) and in silico DNA-DNA hybridization (http://ggdc.dsmz.de/ggdc.php#) estimated using the GGDC version 2.0 online tool yielded 84.20% and 28.4% sequence similarity with E. phocaeensis, 80.77% and 25.3% with E. timonensis, 78.68% and 24.9% with E. massiliensis, 77.35% and 23.7% with C. ihuae, and 74.57% and 22.2% with C. tanakaei, respectively.

Data availability.

The genome sequence reported here and the raw reads have been deposited at EMBL/GenBank under the accession numbers CABFVT000000000 and ERR3427549, respectively.