Draft Genome Sequence of Megamonas funiformis Strain Marseille-P3344, Isolated from a Human Fecal Microbiota.

In this article, we present the draft genome sequence of Megamonas funiformis strain Marseille-P3344, isolated from a human fecal sample. The genome described here is composed of 2,464,704 nucleotides, with 2,230 protein-coding genes and 76 RNA genes.

GENOME ANNOUNCEMENT

Megamonas hypermegale was the first species of the Megamonas genus described. The bacterium was isolated from chicken cecum and first described in 1936 as Bacteroides hypermegas by Harrison and Hansen (1), and the original name was changed to Megamonas hypermegale by Euzéby in 1998 (2). This microorganism is strictly anaerobic and nonmotile. Its optimal growth temperature is 37°C. The species Megamonas funiformis was identified in human feces in 2008 in Japan by Sakon et al. (3). Cells from this bacterium are large Gram-negative rods, 5 to 10 μm in size. Some of the cells exhibit a central, subterminal, or terminal swelling of 2- to 4-μm diameter when grown in a broth medium supplemented with glucose.

In August 2016, as part of a microbial culturomics study, we cultivated strain Marseille-P3344 from a fecal sample of a healthy woman. This bacterium exhibited a 99.08% 16S rRNA sequence similarity with M. funiformis strain YIT 11815T (=JCM 14723 =DSM 19343), its closest phylogenetic neighbor. Genomic DNA (gDNA) from M. funiformis strain Marseille-P3344, isolated from a human fecal specimen, was sequenced using a MiSeq sequencer and the mate pair strategy (Illumina, Inc., San Diego, CA, USA). The gDNA from M. funiformis strain Marseille-P3344 was barcoded in order to be mixed with 11 other projects with the Nextera mate pair sample prep kit (Illumina). The gDNA quantification by a Qubit assay with a high-sensitivity kit (Life Technologies, Inc., Carlsbad, CA, USA) was 148.7 ng/µL.

A total of 6.3 Gb was obtained from a 673,000/mm2 cluster density with a cluster passing quality control filters of 95.4% (12,453,000 clusters). Within this run, the index representation for M. funiformis was 7.99%. The 995,543 mate pair reads were filtered according to the read quality.

The draft genome sequence of M. funiformis strain Marseille-P3344 is composed of 7 scaffolds for a total of 2,464,704 nucleotides (nt) and a G+C content of 31.4%. The coding capacity is 2,099,846 nt (85.1% of the total genome). Predicted genes include 2,230 protein-coding genes, of which 1,701 are assigned to clusters of orthologous groups and 76 (3.29%) are RNA genes (17 rRNAs and 59 tRNAs). A total of 228 genes (10.2%) have peptide signals, and 481 (21.5%) have transmembrane helices. In addition, 46 virulence genes are predicted, including 30 genes associated with antibiotic resistance, including 3 beta-lactamases. No toxin/antitoxin module or bacteriocin-associated gene could be found.

The genomes of M. funiformis strains Marseille-P3344 and YIT 11815T (=JCM 14723 =DSM 19343) were compared using GGDC and OrthoANI softwares (4, 5). Digital DNA-DNA hybridization and OrthoANI values of 84.1% ± 2.6 (>70%) and 98.18% (>95.96%), respectively, were obtained, thus confirming that these strains belong to the same species.

Accession number(s).

The 16S rRNA and whole-genome sequences reported here have been deposited in GenBank under accession numbers LT628480 and FQRY00000000, respectively.