Genome sequence and description of Gracilibacillus timonensis sp. nov. strain Marseille-P2481 T , a moderate halophilic bacterium isolated from the human gut microflora

Microbiologyopen. 2019 Feb;8(2):e00638. doi: 10.1002/mbo3.638. Epub 2018 Apr 19.


Microbial culturomics represents an ongoing revolution in the characterization of the human gut microbiota. By using three culture media containing high salt concentrations (10, 15, and 20% [w/v] NaCl), we attempted an exhaustive exploration of the halophilic microbial diversity of the human gut and isolated strain Marseille-P2481 (= CSUR P2481 = DSM 103076), a new moderately halophilic bacterium. This bacterium is a Gram-positive, strictly aerobic, spore-forming rod that is motile by use of a flagellum and exhibits catalase, but not oxidase activity. Strain Marseille-P2481 was cultivated in media containing up to 20% (w/v) NaCl, with optimal growth being obtained at 37°C, pH 7.0-8.0, and 7.5% [w/v] NaCl). The major fatty acids were 12-methyl-tetradecanoic acid and hexadecanoic acid. Its draft genome is 4,548,390 bp long, composed of 11 scaffolds, with a G+C content of 39.8%. It contains 4,335 predicted genes (4,266 protein coding including 89 pseudogenes and 69 RNA genes). Strain Marseille-P2481 showed 96.57% 16S rRNA sequence similarity with Gracilibacillus alcaliphilus strain SG103T , the phylogenetically closest species with standing in nomenclature. On the basis of its specific features, strain Marseille-P2481T was classified as type strain of a new species within the genus Gracilibacillus for which the name Gracilibacillus timonensis sp. nov. is formally proposed.

Keywords: Gracilibacillus timonensis; halophilic; human gut flora; microbial culturomics; taxonogenomics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aerobiosis
  • Bacillaceae / classification
  • Bacillaceae / genetics*
  • Bacillaceae / isolation & purification
  • Bacillaceae / physiology
  • Base Composition
  • Child
  • Cluster Analysis
  • Computational Biology
  • Cytosol / chemistry
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / genetics
  • DNA, Ribosomal / chemistry
  • DNA, Ribosomal / genetics
  • Fatty Acids / analysis
  • Gastrointestinal Microbiome
  • Genome, Bacterial*
  • Healthy Volunteers
  • Humans
  • Hydrogen-Ion Concentration
  • Locomotion
  • Male
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics
  • Senegal
  • Sequence Analysis, DNA*
  • Sodium Chloride / metabolism
  • Temperature


  • DNA, Bacterial
  • DNA, Ribosomal
  • Fatty Acids
  • RNA, Ribosomal, 16S
  • Sodium Chloride