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

Abstract

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 SG103 , the phylogenetically closest species with standing in nomenclature. On the basis of its specific features, strain Marseille-P2481 was classified as type strain of a new species within the genus Gracilibacillus for which the name Gracilibacillus timonensis sp. nov. is formally proposed.

Description of Gracilibacillus phocaeensis sp. nov., a new halophilic bacterium isolated from Senegalian human stool

“…However, it has been demonstrated to favour the emergence and growth of other, mainly halophilic, bacteria, including Gracilibacillus [ 4 ]. Halophilic and halotolerant bacteria are most commonly isolated from the human gut microbiota [ 5 , 6 ].…”

“…The genus Gracilibacillus currently compromises 13 species with valid standing in nomenclature [ 9 ]. Gracilibacillus species were isolated from diverse salty environmental samples, including seawater, salty lakes [ 4 , 10 , 11 ], soil [ 12 , 13 ], food [ 1 , 14 , 15 ] and gut microbiota [ 6 ].…”

The Methods of Digging for “Gold” within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools

“…There are numerous and continual scientific reports on isolating new halophilic microorganisms, the diversity and properties of halophilic Bacteria and Archaea, as well as genomic analyses from commercial salt [70][71][72][73], cheeses [74][75][76][77], table olives [78], kimchi (Asian fermented vegetables) [79][80][81], and shrimp paste [82,83]. Recent years have also brought interest in the halophilic and halotolerant prokaryotes contributing to the human gut microbiota [73,[84][85][86]. This attention results in part from observing a hazardous tendency to consume increasing amounts of salt delivered with food and its tremendous consequences on human health, including obesity, hypertension, cardiovascular disorders, and stomach cancers [69].…”

Gracilibacillus suaedae sp. nov., an indole acetic acid-producing endophyte isolated from a root of Suaeda salsa

“…Most Gracilibacillus strains were isolated from salt lake water [4,6,8,[10][11][12]. A small number were isolated from soil [7,13,14], and the others were from fermented fish [5], rice seeds [15], kimchi [16], indigo fermentation liquor for dyeing [17], and human gut or stools [18,19]. Some Gracilibacillus strains were reported to produce indole acetic acid (IAA), fix nitrogen, solubilize phosphate, secrete siderophore and auxins, and control nematodes [20,21].…”