Microbial culturomics unravels the halophilic microbiota repertoire of table salt: description of Gracilibacillus massiliensis sp. nov.

Abstract

BackgroundMicrobial culturomics represents an ongoing revolution in the characterization of environmental and human microbiome.MethodsBy using three media containing high salt concentration (100, 150, and 200 g/L), the halophilic microbial culturome of a commercial table salt was determined.ResultsEighteen species belonging to the Terrabacteria group were isolated including eight moderate halophilic and 10 halotolerant bacteria. Gracilibacillus massiliensis sp. nov., type strain Awa-1T (=CSUR P1441=DSM 29726), is a moderately halophilic gram-positive, non-spore-forming rod, and is motile by using a flagellum. Strain Awa-1T shows catalase activity but no oxidase activity. It is not only an aerobic bacterium but also able to grow in anaerobic and microaerophilic atmospheres. The draft genome of G. massiliensis is 4,207,226 bp long, composed of 13 scaffolds with 36.05% of G+C content. It contains 3,908 genes (3,839 protein-coding and 69 RNA genes). At least 1,983 (52%) orthologous proteins were not shared with the closest phylogenetic species. Hundred twenty-six genes (3.3%) were identified as ORFans.ConclusionsMicrobial culturomics can dramatically improve the characterization of the food and environmental microbiota repertoire, deciphering new bacterial species and new genes. Further studies will clarify the geographic specificity and the putative role of these new microbes and their related functional genetic content in environment, health, and disease.

Genome sequence and description of Haloferax massiliense sp. nov., a new halophilic archaeon isolated from the human gut

“…Bacterial halophilism has become a subject of considerable interest for microbiologists and molecular biologists during the past 20 years, because of their development on salty foods (Fukushima et al 2007 ). Indeed, these organizations have also been detected in refined salt (Diop et al 2016 ) as well as food products where salt is used in large quantities in the process of their conservation such as salted fish, pork ham, sausages and fish sauces (Tanasupawat et al 2009 ; Kim et al 2010 ). Additionally, the limitation of these organisms to extreme environments has been recently contested after their detection in habitats with relatively low salinity, suggesting an ability of adaptation to survive in more moderate environments (Purdy et al 2004 ).…”

Microbial culturomics to isolate halophilic bacteria from table salt: genome sequence and description of the moderately halophilic bacterium Bacillus salis sp. nov.

“…Culture was realized in an aerobic atmosphere on a homemade culture medium consisting of a Columbia agar culture (Sigma-Aldrich, Saint-Quentin Fallavier, France) modified by adding (per liter): MgCl 2 6H 2 O, 5 g; MgSO 4 7H 2 O, 5 g; KCl, 2 g; CaCl 2 2H 2 O, 1 g; NaBr, 0.5 g; NaHCO 3 , 0.5 g, glucose, 2 g and 100 g/L of NaCl. The pH was adjusted to 7.5 with 10 M NaOH before autoclaving [3] .…”

“…They are involved in centuries-old processes, such as production of salt and fermentation of food consumed by humans [1] , [2] . Today, with the emergence of new biologic technologies, these organisms have been isolated and described from many traditional foods [2] such as salt [3] .…”

Investigations by the Institut Hospitalo-Universitaire Méditerranée Infection of food and food-borne infections in the Mediterranean Basin and in sub-Saharan Africa

“…Indeed, we were the first to identify Gracilibacillus massiliensis sp. nov., a moderately halophilic Gram-positive bacterium in commercial table salt originating from the saline of Aigues-Mortes, Southern France [13] . Moreover, we identified in fermented cow's milk products from Algeria a new strain of Lactococcus garvieae, a bacterial species commonly used in the manufacture of fermented milk products and meats [14] .…”