Microbial Culturomics to Map Halophilic Bacterium in Human Gut: Genome Sequence and Description of Oceanobacillus jeddahense sp. nov.
Culturomics is a new omics subspecialty to map the microbial diversity of human gut, coupled with a taxono-genomic strategy. We report here the description of a new bacterial species using microbial culturomics: strain S5T, (= CSUR P1091=DSM 28586) isolated from a stool specimen of a 25-year-old obese patient from Saudi Arabia. The strain S5T was a Gram-positive, strictly aerobic rod, which was motile by a polar flagellum, spore-forming, and exhibited catalase and oxidase activities. It grows optimally at 37°C, with a pH of 7.5 and 10% of NaCl. 16S rRNA gene-based identification revealed that strain S5T has 98.6% 16S rRNA sequence similarity with the reference O. oncorhynchi, phylogenetically the closest validated Oceanobacillus species. Here, we further describe the phenotypic characteristics of this organism and its complete genome sequence and annotation. The 5,388,285 bp long genome exhibits a G+C content of 37.24% and contains 5109 protein-coding genes and 198 RNA genes. Based on the characteristics reported here, we propose classifying this novel bacterium as representative of a new species belonging to the genus Oceanobacillus, Oceanobacillus jeddahense sp. nov. In a broader context, it is noteworthy that halophilic bacteria have long been overlooked in the human gut, and their role in human health and disease has not yet been investigated. This study thus further underscores the usefulness of the culturomics approach exploring the bacterial diversity of the gut.
1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université , Marseille, Franca.
Saber
S
Khelaifia
1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université , Marseille, Franca.
Jean-Christophe
JC
Lagier
2 Special Infectious Agents Unit, King Fahd Medical Research Center, Faculty of Medicine, King Abdulaziz University , Jeddah, Saudi Arabia .
Fehmida
F
Bibi
2 Special Infectious Agents Unit, King Fahd Medical Research Center, Faculty of Medicine, King Abdulaziz University , Jeddah, Saudi Arabia .|3 Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Faculty of Medicine, King Abdulaziz University , Jeddah, Saudi Arabia .
Esam Ibraheem
EI
Azhar
1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université , Marseille, Franca.
Olivier
O
Croce
1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université , Marseille, Franca.
Roshan
R
Padmanabhan
4 Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University , Jeddah, Saudi Arabia .
Asif Ahmad
AA
Jiman-Fatani
2 Special Infectious Agents Unit, King Fahd Medical Research Center, Faculty of Medicine, King Abdulaziz University , Jeddah, Saudi Arabia .
Muhammad
M
Yasir
1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université , Marseille, Franca.
Catherine
C
Robert
1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université , Marseille, Franca.
Claudia
C
Andrieu
1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université , Marseille, Franca.
Pierre-Edouard
PE
Fournier
1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université , Marseille, Franca.|2 Special Infectious Agents Unit, King Fahd Medical Research Center, Faculty of Medicine, King Abdulaziz University , Jeddah, Saudi Arabia .
Didier
D
Raoult
D001407:Bacillus / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D007422:Intestines / Q000382:microbiology*; D010802:Phylogeny; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization