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Microbial Culturomics to Map Halophilic Bacterium in Human Gut: Genome Sequence and Description of Oceanobacillus Jeddahense Sp

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Microbial Culturomics to Map Halophilic Bacterium in Human Gut: Genome Sequence and Description of Oceanobacillus Jeddahense Sp See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/301533830 Microbial Culturomics to Map Halophilic Bacterium in Human Gut: Genome Sequence and Description of Oceanobacillus jeddahense sp. nov Article in Omics: a journal of integrative biology · April 2016 Impact Factor: 2.36 · DOI: 10.1089/omi.2016.0004 READS 45 12 authors, including: Fehmeeda Imran Olivier Croce King Abdulaziz University French National Centre for Scientific Research 34 PUBLICATIONS 135 CITATIONS 62 PUBLICATIONS 190 CITATIONS SEE PROFILE SEE PROFILE Asif Jiman-Fatani Catherine Robert King Abdulaziz University Aix-Marseille Université 34 PUBLICATIONS 75 CITATIONS 273 PUBLICATIONS 21,597 CITATIONS SEE PROFILE SEE PROFILE All in-text references underlined in blue are linked to publications on ResearchGate, Available from: Jean-Christophe Lagier letting you access and read them immediately. Retrieved on: 02 May 2016 OMICS A Journal of Integrative Biology Volume 20, Number 4, 2016 ª Mary Ann Liebert, Inc. DOI: 10.1089/omi.2016.0004 Microbial Culturomics to Map Halophilic Bacterium in Human Gut: Genome Sequence and Description of Oceanobacillus jeddahense sp. nov. Saber Khelaifia,1* Jean-Christophe Lagier,1* Fehmida Bibi,2* Esam Ibraheem Azhar,2,3 Olivier Croce,1 Roshan Padmanabhan,1 Asif Ahmad Jiman-Fatani,4 Muhammad Yasir,2 Catherine Robert,1 Claudia Andrieu,1 Pierre-Edouard Fournier,1 and Didier Raoult1,2 Abstract 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 anno- tation. 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 jedda- hense 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. Introduction genera, leading to some limitations (Kokcha et al., 2012). Genomic data for many bacterial species are now available culture-based emerging omics concept is the field due to the emergence of high-throughput sequencing tech- Aof ‘‘culturomics’’ that has recently been introduced, niques (Mishra et al., 2012). revealing high bacterial diversity in human stool samples, We have recently outlined a new method (taxono- including halophilic organisms (Lagier et al., 2012a). Cul- genomics), including genomic data in a polyphasic approach turomics has helped to map the microbial diversity of human in order to describe new bacterial species (Ramasamy et al., gut, coupled with a taxono-genomic strategy. Notably, 16S 2014). This strategy combines phenotypic characteristics rRNA sequence identity and phylogeny (Rossello-Mora, with MALDI-TOF MS spectrum and genomic analysis (La- 2006; Wayne et al., 1987), genomic G + C content diversity gier et al., 2012b; Mishra et al., 2012). Using this method, we and DNA–DNA hybridization (DDH) (Ramasamy et al., isolated the strain S5T belonging to the genus Oceanoba- 2014; Welker and Moore, 2011) have been the traditional cillus. The first description of genus Oceanobacillus was parameters used to delineate a bacterial species. However, made by Lu et al. (2001) and was then amended (Yumoto the cut-off values vary dramatically between species and et al., 2005). These bacteria belong to the phylum Firmicutes 1Unite´ de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Me´diterrane´e-Infection, Faculte´ de Me´decine, Aix-Marseille Universite´, Marseille, Franca. 2Special Infectious Agents Unit, King Fahd Medical Research Center, and Departments of 3Medical Laboratory Technology, Faculty of Applied Medical Sciences, and 4Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia. *These three authors contributed equally. 248 CULTUROMICS OF OCEANOBACILLUS JEDDAHENSE 249 within the Bacillaceae family. The Oceanobacillus genus Strain identification using MALDI-TOF currently includes 13 recognized species and two subspecies. and 16S rRNA sequencing These bacteria are Gram-positive, motile rods, obligate MALDI-TOF MS (matrix-assisted laser-desorption/ aerobic or facultative anaerobic, and obligate or facultative ionization time-of-flight) protein analysis was carried out as alkaliphilic. previously described (Seng et al., 2009). The resulting twelve Oceanobacillus T Bacteria from the genus were essentially spectra of strain S5 were imported into the MALDI Bio- ., isolated from deep-sea sediment core (Lu et al 2001; Kim Typer software (version 2.0, Bruker) and analyzed using et al., 2007; Yumoto et al., 2005), deteriorated mural paint- standard pattern matching (with default parameter settings) ings (Heyrman et al., 2003), salt fields (Lee et al., 2006), against the main spectra of over 6252 bacteria, including freshwater fish (Yumoto et al., 2005), algal mat (Romano the spectra from the most closely related species: Oceano- et al., 2006), freshwater insects (Raats and Halpern, 2007), a bacillus oncorhynchi CIP108867T, O. picturae CIP 108264T, Bacillus -dominated wastewater treatment system in Korea O. profundus CIP 109535T, O. chironomi CIP 109536T, O. (Nam et al., 2008), fermented shrimp paste samples (Nam- iheyensis CIP 107618T, and O. oncorhynchi subsp. in- wong et al., 2009), soy sauce production equipment (Tomi- caldanensis CIP 109235T. The 16S rRNA PCR and sequenc- naga et al., 2009), marine solar saltern (Lee et al., 2010), ing were performed as previously described (Mourembou activated sludge in a bioreactor (Whon et al., 2010), tradi- et al., 2015). tional Korean fermented food (Hirota et al., 2013), fermented Polygonum indigo liquor sample (Yang et al., 2010), and, finally, a human stool sample (Roux et al., 2013). Growth conditions Here, we used high salt culture conditions in order to The optimum growth temperature of the strain S5T was cultivate halophilic bacteria from human faeces and a novel tested on our home-made solid medium by inoculating 105 Oceanobacillus isolate, strain S5T ( = CSUR P1091 = DSM CFU/mL of an exponentially growing culture incubated 28586), was isolated from a stool sample of a 25-year- aerobically at 28°,37°,45°, and 55°C. The growth atmo- old obese Saudi patient, as part of culturomics study of in- sphere was tested under aerobic conditions, in the presence of testinal microflora, as a new representative of the genus 5% CO2, and also in microaerophilic and anaerobic condi- Oceanobacillus. tions created using GENbag microaer and GENbag anaer (BioMe´rieux, Marcy l’Etoile, France), respectively. The Materials and Methods optimum NaCl concentration required for growth was tested at 0%, 0.5%, 1.5%, 5%, 7.5%, 10%, 15%, and 20% of NaCl. Ethics and collection of the strain The optimum pH was determined by growth testing at pH 5, The stool specimens were collected from a 25-year-old 6, 7, 7.5, 8. and 9. obese Saudi patient after defecation into sterile plastic con- tainers, which were sampled and stored at -80°C until use. Biochemical, sporulation, and motility assays (Supplementary Table S1. Supplementary material is available The commercially available Api ZYM, Api 20 NE, Api 50 online at www.liebertpub.com/omi). Informed and signed CH strips (bioMe´rieux), supplemented by 10% NaCl (w/v), consent was obtained from the patient. The study and consent were used to characterize the biochemical properties of the procedure were approved by the Ethics Committees of the strain according to the manufacturer’s instructions. Strain King Abdulaziz University (King Fahd Medical Research sporulation was tested by thermic-shock at 60°C for 20 Center, Saudi Arabia), under agreement number 014- T minutes. A fresh culture of the strain S5 was observed under CEGMR-2-ETH-P, and by the Institut Fe´de´ratif de Recherche DM1000 photonic microscope (Leica Microsystems, Nan- 48 (Faculty of Medicine, Marseille, France), under agreement terre, France) at 100X to assess the motility of the bacteria. number 09-022. The salt concentration of the stool specimen The colony’s surface was observed on our home-made cul- was determined using a digital refractometer (Fisher Scientific, ture medium after 24 h incubation under aerobic conditions at Illkirch, France) and the pH by using a pH-meter. 37°C. Isolation of the strain Antibiotic susceptibility testing T Strain S5 was isolated in December 2013 using aerobic Susceptibility to antibiotics was tested
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