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View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Archive Ouverte en Sciences de l'Information et de la Communication Genome analysis and description of Xanthomonas massiliensis sp. nov., a new species isolated from human faeces S Ndongo, M Beye, Gregory Dubourg, Tt Nguyen, Carine Couderc, Fabrizio Di Pinto, Pierre-Edouard Fournier, Didier Raoult, Emmanouil Angelakis To cite this version: S Ndongo, M Beye, Gregory Dubourg, Tt Nguyen, Carine Couderc, et al.. Genome analysis and description of Xanthomonas massiliensis sp. nov., a new species isolated from human faeces. New Microbes and New Infections, Wiley Online Library 2018, 26, pp.63-72. 10.1016/j.nmni.2018.06.005. hal-02100374 HAL Id: hal-02100374 https://hal-amu.archives-ouvertes.fr/hal-02100374 Submitted on 15 Apr 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. TAXONOGENOMICS: GENOME OF A KNOWN ORGANISM Genome analysis and description of Xanthomonas massiliensis sp. nov., a new species isolated from human faeces S. Ndongo1, M. Beye1, G. Dubourg1, T. T. Nguyen1, C. Couderc1, D. P. Fabrizio1, P.-E. Fournier2, D. Raoult1,3 and E. Angelakis2,4 1) Aix-Marseille Université, IRD, AP-HM, MEPHI, 2) Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France, 3) Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia and 4) Laboratory of Medical Microbiology, Hellenic Pasteur Institute, Athens, Greece Abstract Xanthomonas massiliensis strain SN6T is a Gram-negative bacterium which is aerobic, motile and nonsporulating. This new species isolated from human faeces exhibited the characteristic traits of members of this genus, such as yellow pigmentation and viscosity. Here we present the main phenotypic characteristics and the taxonogenomics description of this strain. The genome is 3 690 720 bp long with DNA G + C content of about 70.52%. © 2018 Published by Elsevier Ltd. Keywords: Culturomics, genome, human gut microbiota, taxonogenomics, Xanthomonas massiliensis Original Submission: 12 April 2018; Revised Submission: 8 June 2018; Accepted: 13 June 2018 Article published online: 21 June 2018 axonopodis, X. fragariae and X. albilineans, and 62 pathovars of X. Corresponding author: S. Ndongo, MEPHI, Institut Hospitalo- campestris, on the basis of DNA ± DNA hybridization data and Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin 13005 Marseille, France. biochemical and physiological tests. However, members of the E-mail: [email protected] genus Xanthomonas can be differentiated from members of the phylogenetically closest genus Pseudoxanthomonas by the absence of reduction of nitrates to nitrites and the presence of C13:0 iso 3-OH fatty acid [4]. Members of the Xanthomonas genus were known exclusively Introduction as plant-associated organisms and did not durably colonize other niches [5]. However, during the study of the bacterial diversity of The first member of the genus Xanthomonas was described by the human microbiota by culturomics [6], a strain of Xanthomo- Dowson [1], and the genus [2] contains plant-associated bac- nas was isolated from the stool sample of an obese French patient. teria that establish neutral, commensal or pathogenic relation- It is the first Xanthomonas isolate identified in humans to date. ships with plants. Taxonomically, the members of this genus Here we report the characterization of strain SN6 as a novel were revised several times because the taxonomy had been species of the genus Xanthomonas, Xanthomonas massiliensis previously based on host specificity. Each bacterium isolated strain SN6 (= CSUR P2129 = DSM 100900), with a description of from a new host was considered as a new species. Dye and the complete genomic sequence and its annotation. Lelliott [2] reduced the number of species from about 120 to fi the following ve: Xanthomonas campestris, Xanthomonas albili- Materials and methods neans, Xanthomonas axonopodis, Xanthomonas fragariae and Xanthomonas ampelina. The others were grouped together as nomenspecies in the X. campestris group (pathovar). In 1995, Organism information and strain isolation Vauterin et al. [3] partially clarified the classification and Strain SN6 was discovered in the context of a study on the described 20 species among the three former species, X. microaerophilic bacteria of the human digestive microbiota by New Microbe and New Infect 2018; 26: 63–72 © 2018 Published by Elsevier Ltd This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/) https://doi.org/10.1016/j.nmni.2018.06.005 64 New Microbes and New Infections, Volume 26 Number C, November 2018 NMNI culturomics in September 2015. The strain was isolated from a supplemented with 5% sheep’s blood (COS) agar (bioMérieux) 41-year-old obese Frenchwoman hospitalized in September and we also tested its growth under aerobic and anaerobic 2012 at the La Timone Hospital in Marseille, France. This study conditions generated by AnaeroGen (bioMérieux). The mini- and the assent procedure were validated by the ethics com- mum and maximum growth temperature ranges (28°C, 37°C, mittee of the IFR48 Federative Research Institute Marseille 45°C, 55°C) were determined as well as maximum salinity under number 09-022, and we obtained the signed consent of levels (0–5, 50–75, 100 g/L NaCl). The ability of the strain to the patient. grow on media with different pH was also tested. The colonies After collecting the stool, a portion of a sample was stored appeared on day 3 after culture on Columbia agar, and their at −80°C until use. In June 2015, the stool sample was cultivated diameter was measured. Cell morphology, Gram staining and as part of an exploration of the human microbiome centred on motility were observed in fresh colonies using a DM1000 microaerophilic bacteria the. Part of the frozen aliquot of the photonic microscope (Leica Microsystems, Nanterre, France) specimen (approximately 1 g) was taken out and diluted in 900 μL with a 40 × objective lens. Sporulation was tested by thermal of phosphate-buffered saline (Life Technologies, Carlsbad, CA, shock, which consists of exposing the bacterium to a temper- USA) following ten serial dilutions to obtain 1/10. Inoculum (50 ature of 60°C for 20 minutes and then watching its growth after μL) was seeded on Columbia agar supplemented with 5% sheep’s 48 hours. Negative staining was carried out with detection blood (bioMérieux, Marcy l’Etoile, France) and incubated under Formvar-coated grids placed on a drop of 40 μL of bacterial microaerophilic conditions (7% O2,5%H2, 10% CO2, 85% N2) suspension (after an overnight fixation in glutaraldehyde 2.5%) using the generator CampyGen (Thermo Scientific, Villebon-sur- and incubated at 37°C for 30 minutes, followed by a 10-second Yvette, France) at 37°C for 48 hours. incubation in 1% ammonium molybdate. The grids were dried on blotting paper and finally observed using a Tecnai G20 Strain identification transmission electron microscope (FEI Company, Limeil-Bré- After 48 hours of incubation in microaerophilic conditions, vannes, France). pure colonies were isolated on Columbia agar and identified by proteomic analysis using matrix-assisted desorption Biochemical characterization ionization–time of flight mass spectrometry (MALDI-TOF MS) The biochemical properties of strain SN6 were characterized following the same protocol as previously described by Seng using API ZYM, API 20NE and API 50CH strips, according to et al. [7] with a Microflex spectrometer (Bruker Daltonics, the manufacturer’s instructions (bioMérieux) for testing of Leipzig, Germany). All obtained spectra of strain SN6 were carbon source utilization and enzyme activity. The presence of imported into the MALDI BioTyper software (version 2.0; catalase and oxidase activities was tested by using a BBL Dry- Bruker) and analysed by standard pattern matching (with Slide (Becton, Le Pont de Claix, France) according to the default parameter settings) and compared to those of the manufacturer’s instructions. The analysis of cellular fatty acid BioTyper database and our own collection. Thus, a score of >2 methyl ester composition was performed by gas chromatog- allowed identification at the species level, and a score of <1.7 raphy/mass spectrometry (GC/MS). Two samples of approxi- did not allow any identification. mately 100 mg of bacterial biomass per tube collected from five If the identification of the spectrum from colonies selected fresh culture plates were used for the extraction of cellular and purified several times by subculturing on Columbia agar fatty acid methyl esters with the protocol described by Sasser failed, then the 16S rRNA gene was amplified and complete [11]. GC/MS analyses were carried out as described by Dione genome sequencing was carried out as previously described [8]. et al. [12]. The nucleotide sequence obtained was corrected using Chromas Pro 1.34 software (Technelysium, Tewantin, Australia) Antibiotic susceptibility and compared to the nucleotide database using the BLAST The sensitivity to classical antibiotics was tested to determine similarities web services in the online PubMed National Center the antibiogram profile of strain SN6 using the disc diffusion for Biotechnology Information (NCBI) database (http://blast. method following the European Committee on Antimicrobial ncbi.nlm.nih.gov.gate1.inist.fr/Blast.cgi). As suggested previ- Susceptibility Testing 2016 recommendations (http://www. ously, similarity level thresholds of 98.65% and 95% allowed the eucast.org). A suspension of 0.5 McFarland of the species was definition of a new species or a new genus, respectively [9,10].
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  • Genomic Insights Into Strategies Used by Xanthomonas

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    Pieretti et al. BMC Genomics 2012, 13:658 http://www.biomedcentral.com/1471-2164/13/658 RESEARCH ARTICLE Open Access Genomic insights into strategies used by Xanthomonas albilineans with its reduced artillery to spread within sugarcane xylem vessels Isabelle Pieretti1, Monique Royer1, Valérie Barbe2, Sébastien Carrere3, Ralf Koebnik4, Arnaud Couloux2, Armelle Darrasse5, Jérôme Gouzy3, Marie-Agnès Jacques5, Emmanuelle Lauber6, Charles Manceau5, Sophie Mangenot2, Stéphane Poussier7, Béatrice Segurens2, Boris Szurek4, Valérie Verdier4, Matthieu Arlat8, Dean W Gabriel9, Philippe Rott1 and Stéphane Cociancich1,10* Abstract Background: Xanthomonas albilineans causes leaf scald, a lethal disease of sugarcane. X. albilineans exhibits distinctive pathogenic mechanisms, ecology and taxonomy compared to other species of Xanthomonas. For example, this species produces a potent DNA gyrase inhibitor called albicidin that is largely responsible for inducing disease symptoms; its habitat is limited to xylem; and the species exhibits large variability. A first manuscript on the complete genome sequence of the highly pathogenic X. albilineans strain GPE PC73 focused exclusively on distinctive genomic features shared with Xylella fastidiosa—another xylem-limited Xanthomonadaceae. The present manuscript on the same genome sequence aims to describe all other pathogenicity-related genomic features of X. albilineans, and to compare, using suppression subtractive hybridization (SSH), genomic features of two strains differing in pathogenicity. Results: Comparative genomic analyses showed that most of the known pathogenicity factors from other Xanthomonas species are conserved in X. albilineans, with the notable absence of two major determinants of the “artillery” of other plant pathogenic species of Xanthomonas: the xanthan gum biosynthesis gene cluster, and the type III secretion system Hrp (hypersensitive response and pathogenicity).
  • Metagenomics and Metatranscriptomics of Lake Erie Ice

    Metagenomics and Metatranscriptomics of Lake Erie Ice

    METAGENOMICS AND METATRANSCRIPTOMICS OF LAKE ERIE ICE Opeoluwa F. Iwaloye A Thesis Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE August 2021 Committee: Scott Rogers, Advisor Paul Morris Vipaporn Phuntumart © 2021 Opeoluwa Iwaloye All Rights Reserved iii ABSTRACT Scott Rogers, Lake Erie is one of the five Laurentian Great Lakes, that includes three basins. The central basin is the largest, with a mean volume of 305 km2, covering an area of 16,138 km2. The ice used for this research was collected from the central basin in the winter of 2010. DNA and RNA were extracted from this ice. cDNA was synthesized from the extracted RNA, followed by the ligation of EcoRI (NotI) adapters onto the ends of the nucleic acids. These were subjected to fractionation, and the resulting nucleic acids were amplified by PCR with EcoRI (NotI) primers. The resulting amplified nucleic acids were subject to PCR amplification using 454 primers, and then were sequenced. The sequences were analyzed using BLAST, and taxonomic affiliations were determined. Information about the taxonomic affiliations, important metabolic capabilities, habitat, and special functions were compiled. With a watershed of 78,000 km2, Lake Erie is used for agricultural, forest, recreational, transportation, and industrial purposes. Among the five great lakes, it has the largest input from human activities, has a long history of eutrophication, and serves as a water source for millions of people. These anthropogenic activities have significant influences on the biological community. Multiple studies have found diverse microbial communities in Lake Erie water and sediments, including large numbers of species from the Verrucomicrobia, Proteobacteria, Bacteroidetes, and Cyanobacteria, as well as a diverse set of eukaryotic taxa.