DOCSLIB.ORG

Genome Analysis and Description of Xanthomonas Massiliensis Sp. Nov

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Genome Analysis and Description of Xanthomonas Massiliensis Sp. Nov 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]. grown on Mueller-Hinton agar in a petri dish (bioMérieux), and the discs used were provided by i2a (Montpellier, France).
Load more

Recommended publications
  • Identification and Lead-In Characterization of Novel B3 Metallo-Β- Lactamases
    Identification and lead-in characterization of novel B3 metallo-β- lactamases Irsa Mateen1*, Faisal Saeed Awan1, Azeem Iqbal Khan2 and Muhammad Anjum Zia3 1Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan 2Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan 3Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan Abstract: Metallo-β-lactamases (MBLs) are zinc ion dependent enzymes that are responsible for the emergence and spread of β-lactam resistance among bacterial pathogens. There are uncharacterized putative MBLs in the environment and their emergence is major interference in the generation of universal MBL inhibitors so it is important to identify and characterize novel MBLs. In this study two novel MBLs from Luteimonas sp. J29 and Pseudoxanthomonas mexicana were identified using B3 MBLs as query in BLAST database search. 3D models of putative MBLs generated by SWISS- MODEL server taking AIM-1 as a structural template were verified using web based structure assessment and validation programs. Multiple sequence alignment revealed that residues important for substrate binding were conserved and loop region residues (156-162 and 223-230) important for catalysis are variable in these novel MBLs. Homology models showed typical MBL α/β/β/α sandwich fold containing six α helices, twelve β strands and metal interacting residues are conserved in similar way as with other B3 MBLs. We report promising putative B3 MBLs with some variations and substrate docking studies revealed that novel MBLs have attributes close to acquired B3 MBLs. Keywords: β-lactam antibiotics; Luteimonas sp. J29; Pseudoxanthomonas mexicana; homology modeling. INTRODUCTION L1 from Stenotrophomonas maltophilia are some representatives of B3 subgroup (Wachino et al., 2013; Accession of β-lactamases is the most common Docquier et al., 2004; Costello et al., 2006).
    [Show full text]
  • Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
    Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg
    [Show full text]
  • Genome Mining Reveals the Genus Xanthomonas to Be A
    Royer et al. BMC Genomics 2013, 14:658 http://www.biomedcentral.com/1471-2164/14/658 RESEARCH ARTICLE Open Access Genome mining reveals the genus Xanthomonas to be a promising reservoir for new bioactive non-ribosomally synthesized peptides Monique Royer1, Ralf Koebnik2, Mélanie Marguerettaz1, Valérie Barbe3, Guillaume P Robin2, Chrystelle Brin4, Sébastien Carrere5, Camila Gomez1, Manuela Hügelland6, Ginka H Völler6, Julie Noëll1, Isabelle Pieretti1, Saskia Rausch6, Valérie Verdier2, Stéphane Poussier7, Philippe Rott1, Roderich D Süssmuth6 and Stéphane Cociancich1* Abstract Background: Various bacteria can use non-ribosomal peptide synthesis (NRPS) to produce peptides or other small molecules. Conserved features within the NRPS machinery allow the type, and sometimes even the structure, of the synthesized polypeptide to be predicted. Thus, bacterial genome mining via in silico analyses of NRPS genes offers an attractive opportunity to uncover new bioactive non-ribosomally synthesized peptides. Xanthomonas is a large genus of Gram-negative bacteria that cause disease in hundreds of plant species. To date, the only known small molecule synthesized by NRPS in this genus is albicidin produced by Xanthomonas albilineans. This study aims to estimate the biosynthetic potential of Xanthomonas spp. by in silico analyses of NRPS genes with unknown function recently identified in the sequenced genomes of X. albilineans and related species of Xanthomonas. Results: We performed in silico analyses of NRPS genes present in all published genome sequences of Xanthomonas spp., as well as in unpublished draft genome sequences of Xanthomonas oryzae pv. oryzae strain BAI3 and Xanthomonas spp. strain XaS3. These two latter strains, together with X. albilineans strain GPE PC73 and X.
    [Show full text]
  • 20640Edfcb19c0bfb828686027c
    FEMS Microbiology Reviews, fuz024, 44, 2020, 1–32 doi: 10.1093/femsre/fuz024 Advance Access Publication Date: 3 October 2019 Review article REVIEW ARTICLE Mechanistic insights into host adaptation, virulence and epidemiology of the phytopathogen Xanthomonas Shi-Qi An1, Neha Potnis2,MaxDow3,Frank-Jorg¨ Vorholter¨ 4, Yong-Qiang He5, Anke Becker6, Doron Teper7,YiLi8,9,NianWang7, Leonidas Bleris8,9,10 and Ji-Liang Tang5,* 1National Biofilms Innovation Centre (NBIC), Biological Sciences, University of Southampton, University Road, Southampton SO17 1BJ, UK, 2Department of Entomology and Plant Pathology, Rouse Life Science Building, Auburn University, Auburn AL36849, USA, 3School of Microbiology, Food Science & Technology Building, University College Cork, Cork T12 K8AF, Ireland, 4MVZ Dr. Eberhard & Partner Dortmund, Brauhausstraße 4, Dortmund 44137, Germany, 5State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China, 6Loewe Center for Synthetic Microbiology and Department of Biology, Philipps-Universitat¨ Marburg, Hans-Meerwein-Straße 6, Marburg 35032, Germany, 7Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred 33850, USA, 8Bioengineering Department, University of Texas at Dallas, 2851 Rutford Ave, Richardson, TX 75080, USA, 9Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA and 10Department of Biological Sciences, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX75080, USA ∗Corresponding author: State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China.
    [Show full text]
  • The Microbiota Continuum Along the Female Reproductive Tract and Its Relation to Uterine-Related Diseases
    ARTICLE DOI: 10.1038/s41467-017-00901-0 OPEN The microbiota continuum along the female reproductive tract and its relation to uterine-related diseases Chen Chen1,2, Xiaolei Song1,3, Weixia Wei4,5, Huanzi Zhong 1,2,6, Juanjuan Dai4,5, Zhou Lan1, Fei Li1,2,3, Xinlei Yu1,2, Qiang Feng1,7, Zirong Wang1, Hailiang Xie1, Xiaomin Chen1, Chunwei Zeng1, Bo Wen1,2, Liping Zeng4,5, Hui Du4,5, Huiru Tang4,5, Changlu Xu1,8, Yan Xia1,3, Huihua Xia1,2,9, Huanming Yang1,10, Jian Wang1,10, Jun Wang1,11, Lise Madsen 1,6,12, Susanne Brix 13, Karsten Kristiansen1,6, Xun Xu1,2, Junhua Li 1,2,9,14, Ruifang Wu4,5 & Huijue Jia 1,2,9,11 Reports on bacteria detected in maternal fluids during pregnancy are typically associated with adverse consequences, and whether the female reproductive tract harbours distinct microbial communities beyond the vagina has been a matter of debate. Here we systematically sample the microbiota within the female reproductive tract in 110 women of reproductive age, and examine the nature of colonisation by 16S rRNA gene amplicon sequencing and cultivation. We find distinct microbial communities in cervical canal, uterus, fallopian tubes and perito- neal fluid, differing from that of the vagina. The results reflect a microbiota continuum along the female reproductive tract, indicative of a non-sterile environment. We also identify microbial taxa and potential functions that correlate with the menstrual cycle or are over- represented in subjects with adenomyosis or infertility due to endometriosis. The study provides insight into the nature of the vagino-uterine microbiome, and suggests that sur- veying the vaginal or cervical microbiota might be useful for detection of common diseases in the upper reproductive tract.
    [Show full text]
  • Identification and Analysis of Seven Effector Protein Families with Different Adaptive and Evolutionary Histories in Plant-Associated Members of the Xanthomonadaceae
    UC Davis UC Davis Previously Published Works Title Identification and analysis of seven effector protein families with different adaptive and evolutionary histories in plant-associated members of the Xanthomonadaceae. Permalink https://escholarship.org/uc/item/1t8016h3 Journal Scientific reports, 7(1) ISSN 2045-2322 Authors Assis, Renata de AB Polloni, Lorraine Cristina Patané, José SL et al. Publication Date 2017-11-23 DOI 10.1038/s41598-017-16325-1 Peer reviewed eScholarship.org Powered by the California Digital Library University of California www.nature.com/scientificreports OPEN Identifcation and analysis of seven efector protein families with diferent adaptive and Received: 8 August 2017 Accepted: 9 November 2017 evolutionary histories in plant- Published: xx xx xxxx associated members of the Xanthomonadaceae Renata de A. B. Assis 1, Lorraine Cristina Polloni2, José S. L. Patané3, Shalabh Thakur4, Érica B. Felestrino1, Julio Diaz-Caballero4, Luciano Antonio Digiampietri 5, Luiz Ricardo Goulart2, Nalvo F. Almeida 6, Rafael Nascimento2, Abhaya M. Dandekar7, Paulo A. Zaini2,7, João C. Setubal3, David S. Guttman 4,8 & Leandro Marcio Moreira1,9 The Xanthomonadaceae family consists of species of non-pathogenic and pathogenic γ-proteobacteria that infect diferent hosts, including humans and plants. In this study, we performed a comparative analysis using 69 fully sequenced genomes belonging to this family, with a focus on identifying proteins enriched in phytopathogens that could explain the lifestyle and the ability to infect plants. Using a computational approach, we identifed seven phytopathogen-enriched protein families putatively secreted by type II secretory system: PheA (CM-sec), LipA/LesA, VirK, and four families involved in N-glycan degradation, NixE, NixF, NixL, and FucA1.
    [Show full text]
  • Genome Sequencing of Xanthomonas Vasicola Pathovar Vasculorum Reveals Variation in Plasmids and Genes Encoding Lipopolysaccharid
    Pathogens 2014, 3, 211-237; doi:10.3390/pathogens3010211 OPEN ACCESS pathogens ISSN 2076-0817 www.mdpi.com/journal/pathogens Article Genome Sequencing of Xanthomonas vasicola Pathovar vasculorum Reveals Variation in Plasmids and Genes Encoding Lipopolysaccharide Synthesis, Type-IV Pilus and Type-III Secretion Effectors Arthur Wasukira 1,2, Max Coulter 1, Noorah Al-Sowayeh 1, Richard Thwaites 3, Konrad Paszkiewicz 1, Jerome Kubiriba 2, Julian Smith 3, Murray Grant 1 and David J. Studholme 1,* 1 Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK; E-Mails: [email protected] (A.W.); [email protected] (M.C.); [email protected] (N.A.-S.); [email protected] (K.P.); [email protected] (M.G.) 2 National Crops Resources Research Institute (NaCRRI), Kampala 7084, Uganda; E-Mail: [email protected] 3 The Food and Environment Research Agency, Sand Hutton, York YO41 1LZ, UK; E-Mails: [email protected] (R.T.); [email protected] (J.S.) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +44-(0)-1392-72-4678. Received: 13 December 2013; in revised form: 10 February 2014 / Accepted: 3 March 2014 / Published: 18 March 2014 Abstract: Xanthomonas vasicola pathovar vasculorum (Xvv) is the bacterial agent causing gumming disease in sugarcane. Here, we compare complete genome sequences for five isolates of Xvv originating from sugarcane and one from maize. This identified two distinct types of lipopolysaccharide synthesis gene clusters among Xvv isolates: one is similar to that of Xanthomonas axonopodis pathovar citri (Xac) and is probably the ancestral type, while the other is similar to those of the sugarcane-inhabiting species, Xanthomonas sacchari.
    [Show full text]
  • Bacteria-Killing Type IV Secretion Systems
    fmicb-10-01078 May 18, 2019 Time: 16:6 # 1 REVIEW published: 21 May 2019 doi: 10.3389/fmicb.2019.01078 Bacteria-Killing Type IV Secretion Systems Germán G. Sgro1†, Gabriel U. Oka1†, Diorge P. Souza1‡, William Cenens1, Ethel Bayer-Santos1‡, Bruno Y. Matsuyama1, Natalia F. Bueno1, Thiago Rodrigo dos Santos1, Cristina E. Alvarez-Martinez2, Roberto K. Salinas1 and Chuck S. Farah1* 1 Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil, 2 Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, University of Campinas (UNICAMP), Edited by: Campinas, Brazil Ignacio Arechaga, University of Cantabria, Spain Reviewed by: Bacteria have been constantly competing for nutrients and space for billions of years. Elisabeth Grohmann, During this time, they have evolved many different molecular mechanisms by which Beuth Hochschule für Technik Berlin, to secrete proteinaceous effectors in order to manipulate and often kill rival bacterial Germany Xiancai Rao, and eukaryotic cells. These processes often employ large multimeric transmembrane Army Medical University, China nanomachines that have been classified as types I–IX secretion systems. One of the *Correspondence: most evolutionarily versatile are the Type IV secretion systems (T4SSs), which have Chuck S. Farah [email protected] been shown to be able to secrete macromolecules directly into both eukaryotic and †These authors have contributed prokaryotic cells. Until recently, examples of T4SS-mediated macromolecule transfer equally to this work from one bacterium to another was restricted to protein-DNA complexes during ‡ Present address: bacterial conjugation. This view changed when it was shown by our group that many Diorge P.
    [Show full text]
  • Arenimonas Halophila Sp. Nov., Isolated from Soil
    TAXONOMIC DESCRIPTION Kanjanasuntree et al., Int J Syst Evol Microbiol 2018;68:2188–2193 DOI 10.1099/ijsem.0.002801 Arenimonas halophila sp. nov., isolated from soil Rungravee Kanjanasuntree,1 Jong-Hwa Kim,1 Jung-Hoon Yoon,2 Ampaitip Sukhoom,3 Duangporn Kantachote3 and Wonyong Kim1,* Abstract A Gram-staining-negative, aerobic, non-motile, rod-shaped bacterium, designated CAU 1453T, was isolated from soil and its taxonomic position was investigated using a polyphasic approach. Strain CAU 1453T grew optimally at 30 C and at pH 6.5 in the presence of 1 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that CAU 1453T represented a member of the genus Arenimonas and was most closely related to Arenimonas donghaensis KACC 11381T (97.2 % similarity). T CAU 1453 contained ubiquinone-8 (Q-8) as the predominant isoprenoid quinone and iso-C15 : 0 and iso-C16 : 0 as the major cellular fatty acids. The polar lipids consisted of diphosphatidylglycerol, a phosphoglycolipid, an aminophospholipid, two unidentified phospholipids and two unidentified glycolipids. CAU 1453T showed low DNA–DNA relatedness with the most closely related strain, A. donghaensis KACC 11381T (26.5 %). The DNA G+C content was 67.3 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, CAU 1453T represents a novel species of the genus Arenimonas, for which the name Arenimonas halophila sp. nov. is proposed. The type strain is CAU 1453T (=KCTC 62235T=NBRC 113093T). The genus Arenimonas, a member of the family Xantho- CAU 1453T was isolated from soil by the dilution plating monadaceae in the class Gammaproteobacteria was pro- method using marine agar 2216 (MA; Difco) [14].
    [Show full text]
  • Genes 2011, 2, 1050-1065; Doi:10.3390/Genes2041050
    Genes 2011, 2, 1050-1065; doi:10.3390/genes2041050 OPEN ACCESS genes ISSN 2073-4425 www.mdpi.com/journal/genes Communication Draft Genome Sequences of Xanthomonas sacchari and Two Banana-Associated Xanthomonads Reveal Insights into the Xanthomonas Group 1 Clade David J. Studholme 1,*, Arthur Wasukira 1,2, Konrad Paszkiewicz 1, Valente Aritua 2,3,†, Richard Thwaites 3, Julian Smith 3 and Murray Grant 1 1 Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK; E-Mails: [email protected] (A.W.); [email protected] (K.P.); [email protected] (M.G.) 2 National Crops Resources Research Institute (NaCRRI), P.O. Box 7084, Kampala, Uganda; E-Mail: [email protected] 3 The Food and Environment Research Agency, Sand Hutton, York, YO41 1LZ, UK; E-Mails: [email protected] (R.T.); [email protected] (J.S.) † Present address: Department of Plant Pathology, Citrus Research and Education Center, University of Florida, 700 Experiment Station Road, Lake Alfred 33850, FL, USA. * Author to whom correspondence should be addressed; E-Mail: [email protected]. Received: 23 October 2011; in revised form: 4 November 2011 / Accepted: 21 November 2011 / Published: 2 December 2011 Abstract: We present draft genome sequences for three strains of Xanthomonas species, each of which was associated with banana plants (Musa species) but is not closely related to the previously sequenced banana-pathogen Xanthomonas campestris pathovar musacearum. Strain NCPPB4393 had been deposited as Xanthomonas campestris pathovar musacearum but in fact falls within the species Xanthomonas sacchari.
    [Show full text]
  • Full Genome Sequence Analysis of Two Isolates Reveals a Novel Xanthomonas Species Close to the Sugarcane Pathogen Xanthomonas Albilineans
    Genes 2015, 6, 714-733; doi:10.3390/genes6030714 OPEN ACCESS genes ISSN 2073-4425 www.mdpi.com/journal/genes Article Full Genome Sequence Analysis of Two Isolates Reveals a Novel Xanthomonas Species Close to the Sugarcane Pathogen Xanthomonas albilineans Isabelle Pieretti 1, Stéphane Cociancich 1, Stéphanie Bolot 2,3, Sébastien Carrère 2,3, Alexandre Morisset 1, Philippe Rott 1,† and Monique Royer 1,* 1 CIRAD UMR BGPI, TA A-54/K, Campus International de Baillarguet, F-34398 Montpellier Cedex 5, France; E-Mails: [email protected] (I.P.); [email protected] (S.C.); [email protected] (A.M.); [email protected] (P.R.) 2 INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, 24 Chemin de Borde Rouge—Auzeville CS52627, F-31326 Castanet Tolosan Cedex, France; E-Mails: [email protected] (S.B.); [email protected] (S.C.) 3 CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, 24 Chemin de Borde Rouge—Auzeville CS52627, F-31326 Castanet Tolosan Cedex, France † Present Address: University of Florida, IFAS, Everglades Research and Education Center, Belle Glade, FL 33430, USA; E-Mail: [email protected]. * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +33-499-624-844. Academic Editor: J. Peter W. Young Received: 30 April 2015 / Accepted: 14 July 2015 / Published: 23 July 2015 Abstract: Xanthomonas albilineans is the bacterium responsible for leaf scald, a lethal disease of sugarcane. Within the Xanthomonas genus, X. albilineans exhibits distinctive genomic characteristics including the presence of significant genome erosion, a non-ribosomal peptide synthesis (NRPS) locus involved in albicidin biosynthesis, and a type 3 secretion system (T3SS) of the Salmonella pathogenicity island-1 (SPI-1) family.
    [Show full text]
  • Unveiling Bacterial Interactions Through Multidimensional Scaling and Dynamics Modeling Received: 06 May 2015 Pedro Dorado-Morales1, Cristina Vilanova1, Carlos P
    www.nature.com/scientificreports OPEN Unveiling Bacterial Interactions through Multidimensional Scaling and Dynamics Modeling Received: 06 May 2015 Pedro Dorado-Morales1, Cristina Vilanova1, Carlos P. Garay3, Jose Manuel Martí3 Accepted: 17 November 2015 & Manuel Porcar1,2 Published: 16 December 2015 We propose a new strategy to identify and visualize bacterial consortia by conducting replicated culturing of environmental samples coupled with high-throughput sequencing and multidimensional scaling analysis, followed by identification of bacteria-bacteria correlations and interactions. We conducted a proof of concept assay with pine-tree resin-based media in ten replicates, which allowed detecting and visualizing dynamical bacterial associations in the form of statistically significant and yet biologically relevant bacterial consortia. There is a growing interest on disentangling the complexity of microbial interactions in order to both optimize reactions performed by natural consortia and to pave the way towards the development of synthetic consor- tia with improved biotechnological properties1,2. Despite the enormous amount of metagenomic data on both natural and artificial microbial ecosystems, bacterial consortia are not necessarily deduced from those data. In fact, the flexibility of the bacterial interactions, the lack of replicated assays and/or biases associated with differ- ent DNA isolation technologies and taxonomic bioinformatics tools hamper the clear identification of bacterial consortia. We propose here a holistic approach aiming at identifying bacterial interactions in laboratory-selected microbial complex cultures. The method requires multi-replicated taxonomic data on independent subcultures, and high-throughput sequencing-based taxonomic data. From this data matrix, randomness of replicates can be verified, linear correlations can be visualized and interactions can emerge from statistical correlations.
    [Show full text]