DOCSLIB.ORG

`Lascolabacter Vaginalis' Strain KHD1, a New Bacterial Species Cultivated from Human Female Genital Tract

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
`Lascolabacter Vaginalis' Strain KHD1, a New Bacterial Species Cultivated from Human Female Genital Tract NEW SPECIES ‘Lascolabacter vaginalis’ strain KHD1, a new bacterial species cultivated from human female genital tract K. Diop1,2, O. Mediannikov1,2, P.-E. Fournier1, D. Raoult1,2,3, F. Bretelle1,3 and F. Fenollar1,2 1) Aix-Marseille Université, Institut hospitalo-universitaire Méditerranée-infection, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France, 2) Campus International UCAD-IRD, Dakar, Senegal and 3) Department of Gynecology and Obstetrics, Gynépole, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, AMU, Aix-Marseille Université, Marseille, France Abstract We present the major characteristics of ‘Lascolabacter vaginalis’ strain KHD1 (= CSUR P0109 = DSM 101752), a new member of the family Prevotellaceae that was cultivated from a vaginal sample of a 33-year-old woman with bacterial vaginosis. © 2016 The Author(s). Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases. Keywords: Bacterial vaginosis, culturomics, Lascolabacter vaginalis, taxonomy, vaginal flora Original Submission: 20 May 2016; Revised Submission: 27 May 2016; Accepted: 30 May 2016 Article published online: 6 June 2016 blood agar (bioMérieux), colonies were grey, shiny, smooth and Corresponding author: F. Fenollar, Aix-Marseille Université, circular with a diameter of 1.4–2 mm. Strain KHD1 is strictly Institut hospitalo-universitaire Méditerranée-infection, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 anaerobic. Bacterial cells were Gram-negative rod-shaped Boulevard Jean Moulin, 13385 Marseille Cedex 05, France bacilli or coccobacilli, non-motile, and non-spore-forming with fl E-mail: [email protected] a mean diameter of 0.36 μm and a mean length of 0.57 μm. Strain KHD1 exhibited positive oxidase activity but catalase was negative. The 16S rRNA gene sequence was obtained after As part of the study of the human microbiota thanks to the amplification using the universal primer pair (fD1 and rp2) and a approach of microbial culturomics [1], we analysed the vaginal 3130-XL sequencer (Applied Biosciences, Saint-Aubin, France), flora of women with bacterial vaginosis [2]. In October 2015, as previously reported [4]. 16S rRNA gene sequence-based we isolated in the vaginal swab of a 33-year-old French woman identification of strain KHD1 showed 90% of identity with a bacterial strain that could not be identified using matrix- Prevotella loescheii strain JCM 12249 (GenBank Accession assisted laser desorption-ionization time-of-flight mass spec- number NR_113108.1), the phylogenetically closest bacterium trometry (MALDI-TOF MS) (Microflex spectrometer; Bruker with a validly published name (Fig. 1). As this sequence was Daltonics, Bremen, Germany) [3]. The study was authorized by below the 95% threshold set by Stackebrandt and Elbers to the local ethics committee of the IFR48 (Marseille, France; define a new genus without carrying out DNA–DNA hybridi- agreement 09-022) and the patient gave her written consent. zation [5], strain KHD1 was classified as the representative The initial growth of strain KHD1 was obtained at 37°C strain of a new genus belonging to the family Prevotellaceae in under anaerobic conditions after 4 days of culture on Schaedler the phylum Bacteroidetes [6]. agar enriched with sheep blood and vitamin K (BD Diagnostics, Described by Holdeman and Johnson in 1982, Prevotella loe- Le Pont-de-Claix, France) after 24 h of pre-incubation in a schi is a Gram-negative rod, non-motile, and non-spore-forming, blood culture bottle (BD Diagnostics) enriched with 4 mL of with no catalase activity [7]. This strictly anaerobic bacterium rumen that was filter-sterilized through at 0.2-μm pore filter was isolated from the human oral cavity. Hallella sergens, another (Thermo Fisher Scientific, Villebon-sur-Yvette, France) and closely related anaerobic species, is also a Gram-negative rod, 3 mL of sheep blood (bioMérieux, Marcy l’Etoile, France). After non-motile, non-spore-forming bacterium, catalase-negative, 2 days of incubation at 37°C under anaerobic conditions on that was isolated from the human gingival crevice [8]. New Microbe and New Infect 2016; 13: 22–24 © 2016 The Author(s). Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/) http://dx.doi.org/10.1016/j.nmni.2016.05.017 NMNI Diop et al. ‘Lascolabacter vaginalis’ 23 AcetomicrobiumflavidumDSM20664T (FR733692) 100 Rikenella microfusus ATCC 29728 (L16498) Alistipes timonensis JC136 (JF824799) Porphyromonas asaccharolytica DSM 20707 (L16490) Barnesiella viscericola (AB267809) Bacteroides acidofaciens A40 (AB021164) PhocaeicolaabscessusCCUG 55929 (EU694176) 100 100 Paraprevotella clara (AB331896) 99 Paraprevotellaxylaniphila(AB331897) 100 Alloprevotellarava81/4-12 (JQ039189) 100 AlloprevotellatanneraeATCC 51259 (AJ005634) Xylanibacter oryzae (AB078826) 100 100 Prevotella melaninogenica ATCC 25845 (NR_102895) 100 Hallella seregens (X81877) 100 LascolabactervaginalisKHD1 Prevotella timonensis 4401737 (NR_113123) Prevotella stercoreaCB35 (NR_041364) 95 Prevotella saccharolytica JCM 17484 (NR_113320) 97 Prevotella loescheii JCM 12249 (NR_113108) 100 Prevotella shahii EHS11 (NR_024815) 0.20 FIG. 1. Phylogenetic tree highlighting the position of Lascolabacter vaginalis strain KHD1T described in the present study relative to other species of the family Prevotellaceae. The 16S rRNA gene sequences were aligned using CLUSTALW, and phylogenetic inferences were obtained from a Bayesian phylogenetic analysis with the SYM+I+G substitution model. GenBank Accession numbers areindicatedafterthenameinbrackets.The numbers at the nodes are the bootstrap values obtained by repeating the analysis 100 times to generate a majority consensus tree. Only the bootstraps scoring at least 95% were retained. There were 1414 positions in the final data set. The scale bar indicates a 20% nucleotide sequence divergence. Strain KHD1 presents a 16S rRNA divergence of about 10% Nucleotide Sequence Accession Number with its phylogenetically closest species [9], we propose that gene sequence strain KHD1 may be the representative strain of The 16S rRNA gene sequence was deposited in EMBL-EBI a novel genus named ‘Lascolabacter’ gen. nov. ‘Lascolabacter’ under accession number LN998055. (La.sko.la.bacʹter N. L. masc. n. Lascola (personal name considered as a Latin word), La Scola, named after French microbiologist professor Bernard La Scola, MD; N.L. masc. n. Deposit in Culture Collection bacter, a staff or rod; N.L. masc. n. ‘Lascolabacter’, a rod named after Bernard La Scola). Strain KHD1 is the type strain of the ‘ new species ‘Lascolabacter vaginalis’ gen. nov., sp. nov. Strain KHD1 was deposited in the Collection de Souches de l’Unité des Rickettsies’ (CSUR, WDCM 875) and in the ‘ ’ MALDI-TOF MS Spectrum Accession collection Deutsche Sammlung von Mikroorganismen (DSM) under numbers P0109 and 101752, respectively. Number Conflict of Interest The MALDI-TOF MS spectrum of ‘Lascolabacter vaginalis’ is available at http://www.mediterranee-infection.com/article.php? laref=256&titre=urms-database. The authors have no conflicts of interest to declare. © 2016 The Author(s). Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases, NMNI, 13,22–24 This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). 24 New Microbes and New Infections, Volume 13 Number C, September 2016 NMNI Acknowledgements [4] Drancourt M, Bollet C, Carlioz A, Martelin R, Gayral JP, Raoult D. 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J Clin Microbiol 2000;38: – This research is funded by the Méditerranée-Infection 3623 30. [5] Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold Foundation. standards. Microbiol Today 2006;33:152–5. [6] Euzéby J. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2012;62: References 1–4. [7] Holdeman LV, Johnson JL. Description of Bacteroides loescheii sp. nov. and emendation of the descriptions of Bacteroides melaninogenicus [1] Lagier JC, Hugon P, Khelaifia S, Fournier PE, La Scola B, Raoult D. The (Oliver and Wherry) Roy and Kelly 1939 and Bacteroides denticola Shah rebirth of culture in microbiology through the example of culturomics and Collins 1981. Int J Syst Evol Microbiol 1982;32:399–409. to study human gut microbiota. Clin Microbiol Rev 2015;28:237–64. [8] Moore LV, Moore WE. Oribaculum catoniae gen. nov., sp. nov.; Catonella [2] Menard JP, Fenollar F, Henry M, Bretelle F, Raoult D. Molecular morbi gen. nov., sp. nov.; Hallella seregens gen. nov., sp. nov.; Johnsonella quantification of Gardnerella vaginalis and Atopobium vaginae loads to ignava gen. nov., sp. nov.; and Dialister pneumosintes gen. nov., comb. predict bacterial vaginosis. Clin Infect Dis 2008;20:33–43. nov., nom. rev., anaerobic gram-negative bacilli from the human gingival [3] Seng P, Abat C, Rolain JM, Colson P, Lagier JC, Gouriet F, et al. Iden- crevice. Int J Syst Evol Microbiol 1994;44:187–92. tification of rare pathogenic bacteria in a clinical microbiology labora- [9] Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH, et al. The tory: impact of matrix-assisted laser desorption ionization-time of flight All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of mass spectrometry. J Clin Microbiol 2013;51:2182–94. all sequenced type strains. Syst Appl Microbiol 2008;31:241–50. © 2016 The Author(s). Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases, NMNI, 13,22–24 This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)..
Load more

Recommended publications
  • An Integrated Investigation of Ruminal Microbial Communities
    AN INTEGRATED INVESTIGATION OF RUMINAL MICROBIAL COMMUNITIES USING 16S rRNA GENE-BASED TECHNIQUES DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Min Seok Kim Graduate Program in Animal Sciences The Ohio State University 2011 Dissertation Committee: Dr. Mark Morrison, Advisor Dr. Zhongtang Yu, Co-Advisor Dr. Jeffrey L. Firkins Dr. Michael A. Cotta ABSTRACT Ruminant animals obtain most of their nutrients from fermentation products produced by ruminal microbiome consisting of bacteria, archaea, protozoa and fungi. In the ruminal microbiome, bacteria are the most abundant domain and greatly contribute to production of the fermentation products. Some studies showed that ruminal microbial populations between the liquid and adherent fraction are considerably different. Many cultivation-based studies have been conducted to investigate the ruminal microbiome, but culturable species only accounted for a small portion of the ruminal microbiome. Since the 16S rRNA gene (rrs) was used as a phylogenetic marker in studies of the ruminal microbiome, the ruminal microbiome that is not culturable has been identified. Most of previous studies were dependent on sequences recovered using DGGE and construction of rrs clone libraries, but these two techniques could recover only small number of rrs sequences. Recently microarray or pyrosequencing analysis have been used to examine microbial communities in various environmental samples and greatly contributed to identifying numerous rrs sequences at the same time. However, few studies have used the microarray or pyrosequencing analysis to investigate the ruminal microbiome. The overall objective of my study was to examine ruminal microbial diversity as affected by dietary modification and to compare microbial diversity between the liquid and adherent fractions using the microarray and pyrosequencing analysis.
    [Show full text]
  • Genome-Based Taxonomic Classification Of
    ORIGINAL RESEARCH published: 20 December 2016 doi: 10.3389/fmicb.2016.02003 Genome-Based Taxonomic Classification of Bacteroidetes Richard L. Hahnke 1 †, Jan P. Meier-Kolthoff 1 †, Marina García-López 1, Supratim Mukherjee 2, Marcel Huntemann 2, Natalia N. Ivanova 2, Tanja Woyke 2, Nikos C. Kyrpides 2, 3, Hans-Peter Klenk 4 and Markus Göker 1* 1 Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany, 2 Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA, USA, 3 Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia, 4 School of Biology, Newcastle University, Newcastle upon Tyne, UK The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for Edited by: assessing their taxonomy based on the principles of phylogenetic classification and Martin G. Klotz, Queens College, City University of trees inferred from genome-scale data. No significant conflict between 16S rRNA gene New York, USA and whole-genome phylogenetic analysis is found, whereas many but not all of the Reviewed by: involved taxa are supported as monophyletic groups, particularly in the genome-scale Eddie Cytryn, trees. Phenotypic and phylogenomic features support the separation of Balneolaceae Agricultural Research Organization, Israel as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new John Phillip Bowman, class Saprospiria from Chitinophagia.
    [Show full text]
  • Genome-Based Taxonomic Classification of Bacteroidetes
    Lawrence Berkeley National Laboratory Recent Work Title Genome-Based Taxonomic Classification of Bacteroidetes. Permalink https://escholarship.org/uc/item/2fs841cf Journal Frontiers in microbiology, 7(DEC) ISSN 1664-302X Authors Hahnke, Richard L Meier-Kolthoff, Jan P García-López, Marina et al. Publication Date 2016 DOI 10.3389/fmicb.2016.02003 Peer reviewed eScholarship.org Powered by the California Digital Library University of California ORIGINAL RESEARCH published: 20 December 2016 doi: 10.3389/fmicb.2016.02003 Genome-Based Taxonomic Classification of Bacteroidetes Richard L. Hahnke 1 †, Jan P. Meier-Kolthoff 1 †, Marina García-López 1, Supratim Mukherjee 2, Marcel Huntemann 2, Natalia N. Ivanova 2, Tanja Woyke 2, Nikos C. Kyrpides 2, 3, Hans-Peter Klenk 4 and Markus Göker 1* 1 Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany, 2 Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA, USA, 3 Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia, 4 School of Biology, Newcastle University, Newcastle upon Tyne, UK The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for Edited by: assessing their taxonomy based on the principles of phylogenetic classification and Martin G.
    [Show full text]
  • A Collection of Bacterial Isolates from the Pig Intestine Reveals Functional and Taxonomic Diversity
    ARTICLE https://doi.org/10.1038/s41467-020-19929-w OPEN A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity David Wylensek1,25, Thomas C. A. Hitch 1,25, Thomas Riedel2,3, Afrizal Afrizal1, Neeraj Kumar1,4, Esther Wortmann1, Tianzhe Liu5, Saravanan Devendran6,7, Till R. Lesker8, Sara B. Hernández 9, Viktoria Heine10, Eva M. Buhl11, Paul M. D’Agostino 5, Fabio Cumbo 12, Thomas Fischöder10, Marzena Wyschkon2,3, Torey Looft 13, Valeria R. Parreira14, Birte Abt2,3, Heidi L. Doden6,7, Lindsey Ly6,7, João M. P. Alves15, Markus Reichlin16, Krzysztof Flisikowski17, Laura Navarro Suarez18, Anthony P. Neumann19, Garret Suen 19, Tomas de Wouters16, Sascha Rohn18,24, Ilias Lagkouvardos4,20, Emma Allen-Vercoe 14, 2 2 21 22 21 1234567890():,; Cathrin Spröer , Boyke Bunk , Anja J. Taverne-Thiele , Marcel Giesbers , Jerry M. Wells , Klaus Neuhaus 4, Angelika Schnieke4,17, Felipe Cava9, Nicola Segata 12, Lothar Elling 10, Till Strowig 8,23, ✉ Jason M. Ridlon6,7, Tobias A. M. Gulder5, Jörg Overmann 2,3 & Thomas Clavel 1 Our knowledge about the gut microbiota of pigs is still scarce, despite the importance of these animals for biomedical research and agriculture. Here, we present a collection of cultured bacteria from the pig gut, including 110 species across 40 families and nine phyla. We provide taxonomic descriptions for 22 novel species and 16 genera. Meta-analysis of 16S rRNA amplicon sequence data and metagenome-assembled genomes reveal prevalent and pig-specific species within Lactobacillus, Streptococcus, Clostridium, Desulfovibrio, Enterococcus, Fusobacterium, and several new genera described in this study. Potentially interesting func- tions discovered in these organisms include a fucosyltransferase encoded in the genome of the novel species Clostridium porci, and prevalent gene clusters for biosynthesis of sactipeptide-like peptides.
    [Show full text]