`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

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