Gardnerella vaginalis is a predominant species in bacterial vaginosis, a dysbiosis of the vagina that is associated with adverse health outcomes, including preterm birth. Here, we present the draft genome sequences of 15 Gardnerella vaginalis strains (now available through BEI Resources) isolated from women with and without bacterial vaginosis

Lek, Sai

Lewis, Amanda L

Lewis, Warren G

Perry, Justin

Robinson, Lloyd S

Sodergren, Erica

Weinstock, George

Wollam, Aye

Genome Announcements

English

PubMed

ABSTRACT
          
            Gardnerella vaginalis
            is a predominant species in bacterial vaginosis, a dysbiosis of the vagina that is associated with adverse health outcomes, including preterm birth. Here, we present the draft genome sequences of 15
            Gardnerella vaginalis
            strains (now available through BEI Resources) isolated from women with and without bacterial vaginosis.
          </jats:p

Lloyd S. Robinson

Justin Perry

Sai Lek

Aye Wollam

Erica Sodergren

George Weinstock

Warren G. Lewis

Amanda L. Lewis

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Genome Sequences of 15 Gardnerella vaginalis Strains Isolated from the Vaginas of Women with and without Bacterial Vaginosis

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Washington University School of MedicineDigital Commons@BeckerOpen Access Publications2016Genome sequences of 15 Gardnerella vaginalisstrains isolated from the vaginas of women with andwithout bacterial vaginosisLloyd S. RobinsonWashington University School of Medicine in St. LouisJustin PerryWashington University School of Medicine in St. LouisSai LekWashington University School of Medicine in St. LouisAye WollamWashington University School of Medicine in St. LouisErica SodergrenWashington University School of Medicine in St. LouisSee next page for additional authorsFollow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubsThis Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in OpenAccess Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact engeszer@wustl.edu.Recommended CitationRobinson, Lloyd S.; Perry, Justin; Lek, Sai; Wollam, Aye; Sodergren, Erica; Weinstock, George; Lewis, Warren G.; and Lewis, AmandaL., ,"Genome sequences of 15 Gardnerella vaginalis strains isolated from the vaginas of women with and without bacterial vaginosis."Genome Announcements.4,5. e00879-16. (2016).https://digitalcommons.wustl.edu/open_access_pubs/5627AuthorsLloyd S. Robinson, Justin Perry, Sai Lek, Aye Wollam, Erica Sodergren, George Weinstock, Warren G. Lewis,and Amanda L. LewisThis open access publication is available at Digital Commons@Becker: https://digitalcommons.wustl.edu/open_access_pubs/5627Genome Sequences of 15 Gardnerella vaginalis Strains Isolated fromthe Vaginas of Women with and without Bacterial VaginosisLloyd S. Robinson,a Justin Perry,a Sai Lek,b* Aye Wollam,b Erica Sodergren,b* George Weinstock,b* Warren G. Lewis,cAmanda L. Lewisa,dDepartments of Molecular Microbiology,a Medicine,c and Obstetrics and Gynecology,d Washington University School of Medicine, St. Louis, Missouri, USA; Center forWomen’s Infectious Disease Research, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USAb* Present address: Sai Lek, The Jackson Laboratory, Farmington, Connecticut, USA; Erica Sodergren, The Jackson Laboratory, Farmington, Connecticut, USA; George Weinstock, TheJackson Laboratory, Farmington, Connecticut, USA.For a commentary on this article, see doi:10.1128/genomeA.00890-16.Gardnerella vaginalis is a predominant species in bacterial vaginosis, a dysbiosis of the vagina that is associated with adversehealth outcomes, including preterm birth. Here, we present the draft genome sequences of 15 Gardnerella vaginalis strains (nowavailable through BEI Resources) isolated fromwomen with and without bacterial vaginosis.Received 30 June 2016 Accepted 28 July 2016 Published 29 September 2016Citation Robinson LS, Perry J, Lek S, Wollam A, Sodergren E, Weinstock G, Lewis WG, Lewis AL. 2016. Genome sequences of 15 Gardnerella vaginalis strains isolated from thevaginas of women with and without bacterial vaginosis. Genome Announc 4(5):e00879-16. doi:10.1128/genomeA.00879-16.Copyright © 2016 Robinson et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.Address correspondence to Warren G. Lewis, WarrenGLewisPhD@gmail.com, or Amanda L. Lewis, allewis@wustl.edu.Bacterial vaginosis (BV) is a common condition characterizedby low levels of “healthy” vaginal lactobacilli and overgrowthof diverse anaerobes (1, 2). Women with BV have higher risks ofmany adverse health outcomes, including HIV transmission, in-trauterine infections, and preterm birth (3–7). Unfortunately, thecondition is highly recurrent; most women experience anotherepisode of BV within months of treatment (8, 9). Gardnerella vagi-nalis is a facultative anaerobe in the family Bifidobacteriaceae andis one of the dominant species in BV (10). Recent studies demon-strated that G. vaginalis (strain JCP8151B) was sufficient to causeseveral features of BV in a mouse vaginal infection model (11, 12).To support further studies aimed at understanding the role ofG. vaginalis in BV, we sequenced the genomes of 15 G. vaginalisstrains (including JCP8151B) that were isolated from the vaginalswabs from 12 women enrolled in the institutional review board(IRB)-approved Washington University Contraceptive CHOICEProject (13).Strains were isolated by plating vaginal swabs on Gardnerellasemiselective medium, as described previously (12). After 24 to48 h of growth at 37°C in an anaerobic chamber, pinpointcolonies were subcultured and tested by PCR using Gardnerella-specific primers (14). Full-length 16S rRNA gene sequences con-firmed their identity. All strains were derived from differentwomen, with the exception of three strain pairs sharing the samenumerical identifier (i.e., JCP8151A and JCP8151B, JCP8017Aand JCP8017B, and JCP8481A and JCP8481B).For genome sequencing, strains were grown overnight inNYCIII broth, and DNA was isolated with the Wizard genomicDNA purification kit (Promega). Shotgun libraries were gener-ated and sequenced with Illumina sequencing technology. Contigswere assembled with Velvet 1.1.06. GeneMark and Glimmer3 (15,16) were used to predict coding regions, and the remaining se-quences were examined for homology to sequences in the NCBInonredundant protein database. Putative protein functions werepredicted with a suite of programs, including KEGG (17),PSORTb (18), and InterProScan (19). tRNAscan-SE was used toidentify tRNAs (20), and additional noncoding RNA genes weredetermined with RNAmmer (21) and Rfam (22).The average genome coverage of the sequenced strains was150. The average genome size was 1.6 Mbp. The strains contain,on average, 2,800 protein-coding genes, 15 rRNA genes, and 92tRNA genes, and have a GC content of 42.5%.Accession number(s). The draft genome sequences for the 15G. vaginalis strains have been deposited in GenBank under theaccession numbers listed in Table 1. The sequences described inthis paper are the first versions. We have also made 14 of theseTABLE 1 GenBank and BEI accession numbers of the sequencedG. vaginalis strainsStrain/BEI no. BEI accession no. Nucleotide accession no.JCP7275 HM-1105 ATJS00000000JCP7276 HM-1106 ATJR00000000JCP7659 HM-1107 ATJQ00000000JCP7672 HM-1108 ATJP00000000JCP7719 HM-1109 ATJO00000000JCP8017A HM-1110 ATJN00000000JCP8017B HM-1111 ATJM00000000JCP8066 HM-1112 ATJL00000000JCP8070 HM-1113 ATJK00000000JCP8108 HM-1114 ATJJ00000000JCP8151A HM-1115 ATJI00000000JCP8151B HM-1116 ATJH00000000JCP8481A NAa ATJG00000000JCP8481B HM-1118 ATJF00000000JCP8522 HM-1119 ATJE00000000a NA, not available.crossmarkGenome AnnouncementsSeptember/October 2016 Volume 4 Issue 5 e00879-16 genomea.asm.org 1 on February 28, 2017 by Washington University in St. Louishttp://genomea.asm.org/Downloaded from strains available to the research community by depositing themwith the Biodefense and Emerging Infections (BEI) Research Re-source Repository (see BEI numbers in Table 1).ACKNOWLEDGMENTSWe thank Jeffrey Peipert, Jenifer Allsworth, Gina Secura, Jenifer Bick, andall CHOICE participants who shared their samples for this project.FUNDING INFORMATIONThis work, including the efforts of George Weinstock, was funded byHHS | National Institutes of Health (NIH) (5U54HG00496804). Thiswork, including the efforts of Amanda L. Lewis, was funded by HHS| NIH | National Institute of Allergy and Infectious Diseases (NIAID)(R01 AI114635). This work, including the efforts of Amanda L.Lewis, was funded by Burroughs Wellcome Fund (BWF). This work,including the efforts of Amanda L. Lewis, was funded by March ofDimes Foundation (March of Dimes).This work was funded by the March of Dimes Foundation (A.L.L.), theBarnes Jewish Hospital Foundation, the Burroughs-Wellcome Fund Pre-term Birth Initiative (A.L.L.), NIH grant R01 AI114635 (W.G.L. andA.L.L.), NIH Specialized Centers of Research grant P50 DK064540-11(Scott Hultgren, A.L.L.; project II), and the Human Microbiome Project(5U54HG00496804 to G.W.).REFERENCES1. Allsworth JE, Peipert JF. 2007. Prevalence of bacterial vaginosis:2001–2004 National Health and Nutrition Examination Survey data.O b s t e t G y n e c o l 1 0 9 : 1 1 4 – 1 2 0 . ht tp : / /dx .doi .org/10.1097/01.AOG.0000247627.84791.91.2. Kenyon C, Colebunders R, Crucitti T. 2013. The global epidemiology ofbacterial vaginosis: a systematic review. Am J Obstet Gynecol 209:505–523. http://dx.doi.org/10.1016/j.ajog.2013.05.006.3. Atashili J, Poole C, Ndumbe PM, Adimora AA, Smith JS. 2008. Bacterialvaginosis and HIV acquisition: a meta-analysis of published studies. AIDS22:1493–1501. http://dx.doi.org/10.1097/QAD.0b013e3283021a37.4. Hillier SL, Nugent RP, Eschenbach DA, Krohn MA, Gibbs RS, MartinDH, Cotch MF, Edelman R, Pastorek JG, II, Rao AV, McNellis D,Regan JA, Carey JC, Klebanoff MA, The Vaginal Infections and Pre-maturity Study Group. 1995. Association between bacterial vaginosis andpreterm delivery of a low-birth-weight infant. N Engl J Med 333:1737–1742. http://dx.doi.org/10.1056/NEJM199512283332604.5. DiGiulio DB. 2012. Diversity of microbes in amniotic fluid. Semin FetalNeonatal Med 17:2–11. http://dx.doi.org/10.1016/j.siny.2011.10.001.6. DiGiulio DB, Romero R, Kusanovic JP, Gómez R, Kim CJ, Seok KS,Gotsch F, Mazaki-Tovi S, Vaisbuch E, Sanders K, Bik EM, Chaiworap-ongsa T, Oyarzún E, Relman DA. 2010. Prevalence and diversity ofmicrobes in the amniotic fluid, the fetal inflammatory response, and preg-nancy outcome in women with preterm pre-labor rupture of membranes.Am J Reprod Immunol 64:38 –57. http://dx.doi.org/10.1111/j.1600-0897.2010.00830.x.7. Hitti J, Hillier SL, Agnew KJ, Krohn MA, Reisner DP, Eschenbach DA.2001. Vaginal indicators of amniotic fluid infection in preterm labor. Ob-stet Gynecol 97:211–219.8. Bradshaw CS, Morton AN, Hocking J, Garland SM, Morris MB, MossLM, Horvath LB, Kuzevska I, Fairley CK. 2006. High recurrence rates ofbacterial vaginosis over the course of 12 months after oral metronidazoletherapy and factors associated with recurrence. J Infect Dis 193:1478 –1486. http://dx.doi.org/10.1086/503780.9. Wilson J. 2004. Managing recurrent bacterial vaginosis. 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Nu-cleic Acids Res 33:D121–D124. http://dx.doi.org/10.1093/nar/gki081.Robinson et al.Genome Announcements2 genomea.asm.org September/October 2016 Volume 4 Issue 5 e00879-16 on February 28, 2017 by Washington University in St. Louishttp://genomea.asm.org/Downloaded from 

Genome sequences of 15 Gardnerella vaginalis strains isolated from the vaginas of women with and without bacterial vaginosis

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Genome sequences of 15 Gardnerella vaginalis strains isolated from the vaginas of women with and without bacterial vaginosis

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