Research on vaginal infections is currently limited by a lack of available fully sequenced bacterial reference strains. Here, we present strains (now available through BEI Resources) and genome sequences for a set of 14 vaginal isolates from the phylum Firmicutes. These genome sequences provide a valuable resource for future research in understanding the role of Gram-positive bacteria in vaginal health and disease

Deitzler, Grace E

Hallsworth-Pepin, Kymberlie

Lewis, Amanda L

Lewis, Warren G

Mitreva, Makedonka

Park, SoEun

Robinson, Lloyd

Ruiz, Maria J

Weimer, Cory

Wollam, Aye

Genome Announcements

English

PubMed

ABSTRACT
          
            Research on vaginal infections is currently limited by a lack of available fully sequenced bacterial reference strains. Here, we present strains (now available through BEI Resources) and genome sequences for a set of 14 vaginal isolates from the phylum
            Firmicutes
            . These genome sequences provide a valuable resource for future research in understanding the role of Gram-positive bacteria in vaginal health and disease.
          </jats:p

Grace E. Deitzler

Maria J. Ruiz

Cory Weimer

SoEun Park

Lloyd Robinson

Kymberlie Hallsworth-Pepin

Aye Wollam

Makedonka Mitreva

Amanda L. Lewis

Warren G. Lewis

Crossref

Genome Sequences of 14
            <i>Firmicutes</i>
            Strains Isolated from the Human Vagina

Digital Commons@Becker

Washington University School of MedicineDigital Commons@BeckerOpen Access Publications2016Genome sequences of 14 Firmicutes strainsisolated from the human vaginaGrace E. DeitzlerWashington University School of Medicine in St. LouisMaria J. RuizWashington University School of Medicine in St. LouisCory WeimerWashington University School of Medicine in St. LouisSoEun ParkWashington University School of Medicine in St. LouisLloyd RobinsonWashington 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 CitationDeitzler, Grace E.; Ruiz, Maria J.; Weimer, Cory; Park, SoEun; Robinson, Lloyd; Hallsworth-Pepin, Kymberlie; Wollam, Aye; Mitreva,Makedonka; Lewis, Amanda L.; and Lewis, Warren G., ,"Genome sequences of 14 Firmicutes strains isolated from the human vagina."Genome Announcements.4,5. 2016. (2016).https://digitalcommons.wustl.edu/open_access_pubs/5629AuthorsGrace E. Deitzler, Maria J. Ruiz, Cory Weimer, SoEun Park, Lloyd Robinson, Kymberlie Hallsworth-Pepin,Aye Wollam, Makedonka Mitreva, Amanda L. Lewis, and Warren G. LewisThis open access publication is available at Digital Commons@Becker: https://digitalcommons.wustl.edu/open_access_pubs/5629Genome Sequences of 14 Firmicutes Strains Isolated from the HumanVaginaGrace E. Deitzler,a,d Maria J. Ruiz,a,d Cory Weimer,a,d SoEun Park,a,d Lloyd Robinson,a,d Kymberlie Hallsworth-Pepin,e Aye Wollam,eMakedonka Mitreva,c,e Amanda L. Lewis,a,b,d Warren G. Lewisc,dDepartment of Molecular Microbiology,a Department of Obstetrics and Gynecology,b Department of Medicine,c Center for Women’s Infectious Disease Research,d andMcDonnell Genome Institute,e Washington University School of Medicine, St. Louis, Missouri, USAFor a commentary on this article, see doi:10.1128/genomeA.00890-16.Research on vaginal infections is currently limited by a lack of available fully sequenced bacterial reference strains. Here, wepresent strains (now available through BEI Resources) and genome sequences for a set of 14 vaginal isolates from the phylumFirmicutes. These genome sequences provide a valuable resource for future research in understanding the role of Gram-positivebacteria in vaginal health and disease.Received 3 July 2016 Accepted 4 August 2016 Published 29 September 2016Citation Deitzler GE, Ruiz MJ, Weimer C, Park S, Robinson L, Hallsworth-Pepin K, Wollam A, Mitreva M, Lewis AL, Lewis WG. 2016. Genome sequences of 14 Firmicutes strainsisolated from the human vagina. Genome Announc 4(5):e00888-16. doi:10.1128/genomeA.00888-16.Copyright © 2016 Deitzler et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.Address correspondence to Amanda L. Lewis, allewis@wustl.edu, or Warren G. Lewis, WarrenGLewisPhD@gmail.com.A variety of health outcomes have been associated with specificbacteria or bacterial patterns colonizing the human vagina.For example, bacterial vaginosis (BV) is a common dysbiosis ofthe vaginal microbiota that is associated with increased risks ofsexually transmitted infections and serious complications duringpregnancy, such as intrauterine infections and preterm labor (1–6). BV is generally characterized by the absence of vaginal Lacto-bacillus and overgrowth of diversemicrobes, including Firmicutes,such asAnaerococcus, Finegoldia, Megasphaera, Peptoniphilus, andVeillonella species. However, little is known about the strategiesthese bacteria use to colonize the vagina or whether they are in-volved in the causes and complications associated with BV. Weisolated 15 Firmicutes from vaginal swabs of healthy and BV-affected pregnant and nonpregnant women. While some of thesebacterial species may have sequenced reference strains, there arevery few strains from the human vaginawhose genomes have beenpreviously sequenced.Vaginal swabs were collected from nonpregnant and pregnantwomen according to Washington University institutional reviewboard (IRB)-approved protocols 201108155 and 20110382, re-spectively. Organisms were isolated from these swabs anaerobi-cally on solid medium. Isolation procedures and clinical informa-tion will be described in a future publication. The cultureconditions for each strain have been provided to BEI Resources.Sequencing of 16s rRNA genes 1,400 bp were used to initiallyassign bacteria genus and species identifications by comparisonwith the NCBI ribosomal database. Genomic DNA was obtainedusing the Wizard genomic DNA purification kit (Promega).De novo assembly of genomes were conducted using the OneButton Velvet assembly pipeline (version 1.1.06) (7), with hashsizes of 31, 33, and 35 after downsizing the sample input data to100 coverage. A minimum length for contigs was set (postas-sembly) at 200 bp. We performed a screen for core genes (as de-fined by the HMP [8]) on many of the assemblies to test for com-TABLE 1 Strain names and accession numbersSpecies Strain BEI catalog no. Nucleotide sequence accession no.Anaerococcus tetradius MJR8151 HMS-1268 LRPM00000000Bacillus coagulans GED7749B HMS-1281 LRPN00000000Clostridium perfringens MJR7757A HMS-1290 LRPU00000000Enterococcus faecium MJR8396B HMS-1267 LRPV00000000Finegoldia magna GED7760A HMS-1285 LRPW00000000Megasphaera sp. MJR9396C HMS-1269 LRVC00000000Peptoniphilus harei CMW7756A HMS-1297 LRQE00000000Peptostreptococcus anaerobius MJR8628A HMS-1263 LSQZ00000000Staphylococcus lugdunensis MJR7738 HMS-1293 LRQI00000000Staphylococcus simulans MJR7712 HMS-1283 LRQJ00000000Streptococcus mitis CMW7705B HMS-1296 LRQR00000000Streptococcus pasteurianus GED7275A HMS-1273 LSRA00000000Streptococcus salivarius GED7778A HMS-1287 LRQS00000000Veillonella atypica CMW7756B HMS-1301 LRQT00000000crossmarkGenome AnnouncementsSeptember/October 2016 Volume 4 Issue 5 e00888-16 genomea.asm.org 1 on February 28, 2017 by Washington University in St. Louishttp://genomea.asm.org/Downloaded from pleteness of the genome. Gene annotation was performed usingboth ab initio and evidence-based (BLAST) predictions. Codingsequences were predicted using GeneMark and Glimmer3 (9, 10).Intergenic regions not identified by GeneMark and Glimmer3were searched by BLAST in NCBI’s nonredundant bacterial(NR) database. The best prediction for each open readingframe was selected by evaluating all predictions against the bestevidence (nonredundant bacterial, NR, and Pfam [11]) and re-solving overlaps between adjacent coding genes. tRNA genes weredetermined using tRNAscan-SE (12) and noncoding RNA genesby RNAmmer (13) and Rfam (14). Metabolic pathways andsubcellular localization were predicted using KEGG (15) andPSORTb (16), respectively, and functional domains were evalu-ated using InterProScan (17).Accession number(s). These whole-genome shotgun projectshave been deposited in GenBank under the accession numberslisted in Table 1. The sequences described in this paper are the firstversions. We have also made the strains available to the researchcommunity by depositing them with the Biodefense and Emerg-ing Infections (BEI) Research Resource Repository (see BEI num-bers in Table 1).ACKNOWLEDGMENTSWe thank Justin Perry for technical assistance, Deborah Frank for edito-rial assistance, and the Women’s and Infant’s Health Specimen Consor-tium (especially Michele Landeau) for assistance with the collection ofvaginal swabs frompregnantwomen.We also thank Jenifer Allsworth, JeffPeipert, and Jennifer Bick of the Contraceptive CHOICE project for pro-viding specimens from nonpregnant women.We also appreciate the gen-erosity of the women who participated in this research.This work was funded by the Burroughs-Wellcome Fund pretermBirth Initiative (A.L.L.). Summer stipends were provided by the PlanningCenter for Research in Benign Urology Summer Research ProgramP20DK097798 (G.E.D.) and the Washington University in St. LouisGlobal Health Center of the Institute for Public Health (M.J.R.).FUNDING INFORMATIONThis work, including the efforts of Makedonka Mitreva, was fundedby HHS | National Institutes of Health (NIH) (5U54HG004968). Thiswork, including the efforts of Grace E. Deitzler, was funded byHHS | National Institutes of Health (NIH) (P20DK097798). Thiswork, including the efforts of Amanda L. Lewis and Warren G.Lewis, was funded by HHS | NIH | National Institute of Allergy andInfectious Diseases (NIAID) (NIH R01 AI114635). This work,including the efforts of Amanda L. Lewis, was funded by BurroughsWellcome Fund (BWF).REFERENCES1. Atashili J, Poole C, Ndumbe PM, Adimora AA, Smith JS. 2008. Bacterialvaginosis andHIV acquisition: ameta-analysis of published studies. AIDS22:1493–1501. http://dx.doi.org/10.1097/QAD.0b013e3283021a37.2. Hillier SL, Nugent RP, Eschenbach DA, Krohn MA, Gibbs RS, MartinDH, Cotch MF, Edelman R, Pastorek JG, Jr, Rao AV. 1995. Associationbetween bacterial vaginosis and preterm delivery of a low-birth-weightinfant. The Vaginal Infections and Prematurity Study Group. N Engl JMed 333:1737–1742. http://dx.doi.org/10.1056/NEJM199512283332604.3. 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 97:211–219.4. Holst E, Goffeng AR, Andersch B. 1994. Bacterial vaginosis and vaginalmicroorganisms in idiopathic premature labor and association with preg-nancy outcome. J Clin Microbiol 32:176–186.5. Wiesenfeld HC, Hillier SL, Krohn MA, Landers DV, Sweet RL. 2003.Bacterial vaginosis is a strong predictor ofNeisseria gonorrhoeae andChla-mydia trachomatis infection. Clin Infect Dis 36:663– 668. http://dx.doi.org/10.1086/367658.6. Zhang X, Xu X, Li J, Li N, Yan T, Ju X. 2002. Relationship betweenvaginal sialidase bacteria vaginosis and chorioammionitis. Zhonghua FuChan Ke Za Zhi 37:588–590.7. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short readassembly using de Bruijn graphs. Genome Res 18:821–829. http://dx.doi.org/10.1101/gr.074492.107.8. Human Microbiome Project Consortium. 2012. A framework for humanmicrobiome research. Nature 486:215–221. http://dx.doi.org/10.1038/nature11209.9. Borodovsky M, Mills R, Besemer J, Lomsadze A. 2003. Prokaryotic geneprediction using GeneMark and GeneMark.Hmm. Curr Protoc Bio-informatics Chapter 4:Unit 4.5. http://dx.doi .org/10.1002/0471250953.bi0405s01.10. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. 1999. Improvedmicrobial gene identification with GLIMMER. Nucleic Acids Res 27:4636–4641. http://dx.doi.org/10.1093/nar/27.23.4636.11. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G,Forslund K, Eddy SR, Sonnhammer EL, Bateman A. 2008. The Pfamprotein families database. 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PSORTb 3.0: improvedprotein subcellular localization prediction with refined localization sub-categories and predictive capabilities for all prokaryotes. Bioinformatics26:1608–1615. http://dx.doi.org/10.1093/bioinformatics/btq249.17. Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R,Lopez R. 2005. InterProScan: protein domains identifier. Nucleic AcidsRes 33:W116–W120. http://dx.doi.org/10.1093/nar/gki442.Deitzler et al.Genome Announcements2 genomea.asm.org September/October 2016 Volume 4 Issue 5 e00888-16 on February 28, 2017 by Washington University in St. Louishttp://genomea.asm.org/Downloaded from 

Genome sequences of 14 Firmicutes strains isolated from the human vagina

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Genome sequences of 14 Firmicutes strains isolated from the human vagina

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