The composition of the vaginal microbiota is an important health determinant. Several members of the phylum Actinobacteria have been implicated in bacterial vaginosis, a condition associated with many negative health outcomes. Here, we present 11 strains of vaginal Actinobacteria (now available through BEI Resources) along with draft genome sequences

Deitzler, Grace E

Hallsworth-Pepin, Kymberlie

Lewis, Amanda L

Lewis, Warren G

Mitreva, Makedonka

Park, SoEun

Robinson, Lloyd S

Ruiz, Maria J

Weimer, Cory

Wollam, Aye

Genome Announcements

English

PubMed

ABSTRACT
          
            The composition of the vaginal microbiota is an important health determinant. Several members of the phylum
            Actinobacteria
            have been implicated in bacterial vaginosis, a condition associated with many negative health outcomes. Here, we present 11 strains of vaginal
            Actinobacteria
            (now available through BEI Resources) along with draft genome sequences.
          </jats:p

Amanda L. Lewis

Grace E. Deitzler

Maria J. Ruiz

Cory Weimer

SoEun Park

Lloyd S. Robinson

Kymberlie Hallsworth-Pepin

Aye Wollam

Makedonka Mitreva

Warren G. Lewis

Crossref

Genome Sequences of 11 Human Vaginal
            <i>Actinobacteria</i>
            Strains

Digital Commons@Becker

Washington University School of MedicineDigital Commons@BeckerOpen Access Publications2016Genome sequences of 11 human vaginalActinobacteria strainsAmanda L. LewisWashington University School of Medicine in St. LouisGrace 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. 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 CitationLewis, Amanda L.; Deitzler, Grace E.; Ruiz, Maria J.; Weimer, Cory; Park, SoEun; Robinson, Lloyd S.; Hallsworth-Pepin, Kymberlie;Wollam, Aye; Mitreva, Makedonka; and Lewis, Warren G., ,"Genome sequences of 11 human vaginal Actinobacteria strains." GenomeAnnouncements.4,5. e00887-16. (2016).https://digitalcommons.wustl.edu/open_access_pubs/5630AuthorsAmanda L. Lewis, Grace E. Deitzler, Maria J. Ruiz, Cory Weimer, SoEun Park, Lloyd S. Robinson, KymberlieHallsworth-Pepin, Aye Wollam, Makedonka Mitreva, and Warren G. LewisThis open access publication is available at Digital Commons@Becker: https://digitalcommons.wustl.edu/open_access_pubs/5630Genome Sequences of 11 Human Vaginal Actinobacteria StrainsAmanda L. Lewis,a,b,d Grace E. Deitzler,a,d Maria J. Ruiz,a Cory Weimer,a,d SoEun Park,a,d Lloyd S. Robinson,a,dKymberlie Hallsworth-Pepin,c,e Aye Wollam,c,e Makedonka Mitreva,c,e 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.The composition of the vaginal microbiota is an important health determinant. Several members of the phylum Actinobacteriahave been implicated in bacterial vaginosis, a condition associated with many negative health outcomes. Here, we present 11strains of vaginal Actinobacteria (now available through BEI Resources) along with draft genome sequences.Received 14 July 2016 Accepted 28 July 2016 Published 29 September 2016Citation Lewis AL, Deitzler GE, Ruiz MJ, Weimer C, Park S, Robinson LS, Hallsworth-Pepin K, Wollam A, Mitreva M, Lewis WG. 2016. Genome sequences of 11 human vaginalActinobacteria strains. Genome Announc 4(5):e00887-16. doi:10.1128/genomeA.00887-16.Copyright © 2016 Lewis 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.Bacterial vaginosis (BV) is a vaginal dysbiosis associated withserious health complications (1–6). It is characterized by theabsence of Lactobacillus species in the vagina and overgrowth of apolymicrobial community often containing members of the phy-lum Actinobacteria, including Gardnerella vaginalis, Atopobiumspp., and others. In fact, G. vaginalis was recently shown to elicitseveral features of BV in a mouse vaginal infection model (7, 8).Bifidobacteria are also commonly isolated from the vagina, al-though members of this genus are rarely found in pathologicalcontexts. Here, we isolated 11 vaginal bacteria from the phylumActinobacteria. Vaginal swabs were collected from nonpregnantand pregnant women according to Washington University insti-tutional review board (IRB)-approved protocols (201108155 and20110382). Organisms isolated from vaginal swabs were culturedanaerobically, and identification was performed by 16S rRNAgene sequencing. Genomic DNA was obtained using the Wizardgenomic DNA purification kit (Promega). Methodological detailson isolation and clinical information will be described elsewhere.Genomes were assembled de novo using the One Button Velvetassembly pipeline (version 1.1.06) (9) with hash sizes of 31, 33,and 35 after downsizing the sample input data to 100 coverage.An internal core gene screen on the assembly tested for complete-ness of the genome. After assembly, the minimum length for con-tigs was set to 200 bp, and an internal core gene screen was per-formed as defined by the Human Microbiome Project (HMP)(10). Then, adapters were removed, and low-quality regions weretrimmed. Finally, a screen for contamination was performed. Theprocess of gene annotation included generating both ab initio andevidence-based (BLAST) predictions. Functional predictions ofcoding sequences were made using GeneMark and Glimmer3(11, 12). Loci were then defined by clustering predictions with thesame reading frame. We evaluated predictions using the nonre-dundant (NR) and Pfam databases and resolved overlaps be-tween adjacent coding genes. Intergenic regions not spannedby GeneMark and Glimmer3 were subject to a BLAST searchagainst NCBI’s NR database and predictions generated basedon protein alignments. tRNA genes were determined usingtRNAscan-SE (13) and noncoding RNA genes by RNAmmer (14)and Rfam (15). Metabolic pathways and subcellular localizationwere predicted using KEGG and PSORTb, respectively (16, 17),and functional domains were evaluated using InterProScan (18).Accession number(s). These whole-genome shotgun projectshave been deposited in GenBank under the accession numberslisted in Table 1. We have also made the strains available to theTABLE 1 Identifiers and nucleotide sequences for sequenced strains of vaginal ActinobacteriaGenus/species Strain BEI catalog no. Nucleotide accession no.Actinomyces neuii MJR8396A HMS-1266 LRPJ00000000Alloscardovia omnicolens CMW7705A HMS-1282 LRPK00000000Atopobium vaginae CMW7778A HMS-1300 LSOA00000000Bifidobacterium bifidum MJR8628B HMS-1264 LRPO00000000Bifidobacterium breve GED8481 HMS-1261 LRPP00000000Bifidobacterium longum CMW7750 HMS-1299 LRPQ00000000Corynebacterium sp. CMW7794 HMS-1295 LSRB00000000Gardnerella vaginalis GED7275B HMS-1272 LRPZ00000000Gardnerella vaginalis GED7760B HMS-1284 LRQA00000000Gardnerella vaginalis CMW7778B HMS-1298 LSRC00000000Propionibacterium avidum MJR7694 HMS-1291 LRVD00000000crossmarkGenome AnnouncementsSeptember/October 2016 Volume 4 Issue 5 e00887-16 genomea.asm.org 1 on February 28, 2017 by Washington University in St. Louishttp://genomea.asm.org/Downloaded from research community by depositing them with the Biodefense andEmerging Infections (BEI) Research Resource Repository (see BEInumbers in Table 1).ACKNOWLEDGMENTSWe acknowledge Justin Perry, Deborah Frank, and the Women’s andInfant’s Health Specimen Consortium (especially Michele Landeau). Wealso thank Jeff Peipert, Jenifer Allsworth, and Jennifer Bick of the Contra-ceptive CHOICE project for providing specimens from nonpregnantwomen.FUNDING INFORMATIONThis work, including the efforts of Makedonka Mitreva, was fundedby HHS | National Institutes of Health (NIH) (5U54HG00496804).This work, including the efforts of Amanda L. Lewis and Warren G.Lewis, was funded by HHS | NIH | National Institute of Allergy andInfectious Diseases (NIAID) (R01 AI114635). This work, includingthe efforts of Amanda L. Lewis, was funded by HHS | NIH | NationalInstitute of Diabetes and Digestive and Kidney Diseases (NIDDK)(P50 DK064540-11). This work, including the efforts of Grace E.Deitzler, was funded by HHS | NIH | National Institute of Diabetesand Digestive and Kidney Diseases (NIDDK) (P20DK097798). Thiswork, including the efforts of Amanda L. Lewis, was funded byBurroughs Wellcome Fund (BWF).This work was funded by the Burroughs-Wellcome Fund Preterm BirthInitiative (A.L.L.). Summer stipends were provided by the Planning Cen-ter for Research in Benign Urology Summer Research Program(P20DK097798 to G.E.D.) and the Washington University in St. LouisSummer Research Program in Global Health with the Center for GlobalHealth & Infectious Disease (CGHID)/Institute for Public Health (3054-93396B to M.J.R.).REFERENCES1. Wiesenfeld HC, Hillier SL, Krohn MA, Landers DV, Sweet RL. 2003.Bacterial vaginosis is a strong predictor of Neisseria gonorrhoeae and Chla-mydia trachomatis infection. Clin Infect Dis 36:663– 668. http://dx.doi.org/10.1086/367658.2. Marrazzo JM, Martin DH, Watts DH, Schulte J, Sobel JD, Hillier SL,Deal C, Fredricks DN. 2010. Bacterial vaginosis: identifying researchgaps proceedings of a workshop sponsored by DHHS/NIH/NIAID.S e x T r a n s m D i s 3 7 : 7 3 2 – 7 4 4 . ht tp : / /dx .do i .org /10 .1097/OLQ.0b013e3181fbbc95.3. 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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/btq249.18. 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.Lewis et al.Genome Announcements2 genomea.asm.org September/October 2016 Volume 4 Issue 5 e00887-16 on February 28, 2017 by Washington University in St. Louishttp://genomea.asm.org/Downloaded from 

Genome sequences of 11 human vaginal Actinobacteria strains

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Genome sequences of 11 human vaginal Actinobacteria strains

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