Microbial profiling of cpn60 universal target sequences in artificial mixtures of vaginal bacteria sampled by nylon swabs or self-sampling devices under different storage conditions

Journal of Microbiological Methods

Volumn 136, Issue , 2017, Pages 57-64

  Schellenberg, John J ^a   Oh, Angela Yena ^a   Hill, Janet E ^a  

^a UNIVERSITY OF SASKATCHEWAN   (Canada)

Author keywords

ALDEx2; cpn60 universal target; HerSwab ; Hierarchical clustering; Quantitative microbiome profiling; UniFrac; Vaginal self sampling

Indexed keywords

AMPLICON; ARTICLE; CERVICOVAGINAL SELF-SAMPLING DEVICE; CONTROLLED STUDY; CPN60 GENE; DNA EXTRACTION; FEMALE; GENE; GENE AMPLIFICATION; GENE SEQUENCE; GENETIC VARIATION; HUMAN; HUMAN CELL; HUMAN TISSUE; INTERMETHOD COMPARISON; MICROBIAL COMMUNITY; NYLON SWAB; POLYMERASE CHAIN REACTION; REPRODUCIBILITY; ROOM TEMPERATURE; STORAGE; VAGINA DISCHARGE; VAGINA FLORA; VAGINITIS; BACTERIUM; BODY FLUID; CHEMISTRY; CLASSIFICATION; DEVICES; DNA SEQUENCE; GENE TARGETING; GENETICS; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION; MICROBIAL CONSORTIUM; MICROBIOLOGY; NUCLEOTIDE SEQUENCE; PROCEDURES; SPECIMEN HANDLING; TEMPERATURE; VAGINA;

BACTERIAL DNA; CHAPERONIN 60; NYLON; RNA 16S;

BACTERIA; BASE SEQUENCE; BODY FLUIDS; CHAPERONIN 60; DNA, BACTERIAL; FEMALE; GENE TARGETING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICROBIAL CONSORTIA; NYLONS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SPECIMEN HANDLING; TEMPERATURE; VAGINA;

EID: 85015055005     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2017.03.003     Document Type: Article

References (45)

1. Albert, A.Y., Chaban, B., Wagner, E.C., Schellenberg, J.J., Links, M.G., van Schalkwyk, J., Reid, G., Hemmingsen, S.M., Hill, J.E., Money, D., A study of the vaginal microbiome in healthy Canadian women utilizing cpn60-based molecular profiling reveals distinct Gardnerella subgroup community state types. PLoS ONE, 10, 2015, e0135620.
2. Arias, M., Jang, D., Gilchrist, J., Luinstra, K., Li, J., Smieja, M., Chernesky, M.A., Ease, comfort, and performance of the HerSwab vaginal self-sampling device for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae. Sex. Transm. Dis. 43 (2016), 125–129.
3. Bai, G., Gajer, P., Nandy, M., Ma, B., Yang, H., Sakamoto, J., Blanchard, M.H., Ravel, J., Brotman, R.M., Comparison of storage conditions for human vaginal microbiome studies. PLoS ONE, 7, 2012, e36934.
4. Brotman, R.M., Ravel, J., Ready or not: the molecular diagnosis of bacterial vaginosis. Clin. Infect. Dis. 47 (2008), 44–46.
5. Brotman, R.M., Shardell, M.D., Gajer, P., Fadrosh, D., Chang, K., Silver, M.I., Viscidi, R.P., Burke, A.E., Ravel, J., Gravitt, P.E., Association between the vaginal microbiota, menopause status, and signs of vulvovaginal atrophy. Menopause 21 (2014), 450–458.
6. Chaban, B., Albert, A., Links, M.G., Gardy, J., Tang, P., Hill, J.E., Characterization of the upper respiratory tract microbiomes of patients with pandemic H1N1 influenza. PLoS ONE, 8, 2013, e69559.
7. Chaban, B., Links, M.G., Paramel Jayaprakash, T., Wagner, E.C., Bourque, D.K., Lohn, Z., Albert, A.Y.K., van Schalkwyk, J., Reid, G., Hemmingsen, S.M., Hill, J.E., Money, D.M., Characterization of the vaginal microbiota of healthy Canadian women through the menstrual cycle. Microbiome, 2, 2014, 23.
8. R Core Team, R: A Language and Environment for Statistical Computing, Vienna, Austria. 2015.
9. Dominianni, C., Wu, J., Hayes, R.B., Ahn, J., Comparison of methods for fecal microbiome biospecimen collection. BMC Microbiol., 14, 2014, 103.
10. Fernandes, A.D., Macklaim, J.M., Linn, T.G., Reid, G., Gloor, G.B., ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-Seq. PLoS ONE, 8, 2013, e67019.
11. Fernando, W.M.U., Hill, J.E., Zello, G.A., Tyler, R.T., Dahl, W.J., Van Kessel, A.G., Diets supplemented with chickpea or its main oligosaccharide component raffinose modify fecal microbial composition in healthy adults. Benefic. Microbes 1 (2010), 197–207.
12. Gautam, R., Borgdorff, H., Jespers, V., Francis, S.C., Verhelst, R., Mwaura, M., Delany-Moretlwe, S., Ndayisaba, G., Kyongo, J.K., Hardy, L., Menten, J., Crucitti, T., Tsivtsivadze, E., Schuren, F., van de Wijgert, J.H., Vaginal Biomarkers Study, G., Correlates of the molecular vaginal microbiota composition of African women. BMC Infect. Dis., 15, 2015, 86.
13. Geshnizgani, A.M., Onderdonk, A.B., Defined medium simulating genital tract secretions for growth of vaginal microflora. J. Clin. Microbiol. 30 (1992), 1323–1326.
14. Goh, S.H., Potter, S., Wood, J.O., Hemmingsen, S.M., Reynolds, R.P., Chow, A.W., HSP60 gene sequences as universal targets for microbial species identification: studies with coagulase-negative staphylococci. J. Clin. Microbiol. 34 (1996), 818–823.
15. Greiff, V., Menzel, U., Haessler, U., Cook, S.C., Friedensohn, S., Khan, T.A., Pogson, M., Hellmann, I., Reddy, S.T., Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice. BMC Immunol., 15, 2014, 40.
16. Hill, J.E., Penny, S.L., Crowell, K.G., Goh, S.H., Hemmingsen, S.M., cpnDB: a chaperonin sequence database. Genome Res. 14 (2004), 1669–1675.
17. Hill, J.E., Goh, S.H., Money, D.M., Doyle, M., Li, A., Crosby, W.L., Links, M., Leung, A., Chan, D., Hemmingsen, S.M., Characterization of vaginal microflora of healthy, nonpregnant women by chaperonin-60 sequence-based methods. Am. J. Obstet. Gynecol. 193 (2005), 682–692.
18. Hill, J.E., Town, J.R., Hemmingsen, S.M., Improved template representation in cpn60 PCR product libraries generated from complex templates by application of a specific mixture of PCR primers. Environ. Microbiol. 8 (2006), 741–746.
19. Hill, J.E., Fernando, W.M.U., Zello, G.A., Tyler, R.T., Dahl, W.J., Van Kessel, A.G., Improvement of the representation of bifidobacteria in fecal microbiota metagenomic libraries by application of the cpn60 universal primer cocktail. Appl. Environ. Microbiol. 76 (2010), 4550–4552.
20. Hong, S., Bunge, J., Leslin, C., Jeon, S., Epstein, S.S., Polymerase chain reaction primers miss half of rRNA microbial diversity. ISME J. 3 (2009), 1365–1373.
21. Juarez Tomas, M.S., Nader-Macias, M.E., Effect of a medium simulating vaginal fluid on the growth and expression of beneficial characteristics of potentially probiotic lactobacilli. Vilas, A.-M., (eds.) Communicating Current Research and Educational Topics and Trends in Applied Microbiology, 2007, Formatex, Badajoz, Spain, 732–740.
22. Katsuoka, F., Yokozawa, J., Tsuda, K., Ito, S., Pan, X., Nagasaki, M., Yasuda, J., Yamamoto, M., An efficient quantitation method of next-generation sequencing libraries by using MiSeq sequencer. Anal. Biochem. 466 (2014), 27–29.
23. Katyal, I., Chaban, B., Hill, J.E., Comparative genomics of cpn60 defined Enterococcus hirae ecotypes and relationship of gene content differences to competitive fitness. Microb. Ecol. 72 (2015), 917–930.
24. Langmead, B., Salzberg, S.L., Fast gapped-read alignment with bowtie 2. Nat. Methods 9 (2012), 357–359.
25. Lauber, C.L., Zhou, N., Gordon, J.I., Knight, R., Fierer, N., Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. FEMS Microbiol. Lett. 307 (2010), 80–86.
26. Lee, D.H., Zo, Y.G., Kim, S.J., Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphism. Appl. Environ. Microbiol. 62 (1996), 3112–3120.
27. Links, M.G., Hill, J.E., cpn60 universal target region as a barcode for bacteria. Canadian Society of Microbiologists 62nd Annual Meeting, Vancouver, BC, 2012.
28. Lozupone, C., Lladser, M.E., Knights, D., Stombaugh, J., Knight, R., UniFrac: an effective distance metric for microbial community comparison. ISME J. 5 (2011), 169–172.
29. Lunny, C., Taylor, D., Hoang, L., Wong, T., Gilbert, M., Lester, R., Krajden, M., Ogilvie, G., Self-collected versus clinician-collected sampling for Chlamydia and Gonorrhea screening: a systemic review and meta-analysis. PLoS ONE, 10, 2015, e0132776.
30. Masser, D.R., Berg, A.S., Freeman, W.M., Focused, high accuracy 5-methylcytosine quantitation with base resolution by benchtop next-generation sequencing. Epigenetics Chromatin, 6, 2013, 33.
31. Ravel, J., Brotman, R.M., Gajer, P., Ma, B., Nandy, M., Fadrosh, D.W., Sakamoto, J., Koenig, S.S., Fu, L., Zhou, X., Hickey, R.J., Schwebke, J.R., Forney, L.J., Daily temporal dynamics of vaginal microbiota before, during and after episodes of bacterial vaginosis. Microbiome, 1, 2013, 29.
32. Santiago, G.L., Tency, I., Verstraelen, H., Verhelst, R., Trog, M., Temmerman, M., Vancoillie, L., Decat, E., Cools, P., Vaneechoutte, M., Longitudinal qPCR study of the dynamics of L. crispatus, L. iners, A. vaginae, (sialidase positive) G. vaginalis, and P. bivia in the vagina. PLoS ONE, 7, 2012, e45281.
33. Schellenberg, J., Blake Ball, T., Lane, M., Cheang, M., Plummer, F., Flow cytometric quantification of bacteria in vaginal swab samples self-collected by adolescents attending a gynecology clinic. J. Microbiol. Methods 73 (2008), 216–226.
34. Schellenberg, J., Links, M.G., Hill, J.E., Dumonceaux, T.J., Peters, G.A., Tyler, S., Ball, B., Severini, A., Plummer, F.A., Pyrosequencing of the chaperonin-60 universal target as a tool for determining microbial community composition. Appl. Environ. Microbiol. 75 (2009), 2889–2898.
35. Schellenberg, J.J., Links, M.G., Hill, J.E., Dumonceaux, T.J., Kimani, J., Jaoko, W., Wachihi, C., Mungai, J.N., Peters, G.A., Tyler, S., Graham, M., Severini, A., Fowke, K.R., Ball, T.B., Plummer, F.A., Molecular definition of vaginal microbiota in East African commercial sex workers. Appl. Environ. Microbiol. 77 (2011), 4066–4074.
36. Schellenberg, J.J., Dumonceaux, T.J., Hill, J.E., Kimani, J., Jaoko, W., Wachihi, C., Mungai, J.N., Lane, M., Fowke, K.R., Ball, T.B., Plummer, F.A., Selection, phenotyping and identification of acid and hydrogen peroxide producing bacteria from vaginal samples of Canadian and East African women. PLoS ONE, 7, 2012, e41217.
37. Schellenberg, J.J., Card, C.M., Ball, T.B., Mungai, J.N., Irungu, E., Kimani, J., Jaoko, W., Wachihi, C., Fowke, K.R., Plummer, F.A., Bacterial vaginosis, HIV serostatus and T-cell subset distribution in a cohort of East African commercial sex workers: retrospective analysis. AIDS 26 (2012), 387–393.
38. Schellenberg, J.J., Paramel Jayaprakash, T., Withana Gamage, N., Patterson, M.H., Vaneechoutte, M., Hill, J.E., Gardnerella vaginalis subgroups defined by cpn60 sequencing and sialidase activity in isolates from Canada, Belgium and Kenya. PLoS ONE, 11, 2016, e0146510.
39. Serlin, M., Shafer, M.A., Tebb, K., Gyamfi, A.A., Moncada, J., Schachter, J., Wibbelsman, C., What sexually transmitted disease screening method does the adolescent prefer? Adolescents’ attitudes toward first-void urine, self-collected vaginal swab, and pelvic examination. Arch. Pediatr. Adolesc. Med. 156 (2002), 588–591.
40. Shafer, M.A., Moncada, J., Boyer, C.B., Betsinger, K., Flinn, S.D., Schachter, J., Comparing first-void urine specimens, self-collected vaginal swabs, and endocervical specimens to detect Chlamydia trachomatis and Neisseria gonorrhoeae by a nucleic acid amplification test. J. Clin. Microbiol. 41 (2003), 4395–4399.
41. Song, S.J., Amir, A., Metcalf, J.L., Amato, K.R., Xu, Z.Z., Humphrey, G., Knight, R., Preservation methods differ in fecal microbiome stability, affecting suitability for field studies. mSystems, 1, 2016, e00021-00016.
42. Strauss, R.A., Eucker, B., Savitz, D.A., Thorp, J.M. Jr., Diagnosis of bacterial vaginosis from self-obtained vaginal swabs. Infect. Dis. Obstet. Gynecol. 13 (2005), 31–35.
43. Verbeke, T.J., Sparling, R., Hill, J.E., Links, M.G., Levin, D., Dumonceaux, T.J., Predicting relatedness of bacterial genomes using the chaperonin-60 universal target (cpn60 UT): application to Thermoanaerobacter species. Syst. Appl. Microbiol. 34 (2011), 171–179.
44. van de Wijgert, J.H., Borgdorff, H., Verhelst, R., Crucitti, T., Francis, S., Verstraelen, H., Jespers, V., The vaginal microbiota: what have we learned after a decade of molecular characterization?. PLoS ONE, 9, 2014, e105998.
45. Zheng, W., Tsompana, M., Ruscitto, A., Sharma, A., Genco, R., Sun, Y., Buck, M.J., An accurate and efficient experimental approach for characterization of the complex oral microbiota. Microbiome, 3, 2015, 48.