{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T14:07:28Z","timestamp":1790518048213,"version":"4.1.0"},"reference-count":43,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2020,11,21]],"date-time":"2020-11-21T00:00:00Z","timestamp":1605916800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2020,11,21]],"date-time":"2020-11-21T00:00:00Z","timestamp":1605916800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100000308","name":"Carnegie Corporation of New York","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000308","id-type":"DOI","asserted-by":"publisher"}]},{"name":"South African National Research Foundation"},{"DOI":"10.13039\/501100001323","name":"Poliomyelitis Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001323","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001322","name":"South African Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001322","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001713","name":"European and Developing Countries Clinical Trials Partnership","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001713","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001342","name":"South African Department of Science and Technology","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100001342","id-type":"DOI","asserted-by":"crossref"}]},{"name":"South African National Research Foundation"},{"DOI":"10.13039\/501100001342","name":"South African Department of Science and Technology","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100001342","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Microbiome"],"published-print":{"date-parts":[[2020,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Female genital tract (FGT) inflammation is an important risk factor for HIV acquisition. The FGT microbiome is closely associated with inflammatory profile; however, the relative importance of microbial activities has not been established. Since proteins are key elements representing actual microbial functions, this study utilized metaproteomics to evaluate the relationship between FGT microbial function and inflammation in 113 young and adolescent South African women at high risk of HIV infection. Women were grouped as having low, medium, or high FGT inflammation by K-means clustering according to pro-inflammatory cytokine concentrations.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      A total of 3186 microbial and human proteins were identified in lateral vaginal wall swabs using liquid chromatography-tandem mass spectrometry, while 94 microbial taxa were included in the taxonomic analysis. Both metaproteomics and 16S rRNA gene sequencing analyses showed increased non-optimal bacteria and decreased lactobacilli in women with FGT inflammatory profiles. However, differences in the predicted relative abundance of most bacteria were observed between 16S rRNA gene sequencing and metaproteomics analyses. Bacterial protein functional annotations (gene ontology) predicted inflammatory cytokine profiles more accurately than bacterial relative abundance determined by 16S rRNA gene sequence analysis, as well as functional predictions based on 16S rRNA gene sequence data (\n                      <jats:italic>p<\/jats:italic>\n                      &lt; 0.0001). The majority of microbial biological processes were underrepresented in women with high inflammation compared to those with low inflammation, including a\n                      <jats:italic>Lactobacillus<\/jats:italic>\n                      -associated signature of reduced cell wall organization and peptidoglycan biosynthesis. This signature remained associated with high FGT inflammation in a subset of 74 women 9 weeks later, was upheld after adjusting for\n                      <jats:italic>Lactobacillus<\/jats:italic>\n                      relative abundance, and was associated with in vitro inflammatory cytokine responses to\n                      <jats:italic>Lactobacillus<\/jats:italic>\n                      isolates from the same women. Reduced cell wall organization and peptidoglycan biosynthesis were also associated with high FGT inflammation in an independent sample of ten women.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      Both the presence of specific microbial taxa in the FGT and their properties and activities are critical determinants of FGT inflammation. Our findings support those of previous studies suggesting that peptidoglycan is directly immunosuppressive, and identify a possible avenue for biotherapeutic development to reduce inflammation in the FGT. To facilitate further investigations of microbial activities, we have developed the FGT-DB application that is available at\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/fgtdb.org\/\">http:\/\/fgtdb.org\/<\/jats:ext-link>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s40168-020-00932-8","type":"journal-article","created":{"date-parts":[[2020,11,21]],"date-time":"2020-11-21T07:02:54Z","timestamp":1605942174000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":37,"title":["Microbial function and genital inflammation in young South African women at high risk of HIV infection"],"prefix":"10.1186","volume":"8","author":[{"given":"Arghavan","family":"Alisoltani","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Monalisa T.","family":"Manhanzva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthys","family":"Potgieter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christina","family":"Balle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liam","family":"Bell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth","family":"Ross","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arash","family":"Iranzadeh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle","family":"du Plessis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nina","family":"Radzey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zac","family":"McDonald","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bridget","family":"Calder","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Imane","family":"Allali","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicola","family":"Mulder","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Smritee","family":"Dabee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaun","family":"Barnabas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hoyam","family":"Gamieldien","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam","family":"Godzik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan M.","family":"Blackburn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David L.","family":"Tabb","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linda-Gail","family":"Bekker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heather B.","family":"Jaspan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jo-Ann S.","family":"Passmore","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2539-817X","authenticated-orcid":false,"given":"Lindi","family":"Masson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,11,21]]},"reference":[{"key":"932_CR1","unstructured":"UNAIDS Data 2019. Available at: https:\/\/www.unaids.org\/sites\/default\/files\/media_asset\/2019-UNAIDS-data_en.pdf. Accessed 20\/02\/20."},{"key":"932_CR2","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1093\/cid\/civ298","volume":"61","author":"L Masson","year":"2015","unstructured":"Masson L, Passmore JAS, Liebenberg LJ, Werner L, Baxter C, Arnold KB, et al. Genital inflammation and the risk of HIV acquisition in women. Clin Infect Dis. 2015;61:260\u20139.","journal-title":"Clin Infect Dis"},{"key":"932_CR3","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1038\/nm.4506","volume":"24","author":"LR McKinnon","year":"2018","unstructured":"McKinnon LR, Liebenberg LJ, Yende-Zuma N, Archary D, Ngcapu S, Sivro A, et al. Genital inflammation undermines the effectiveness of tenofovir gel in preventing HIV acquisition in women. Nat Med. 2018;24:491.","journal-title":"Nat Med"},{"key":"932_CR4","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1097\/QAI.0000000000000103","volume":"66","author":"C Morrison","year":"2014","unstructured":"Morrison C, Fichorova RN, Mauck C, Chen PL, Kwok C, Chipato T, et al. Cervical inflammation and immunity associated with hormonal contraception, pregnancy, and HIV-1 seroconversion. J Acquir Immune Defic Syndr. 2014;66:109\u201317.","journal-title":"J Acquir Immune Defic Syndr"},{"key":"932_CR5","doi-asserted-by":"publisher","first-page":"1034","DOI":"10.1038\/nature07831","volume":"458","author":"Q Li","year":"2009","unstructured":"Li Q, Estes JD, Schlievert PM, Duan L, Brosnahan AJ, Southern PJ, et al. Glycerol monolaurate prevents mucosal SIV transmission. Nature. 2009;458:1034\u20138.","journal-title":"Nature."},{"key":"932_CR6","doi-asserted-by":"publisher","first-page":"2336","DOI":"10.1073\/pnas.86.7.2336","volume":"86","author":"L Osborn","year":"1989","unstructured":"Osborn L, Kunkel S, Nabel GJ. Tumor necrosis factor \u03b1 and interleukin 1 stimulate the human immunodeficiency virus enhancer by activation of the nuclear factor \u03baB. Proc Natl Acad Sci U S A. 1989;86:2336\u201340.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"932_CR7","doi-asserted-by":"publisher","first-page":"194","DOI":"10.1038\/mi.2015.51","volume":"9","author":"KB Arnold","year":"2016","unstructured":"Arnold KB, Burgener A, Birse K, Romas L, Dunphy LJ, Shahabi K, et al. Increased levels of inflammatory cytokines in the female reproductive tract are associated with altered expression of proteases, mucosal barrier proteins, and an influx of HIV-susceptible target cells. Mucosal Immunol. 2016;9:194\u2013205.","journal-title":"Mucosal Immunol"},{"key":"932_CR8","doi-asserted-by":"publisher","first-page":"5139","DOI":"10.1021\/pr200596r","volume":"11","author":"A Burgener","year":"2011","unstructured":"Burgener A, Rahman S, Ahmad R, Lajoie J, Ramdahin S, Mesa C, et al. Comprehensive proteomic study identifies serpin and cystatin antiproteases as novel correlates of HIV-1 resistance in the cervicovaginal mucosa of female Sex workers. J Proteome Res. 2011;11:5139\u201349.","journal-title":"J Proteome Res"},{"key":"932_CR9","doi-asserted-by":"publisher","first-page":"580","DOI":"10.1136\/sextrans-2014-051601","volume":"90","author":"L Masson","year":"2014","unstructured":"Masson L, Mlisana K, Little F, Werner L, Mkhize NN, Ronacher K, et al. Defining genital tract cytokine signatures of sexually transmitted infections and bacterial vaginosis in women at high risk of HIV infection: a cross-sectional study. Sex Transm Infect. 2014;90:580\u20137.","journal-title":"Sex Transm Infect"},{"key":"932_CR10","doi-asserted-by":"publisher","first-page":"e00410","DOI":"10.1128\/IAI.00410-17","volume":"86","author":"K Lennard","year":"2018","unstructured":"Lennard K, Dabee S, Barnabas SL, Havyarimana E, Blakney A, Jaumdally SZ, et al. Microbial composition predicts genital tract inflammation and persistent bacterial vaginosis in South African adolescent females. Infect Immun. 2018;86:e00410\u20137.","journal-title":"Infect Immun"},{"key":"932_CR11","doi-asserted-by":"publisher","first-page":"965","DOI":"10.1016\/j.immuni.2015.04.019","volume":"42","author":"MN Anahtar","year":"2015","unstructured":"Anahtar MN, Byrne EH, Doherty KE, Bowman BA, Yamamoto HS, Soumillon M, et al. Cervicovaginal bacteria are a major modulator of host inflammatory responses in the female genital tract. Immunity. 2015;42:965\u201376.","journal-title":"Immunity."},{"key":"932_CR12","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1111\/aji.12415","volume":"74","author":"J Deese","year":"2015","unstructured":"Deese J, Masson L, Miller W, Cohen M, Morrison C, Wang M, et al. Injectable progestin-only contraception is associated with increased levels of pro-inflammatory cytokines in the female genital tract. Am J Reprod Immunol. 2015;74:357\u201367.","journal-title":"Am J Reprod Immunol"},{"key":"932_CR13","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1016\/j.immuni.2016.12.013","volume":"46","author":"C Gosmann","year":"2017","unstructured":"Gosmann C, Anahtar MN, Handley SA, Farcasanu M, Abu-Ali G, Bowman BA, et al. Lactobacillus-deficient cervicovaginal bacterial communities are associated with increased HIV acquisition in young South African women. Immunity. 2017;46:29\u201337.","journal-title":"Immunity."},{"key":"932_CR14","doi-asserted-by":"publisher","first-page":"S9","DOI":"10.1186\/1475-2859-13-S1-S9","volume":"13","author":"MP Chapot-Chartier","year":"2014","unstructured":"Chapot-Chartier MP, Kulakauskas S. Cell wall structure and function in lactic acid bacteria. Microb Cell Factories. 2014;13:S9.","journal-title":"Microb Cell Factories"},{"key":"932_CR15","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-018-38253-4","volume":"9","author":"E Chetwin","year":"2019","unstructured":"Chetwin E, Manhanzva MT, Abrahams AG, Froissart R, Gamieldien H, Jaspan H, et al. Antimicrobial and inflammatory properties of South African clinical Lactobacillus isolates and vaginal probiotics. Sci Rep. 2019;9:1\u201315.","journal-title":"Sci Rep"},{"key":"932_CR16","doi-asserted-by":"publisher","first-page":"1480","DOI":"10.1038\/mi.2017.27","volume":"10","author":"AC Hearps","year":"2017","unstructured":"Hearps AC, Tyssen D, Srbinovski D, Bayigga L, Diaz DJD, Aldunate M, et al. Vaginal lactic acid elicits an anti-inflammatory response from human cervicovaginal epithelial cells and inhibits production of pro-inflammatory mediators associated with HIV acquisition. Mucosal Immunol. 2017;10:1480\u201390.","journal-title":"Mucosal Immunol"},{"issue":"3","key":"932_CR17","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1089\/aid.2018.0304","volume":"35","author":"LR McKinnon","year":"2019","unstructured":"McKinnon LR, Achilles SL, Bradshaw CS, Burgener A, Crucitti T, Fredricks DN, et al. The evolving facets of bacterial vaginosis: implications for HIV transmission. AIDS Res Hum Retrovir. 2019;35(3):219\u201328.","journal-title":"AIDS Res Hum Retrovir"},{"key":"932_CR18","first-page":"219","volume":"35","author":"J Ravel","year":"2011","unstructured":"Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SSK, McCulle SL, et al. Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci U S A. 2011;35:219\u201328.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"932_CR19","doi-asserted-by":"publisher","first-page":"3424","DOI":"10.1002\/pmic.201400571","volume":"15","author":"W Xiong","year":"2015","unstructured":"Xiong W, Abraham PE, Li Z, Pan C, Hettich RL. Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota. Proteomics. 2015;15:3424\u201338.","journal-title":"Proteomics."},{"key":"932_CR20","doi-asserted-by":"publisher","first-page":"938","DOI":"10.1126\/science.aai9383","volume":"356","author":"NR Klatt","year":"2017","unstructured":"Klatt NR, Cheu R, Birse K, Zevin AS, Perner M, No\u00ebl-Romas L, et al. Vaginal bacteria modify HIV tenofovir microbicide efficacy in African women. Science. 2017;356:938\u201345.","journal-title":"Science."},{"key":"932_CR21","doi-asserted-by":"publisher","first-page":"e1005889","DOI":"10.1371\/journal.ppat.1005889","volume":"12","author":"AS Zevin","year":"2016","unstructured":"Zevin AS, Xie IY, Birse K, Arnold K, Romas L, Westmacott G, et al. Microbiome composition and function drives wound-healing impairment in the female genital tract. PLoS Pathog. 2016;12:e1005889.","journal-title":"PLoS Pathog"},{"key":"932_CR22","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1177\/0956462417740487","volume":"29","author":"SL Barnabas","year":"2018","unstructured":"Barnabas SL, Dabee S, Passmore JAS, Jaspan HB, Lewis DA, Jaumdally SZ, et al. Converging epidemics of sexually transmitted infections and bacterial vaginosis in southern African female adolescents at risk of HIV. Int J STD AIDS. 2018;29:531\u20139.","journal-title":"Int J STD AIDS"},{"key":"932_CR23","doi-asserted-by":"publisher","first-page":"e0213975","DOI":"10.1371\/journal.pone.0213975","volume":"14","author":"S Dabee","year":"2019","unstructured":"Dabee S, Barnabas SL, Lennard KS, Jaumdally SZ, Gamieldien H, Balle C, et al. Defining characteristics of genital health in South African adolescent girls and young women at high risk for HIV infection. PLoS One. 2019;14:e0213975.","journal-title":"PLoS One"},{"key":"932_CR24","doi-asserted-by":"publisher","first-page":"1050","DOI":"10.1136\/gut.2010.232918","volume":"60","author":"EM Fernandez","year":"2011","unstructured":"Fernandez EM, Valenti V, Rockel C, Hermann C, Pot B, Boneca IG, et al. Anti-inflammatory capacity of selected lactobacilli in experimental colitis is driven by NOD2-mediated recognition of a specific peptidoglycan-derived muropeptide. Gut. 2011;60:1050\u20139.","journal-title":"Gut."},{"key":"932_CR25","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-020-62184-8","volume":"10","author":"MT Manhanzva","year":"2020","unstructured":"Manhanzva MT, Abrahams AG, Gamieldien H, Froissart R, Jaspan H, Jaumdally SZ, et al. Inflammatory and antimicrobial properties differ between vaginal Lactobacillus isolates from South African women with non-optimal versus optimal microbiota. Sci Rep. 2020;10:1\u201313.","journal-title":"Sci Rep"},{"key":"932_CR26","doi-asserted-by":"publisher","first-page":"280","DOI":"10.4161\/gmic.2.5.18255","volume":"2","author":"E Macho Fernandez","year":"2011","unstructured":"Macho Fernandez E, Pot B, Grangette C. Beneficial effect of probiotics in IBD: are peptidogycan and NOD2 the molecular key effectors? Gut Microbes. 2011;2:280\u20136.","journal-title":"Gut Microbes"},{"key":"932_CR27","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-018-29320-x","volume":"8","author":"C Balle","year":"2018","unstructured":"Balle C, Lennard K, Dabee S, Barnabas SL, Jaumdally SZ, Gasper MA, et al. Endocervical and vaginal microbiota in South African adolescents with asymptomatic Chlamydia trachomatis infection. Sci Rep. 2018;8:1\u20139.","journal-title":"Sci Rep"},{"key":"932_CR28","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1038\/s41579-018-0041-0","volume":"16","author":"JC Lagier","year":"2018","unstructured":"Lagier JC, Dubourg G, Million M, Cadoret F, Bilen M, Fenollar F, et al. Culturing the human microbiota and culturomics. Nat Rev Microbiol. 2018;16:540\u201350.","journal-title":"Nat Rev Microbiol"},{"key":"932_CR29","doi-asserted-by":"crossref","unstructured":"Holm JB, France MT, Ma B, McComb E, Robinson CK, Mehta A, et al. Comparative Metagenome-Assembled Genome Analysis of \u201cCandidatus Lachnocurva vaginae\u201d, Formerly Known as Bacterial Vaginosis-Associated Bacterium\u2212 1 (BVAB1). Front Cellular Infect Microbiol. 2020;10:117.","DOI":"10.3389\/fcimb.2020.00117"},{"key":"932_CR30","doi-asserted-by":"crossref","unstructured":"Huffnagle GB, Noverr MC. The emerging world of the fungal microbiome. Trends Microbiol. 2013;21:334-41.","DOI":"10.1016\/j.tim.2013.04.002"},{"key":"932_CR31","doi-asserted-by":"crossref","unstructured":"Bianco L, Perrotta G. Methodologies and perspectives of proteomics applied to filamentous fungi: From sample preparation to secretome analysis. Int J Mol Sci. 2015;6:5803-29.","DOI":"10.3390\/ijms16035803"},{"key":"932_CR32","doi-asserted-by":"publisher","first-page":"116","DOI":"10.1186\/1471-2180-9-116","volume":"9","author":"H Verstraelen","year":"2009","unstructured":"Verstraelen H, Verhelst R, Claeys G, De Backer E, Temmerman M, Vaneechoutte M. Longitudinal analysis of the vaginal microflora in pregnancy suggests that L. crispatus promotes the stability of the normal vaginal microflora and that L. gasseri and\/or L. iners are more conducive to the occurrence of abnormal vaginal microflora. BMC Microbiol. 2009;9:116.","journal-title":"BMC Microbiol"},{"issue":"2","key":"932_CR33","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1136\/sextrans-2017-053133","volume":"94","author":"R van Houdt","year":"2018","unstructured":"van Houdt R, Ma B, Bruisten SM, Ravel AGCLSJ, de Vries HJC. Lactobacillus iners-dominated vaginal microbiota is associated with increased susceptibility to Chlamydia trachomatis infection in Dutch women: a case\u2013control study. Sex Transm Infect. 2018;94(2):117\u201323.","journal-title":"Sex Transm Infect"},{"key":"932_CR34","doi-asserted-by":"publisher","unstructured":"Potgieter MG, Nel AJM, Tabb DL, Fortuin S, Garnett S, Blackburn JM, et al. MetaNovo: a probabilistic approach to peptide and polymorphism discovery in complex mass spectrometry datasets. bioRxiv. 2019:605550. https:\/\/doi.org\/10.1101\/605550.","DOI":"10.1101\/605550"},{"key":"932_CR35","doi-asserted-by":"publisher","first-page":"10868","DOI":"10.1038\/s41598-018-29092-4","volume":"8","author":"S Afiuni-Zadeh","year":"2018","unstructured":"Afiuni-Zadeh S, Boylan KLM, Jagtap PD, Griffin TJ, Rudney JD, Peterson ML, et al. Evaluating the potential of residual Pap test fluid as a resource for the metaproteomic analysis of the cervical-vaginal microbiome. Sci Rep. 2018;8:10868.","journal-title":"Sci Rep"},{"key":"932_CR36","volume-title":"limma: linear models for microarray data. Bioinforma Comput Biol Solut Using R Bioconductor","author":"GK Smyth","year":"2005","unstructured":"Smyth GK. limma: linear models for microarray data. Bioinforma Comput Biol Solut Using R Bioconductor; 2005."},{"key":"932_CR37","doi-asserted-by":"publisher","first-page":"e1005752","DOI":"10.1371\/journal.pcbi.1005752","volume":"13","author":"F Rohart","year":"2017","unstructured":"Rohart F, Gautier B, Singh A, L\u00ea Cao KA. mixOmics: an R package for \u2018omics feature selection and multiple data integration. PLoS Comput Biol. 2017;13:e1005752.","journal-title":"PLoS Comput Biol"},{"key":"932_CR38","doi-asserted-by":"publisher","first-page":"2847","DOI":"10.1093\/bioinformatics\/btw313","volume":"32","author":"Z Gu","year":"2016","unstructured":"Gu Z, Eils R, Schlesner M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics. 2016;32:2847\u20139.","journal-title":"Bioinformatics."},{"key":"932_CR39","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1186\/1471-2105-9-559","volume":"9","author":"P Langfelder","year":"2008","unstructured":"Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9:559.","journal-title":"BMC Bioinformatics"},{"key":"932_CR40","first-page":"18","volume":"2","author":"A Liaw","year":"2002","unstructured":"Liaw A, Wiener M. Classification and regression by randomForest. R News. 2002;2:18\u201322.","journal-title":"R News"},{"key":"932_CR41","doi-asserted-by":"publisher","first-page":"e01283","DOI":"10.1128\/mBio.01283-14","volume":"5","author":"MM Pearce","year":"2014","unstructured":"Pearce MM, Hilt EE, Rosenfeld AB, Zilliox MJ, Thomas-White K, Fok C, et al. The female urinary microbiome: a comparison of women with and without urgency urinary incontinence. MBio. 2014;5:e01283\u201314.","journal-title":"MBio."},{"key":"932_CR42","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","volume":"13","author":"BJ Callahan","year":"2016","unstructured":"Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581.","journal-title":"Nat Methods"},{"key":"932_CR43","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12864-019-6419-1","volume":"21","author":"NR Narayan","year":"2020","unstructured":"Narayan NR, Weinmaier T, Laserna-Mendieta EJ, Claesson MJ, Shanahan F, Dabbagh K, et al. Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences. BMC Genomics. 2020;21:1\u201312.","journal-title":"BMC Genomics"}],"updated-by":[{"DOI":"10.1186\/s40168-022-01245-8","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2022,3,9]],"date-time":"2022-03-09T00:00:00Z","timestamp":1646784000000}}],"container-title":["Microbiome"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40168-020-00932-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s40168-020-00932-8\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40168-020-00932-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,9]],"date-time":"2022-03-09T16:02:55Z","timestamp":1646841775000},"score":1,"resource":{"primary":{"URL":"https:\/\/microbiomejournal.biomedcentral.com\/articles\/10.1186\/s40168-020-00932-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,11,21]]},"references-count":43,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2020,12]]}},"alternative-id":["932"],"URL":"https:\/\/doi.org\/10.1186\/s40168-020-00932-8","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.03.10.986646","asserted-by":"object"}]},"ISSN":["2049-2618"],"issn-type":[{"value":"2049-2618","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,11,21]]},"assertion":[{"value":"30 June 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 October 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 November 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 March 2022","order":4,"name":"change_date","label":"Change Date","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Correction","order":5,"name":"change_type","label":"Change Type","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"A Correction to this paper has been published:","order":6,"name":"change_details","label":"Change Details","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"https:\/\/doi.org\/10.1186\/s40168-022-01245-8","URL":"https:\/\/doi.org\/10.1186\/s40168-022-01245-8","order":7,"name":"change_details","label":"Change Details","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The University of Cape Town Faculty of Health Sciences Human Research Ethics Committee (HREC REF: 267\/2013) approved this study. Women \u2265 18\u2009years provided written informed consent, and those < 18\u2009years provided informed assent and informed consent was obtained from parents\/guardians.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"165"}}