{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,30]],"date-time":"2026-10-30T08:01:16Z","timestamp":1793347276540,"version":"4.5.0"},"reference-count":66,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,6,12]],"date-time":"2025-06-12T00:00:00Z","timestamp":1749686400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,6,12]],"date-time":"2025-06-12T00:00:00Z","timestamp":1749686400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["npj Biofilms Microbiomes"],"DOI":"10.1038\/s41522-025-00747-1","type":"journal-article","created":{"date-parts":[[2025,6,12]],"date-time":"2025-06-12T12:56:01Z","timestamp":1749732961000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Metagenomic insight into the vaginal microbiome in women infected with HPV 16 and 18"],"prefix":"10.1038","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-6683-0991","authenticated-orcid":false,"given":"Da-Ryung","family":"Jung","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yeseul","family":"Choi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minsoo","family":"Jeong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vineet","family":"Singh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Se Young","family":"Jeon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Incheol","family":"Seo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nora Jee-Young","family":"Park","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yoon Hee","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ji Young","family":"Park","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hyung Soo","family":"Han","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jae-Ho","family":"Shin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gun Oh","family":"Chong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,6,12]]},"reference":[{"key":"747_CR1","doi-asserted-by":"publisher","first-page":"F12","DOI":"10.1016\/j.vaccine.2012.07.055","volume":"30","author":"D Forman","year":"2012","unstructured":"Forman, D. et al. Global burden of human papillomavirus and related diseases. Vaccine 30, F12\u2013F23 (2012).","journal-title":"Vaccine"},{"key":"747_CR2","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1080\/14760584.2019.1568876","volume":"18","author":"M Lehtinen","year":"2019","unstructured":"Lehtinen, M., Baussano, I., Paavonen, J., V\u00e4nsk\u00e4, S. & Dillner, J. Eradication of human papillomavirus and elimination of HPV-related diseases\u2013scientific basis for global public health policies. Expert Rev. Vaccines 18, 153\u2013160 (2019).","journal-title":"Expert Rev. Vaccines"},{"key":"747_CR3","doi-asserted-by":"publisher","first-page":"791","DOI":"10.21037\/tau.2017.06.27","volume":"6","author":"LC Kidd","year":"2017","unstructured":"Kidd, L. C. et al. Relationship between human papillomavirus and penile cancer\u2014implications for prevention and treatment. Transl. Androl. Urol. 6, 791 (2017).","journal-title":"Transl. Androl. Urol."},{"key":"747_CR4","doi-asserted-by":"publisher","first-page":"e1008376","DOI":"10.1371\/journal.ppat.1008376","volume":"16","author":"M Usyk","year":"2020","unstructured":"Usyk, M. et al. Cervicovaginal microbiome and natural history of HPV in a longitudinal study. PLoS Pathog. 16, e1008376 (2020).","journal-title":"PLoS Pathog."},{"key":"747_CR5","doi-asserted-by":"publisher","first-page":"H1","DOI":"10.1016\/j.vaccine.2013.10.003","volume":"31","author":"FX Bosch","year":"2013","unstructured":"Bosch, F. X. et al. Comprehensive control of human papillomavirus infections and related diseases. Vaccine 31, H1\u2013H31 (2013).","journal-title":"Vaccine"},{"key":"747_CR6","doi-asserted-by":"publisher","first-page":"1048","DOI":"10.1016\/S1470-2045(10)70230-8","volume":"11","author":"S de Sanjose","year":"2010","unstructured":"de Sanjose, S. et al. Human papillomavirus genotype attribution in invasive cervical cancer: a retrospective cross-sectional worldwide study. Lancet Oncol. 11, 1048\u20131056 (2010).","journal-title":"Lancet Oncol."},{"key":"747_CR7","doi-asserted-by":"publisher","first-page":"417","DOI":"10.31557\/APJCP.2019.20.2.417","volume":"20","author":"H Aydo\u011fmu\u015f","year":"2019","unstructured":"Aydo\u011fmu\u015f, H. & Aydo\u011fmu\u015f, S. Comparison of colposcopic biopsy results of patients who have cytomorphological normal but HPV 16-18 or other high-risk HPV subtypes positive. Asian Pac. J. Cancer Prev. 20, 417 (2019).","journal-title":"Asian Pac. J. Cancer Prev."},{"key":"747_CR8","doi-asserted-by":"publisher","first-page":"1310","DOI":"10.1038\/mi.2016.129","volume":"10","author":"B Shannon","year":"2017","unstructured":"Shannon, B. et al. Association of HPV infection and clearance with cervicovaginal immunology and the vaginal microbiota. Mucosal Immunol. 10, 1310\u20131319 (2017).","journal-title":"Mucosal Immunol."},{"key":"747_CR9","doi-asserted-by":"publisher","first-page":"40135","DOI":"10.18632\/oncotarget.9510","volume":"7","author":"J Zou","year":"2016","unstructured":"Zou, J. et al. Variants in human papillomavirus receptor and associated genes are associated with type-specific HPV infection and lesion progression of the cervix. Oncotarget 7, 40135 (2016).","journal-title":"Oncotarget"},{"key":"747_CR10","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s40168-020-00934-6","volume":"8","author":"MT France","year":"2020","unstructured":"France, M. T. et al. VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition. Microbiome 8, 1\u201315 (2020).","journal-title":"Microbiome"},{"key":"747_CR11","doi-asserted-by":"publisher","first-page":"132ra152","DOI":"10.1126\/scitranslmed.3003605","volume":"4","author":"P Gajer","year":"2012","unstructured":"Gajer, P. et al. Temporal dynamics of the human vaginal microbiota. Sci. Transl. Med. 4, 132ra152\u2013132ra152 (2012).","journal-title":"Sci. Transl. Med."},{"key":"747_CR12","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1016\/j.chom.2018.01.013","volume":"23","author":"MN Anahtar","year":"2018","unstructured":"Anahtar, M. N., Gootenberg, D. B., Mitchell, C. M. & Kwon, D. S. Cervicovaginal microbiota and reproductive health: the virtue of simplicity. Cell Host Microbe 23, 159\u2013168 (2018).","journal-title":"Cell Host Microbe"},{"key":"747_CR13","doi-asserted-by":"publisher","first-page":"e0215945","DOI":"10.1371\/journal.pone.0215945","volume":"14","author":"EM Bik","year":"2019","unstructured":"Bik, E. M. et al. A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis. PLoS ONE 14, e0215945 (2019).","journal-title":"PLoS ONE"},{"key":"747_CR14","doi-asserted-by":"publisher","first-page":"540900","DOI":"10.3389\/fcimb.2020.540900","volume":"10","author":"E Caselli","year":"2020","unstructured":"Caselli, E. et al. Vaginal microbiota and cytokine microenvironment in HPV clearance\/persistence in women surgically treated for cervical intraepithelial neoplasia: an observational prospective study. Front. cell. infect. microbiol. 10, 540900 (2020).","journal-title":"Front. cell. infect. microbiol."},{"key":"747_CR15","doi-asserted-by":"crossref","unstructured":"Molina, M. A., Leenders, W. P., Huynen, M. A., Melchers, W. J. & Andralojc, K. M. Temporal composition of the cervicovaginal microbiome associates with hrHPV infection outcomes in a longitudinal study. bioRxiv, 2023.2006. 2002.543506 (2023).","DOI":"10.1101\/2023.06.02.543506"},{"key":"747_CR16","doi-asserted-by":"publisher","first-page":"1292230","DOI":"10.3389\/fmicb.2023.1292230","volume":"14","author":"E Sofou","year":"2023","unstructured":"Sofou, E. et al. High risk HPV-positive women cervicovaginal microbial profiles in a Greek cohort: a retrospective analysis of the GRECOSELF study. Front. microbiol. 14, 1292230 (2023).","journal-title":"Front. microbiol."},{"key":"747_CR17","first-page":"e00357","volume":"8","author":"D Vargas-Robles","year":"2023","unstructured":"Vargas-Robles, D. et al. The cervical microbiota of Hispanics living in Puerto Rico is nonoptimal regardless of HPV status. mSystems 8, e00357\u201300323 (2023).","journal-title":"mSystems"},{"key":"747_CR18","doi-asserted-by":"publisher","first-page":"14716","DOI":"10.3390\/ijerph192214716","volume":"19","author":"T Sasivimolrattana","year":"2022","unstructured":"Sasivimolrattana, T. et al. Cervical microbiome in women infected with HPV16 and high-risk HPVs. Int. J. Environ. Res. Public Health 19, 14716 (2022).","journal-title":"Int. J. Environ. Res. Public Health"},{"key":"747_CR19","doi-asserted-by":"crossref","unstructured":"Huang, L. et al. A multi-kingdom collection of 33,804 reference genomes for the human vaginal microbiome. Nat. Microbiol., 1\u201316 (2024).","DOI":"10.1038\/s41564-024-01751-5"},{"key":"747_CR20","doi-asserted-by":"publisher","first-page":"725","DOI":"10.1038\/nbt.3893","volume":"35","author":"RM Bowers","year":"2017","unstructured":"Bowers, R. M. et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat. Biotechnol. 35, 725\u2013731 (2017).","journal-title":"Nat. Biotechnol."},{"key":"747_CR21","doi-asserted-by":"publisher","first-page":"e63514","DOI":"10.1371\/journal.pone.0063514","volume":"8","author":"JE Lee","year":"2013","unstructured":"Lee, J. E. et al. Association of the vaginal microbiota with human papillomavirus infection in a Korean twin cohort. PLoS ONE 8, e63514 (2013).","journal-title":"PLoS ONE"},{"key":"747_CR22","doi-asserted-by":"publisher","DOI":"10.1038\/srep16865","volume":"5","author":"A Mitra","year":"2015","unstructured":"Mitra, A. et al. Cervical intraepithelial neoplasia disease progression is associated with increased vaginal microbiome diversity. Sci. Rep. 5, 16865 (2015).","journal-title":"Sci. Rep."},{"key":"747_CR23","doi-asserted-by":"publisher","DOI":"10.1038\/s41522-020-00146-8","volume":"6","author":"L Cheng","year":"2020","unstructured":"Cheng, L. et al. Vaginal microbiota and human papillomavirus infection among young Swedish women. NPJ Biofilms Microbiomes 6, 39 (2020).","journal-title":"NPJ Biofilms Microbiomes"},{"key":"747_CR24","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-28724-8","volume":"13","author":"A Lebeau","year":"2022","unstructured":"Lebeau, A. et al. HPV infection alters vaginal microbiome through down-regulating host mucosal innate peptides used by Lactobacilli as amino acid sources. Nat. Commun. 13, 1076 (2022).","journal-title":"Nat. Commun."},{"key":"747_CR25","doi-asserted-by":"publisher","first-page":"851670","DOI":"10.3389\/fmicb.2022.851670","volume":"13","author":"MJ Kim","year":"2022","unstructured":"Kim, M. J., Lee, S., Kwon, M. Y. & Kim, M. Clinical significance of composition and functional diversity of the vaginal microbiome in recurrent vaginitis. Front. microbiol. 13, 851670 (2022).","journal-title":"Front. microbiol."},{"key":"747_CR26","doi-asserted-by":"publisher","first-page":"1013","DOI":"10.3390\/diagnostics10121013","volume":"10","author":"YH Lee","year":"2020","unstructured":"Lee, Y. H. et al. Vaginal microbiome-based bacterial signatures for predicting the severity of cervical intraepithelial neoplasia. Diagnostics 10, 1013 (2020).","journal-title":"Diagnostics"},{"key":"747_CR27","doi-asserted-by":"publisher","first-page":"1723","DOI":"10.1093\/infdis\/jiu330","volume":"210","author":"RM Brotman","year":"2014","unstructured":"Brotman, R. M. et al. Interplay between the temporal dynamics of the vaginal microbiota and human papillomavirus detection. J. Infect. Dis. 210, 1723\u20131733 (2014).","journal-title":"J. Infect. Dis."},{"key":"747_CR28","doi-asserted-by":"publisher","unstructured":"Mitra, A. et al. The vaginal microbiota associates with the regression of untreated cervical intraepithelial neoplasia 2 lesions. Nat. Commun. 11, 1999 https:\/\/doi.org\/10.1038\/s41467-020-15856-y (2020).","DOI":"10.1038\/s41467-020-15856-y"},{"key":"747_CR29","doi-asserted-by":"publisher","first-page":"649067","DOI":"10.3389\/fcimb.2021.649067","volume":"11","author":"N Sun","year":"2021","unstructured":"Sun, N. et al. Comprehensive characterization of microbial community in the female genital tract of reproductive-aged women in china. Front. cell. infect. microbiol. 11, 649067 (2021).","journal-title":"Front. cell. infect. microbiol."},{"key":"747_CR30","doi-asserted-by":"publisher","first-page":"e0153274","DOI":"10.1371\/journal.pone.0153274","volume":"11","author":"A Audirac-Chalifour","year":"2016","unstructured":"Audirac-Chalifour, A. et al. Cervical microbiome and cytokine profile at various stages of cervical cancer: a pilot study. PLoS ONE 11, e0153274 (2016).","journal-title":"PLoS ONE"},{"key":"747_CR31","doi-asserted-by":"publisher","first-page":"D499","DOI":"10.1093\/nar\/gkw879","volume":"45","author":"K Van Doorslaer","year":"2017","unstructured":"Van Doorslaer, K. et al. The Papillomavirus Episteme: a major update to the papillomavirus sequence database. Nucleic Acids Res. 45, D499\u2013D506 (2017).","journal-title":"Nucleic Acids Res."},{"key":"747_CR32","doi-asserted-by":"publisher","first-page":"1850","DOI":"10.1099\/vir.0.051722-0","volume":"94","author":"A Trevisan","year":"2013","unstructured":"Trevisan, A. et al. Human papillomavirus type 16 viral load measurement as a predictor of infection clearance. J. Gen. Virol. 94, 1850\u20131857 (2013).","journal-title":"J. Gen. Virol."},{"key":"747_CR33","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12985-020-01474-z","volume":"18","author":"X Lu","year":"2021","unstructured":"Lu, X., Wang, T., Zhang, Y. & Liu, Y. Analysis of influencing factors of viral load in patients with high-risk human papillomavirus. Virol. J. 18, 1\u20138 (2021).","journal-title":"Virol. J."},{"key":"747_CR34","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-024-61942-2","volume":"14","author":"J Norenhag","year":"2024","unstructured":"Norenhag, J. et al. Compositional and functional differences of the vaginal microbiota of women with and without cervical dysplasia. Sci. Rep. 14, 11183 (2024).","journal-title":"Sci. Rep."},{"key":"747_CR35","doi-asserted-by":"publisher","first-page":"2398","DOI":"10.3390\/microorganisms10122398","volume":"10","author":"Y Choi","year":"2022","unstructured":"Choi, Y. et al. Updates on Group B Streptococcus infection in the field of obstetrics and gynecology. Microorganisms 10, 2398 (2022).","journal-title":"Microorganisms"},{"key":"747_CR36","doi-asserted-by":"publisher","DOI":"10.3389\/fpubh.2020.587298","volume":"8","author":"Z-T Wei","year":"2021","unstructured":"Wei, Z.-T. et al. Depiction of vaginal microbiota in women with high-risk human papillomavirus infection. Front. Public Health 8, 587298 (2021).","journal-title":"Front. Public Health"},{"key":"747_CR37","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-14677-3","volume":"11","author":"B Ma","year":"2020","unstructured":"Ma, B. et al. A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina. Nat. Commun. 11, 940 (2020).","journal-title":"Nat. Commun."},{"key":"747_CR38","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1007\/978-94-007-6621-1_14","volume":"786","author":"RR Stine","year":"2013","unstructured":"Stine, R. R. & Matunis, E. L. JAK-STAT signaling in stem cells. Adv. Exp. Med. Biol. 786, 247\u2013267 (2013).","journal-title":"Adv. Exp. Med. Biol."},{"key":"747_CR39","doi-asserted-by":"publisher","first-page":"2297","DOI":"10.3390\/cells9102297","volume":"9","author":"A Guti\u00e9rrez-Hoya","year":"2020","unstructured":"Guti\u00e9rrez-Hoya, A. & Soto-Cruz, I. Role of the JAK\/STAT pathway in cervical cancer: its relationship with HPV E6\/E7 oncoproteins. Cells 9, 2297 (2020).","journal-title":"Cells"},{"key":"747_CR40","doi-asserted-by":"publisher","first-page":"e1002256","DOI":"10.1371\/journal.ppat.1002256","volume":"7","author":"Y Ben Khalifa","year":"2011","unstructured":"Ben Khalifa, Y. et al. The human papillomavirus E6 oncogene represses a cell adhesion pathway and disrupts focal adhesion through degradation of TAp63\u03b2 upon transformation. PLoS Pathog. 7, e1002256 (2011).","journal-title":"PLoS Pathog."},{"key":"747_CR41","doi-asserted-by":"crossref","first-page":"309","DOI":"10.3892\/ijo_00000449","volume":"35","author":"H Yuan","year":"2009","unstructured":"Yuan, H. et al. Human papillomavirus type 16 oncoprotein E7 suppresses cadherin-mediated cell adhesion via ERK and AP-1 signaling. Int. J. Oncol. 35, 309\u2013314 (2009).","journal-title":"Int. J. Oncol."},{"key":"747_CR42","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1111\/imm.12972","volume":"155","author":"H Tomlin","year":"2018","unstructured":"Tomlin, H. & Piccinini, A. M. A complex interplay between the extracellular matrix and the innate immune response to microbial pathogens. Immunology 155, 186\u2013201 (2018).","journal-title":"Immunology"},{"key":"747_CR43","doi-asserted-by":"publisher","first-page":"2590","DOI":"10.1016\/j.jmb.2018.06.024","volume":"430","author":"MS Maginnis","year":"2018","unstructured":"Maginnis, M. S. Virus\u2013receptor interactions: the key to cellular invasion. J. Mol. Biol. 430, 2590\u20132611 (2018).","journal-title":"J. Mol. Biol."},{"key":"747_CR44","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1210\/jcem-11-1-103","volume":"11","author":"WB Ayre","year":"1951","unstructured":"Ayre, W. B. The glycogen-estrogen relationship in the vaginal tract. J. Clin. Endocr. 11, 103\u2013110 (1951).","journal-title":"J. Clin. Endocr."},{"key":"747_CR45","doi-asserted-by":"publisher","first-page":"1641","DOI":"10.1038\/s41564-023-01447-2","volume":"8","author":"DJ Jenkins","year":"2023","unstructured":"Jenkins, D. J. et al. Bacterial amylases enable glycogen degradation by the vaginal microbiome. Nat. Microbiol. 8, 1641\u20131652 (2023).","journal-title":"Nat. Microbiol."},{"key":"747_CR46","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s40168-019-0667-9","volume":"7","author":"C Van Der Veer","year":"2019","unstructured":"Van Der Veer, C. et al. Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: implications for in vivo dominance of the vaginal microbiota. Microbiome 7, 1\u201314 (2019).","journal-title":"Microbiome"},{"key":"747_CR47","doi-asserted-by":"crossref","unstructured":"Segui Perez, C. et al. Prevotella timonensis degrades the vaginal epithelial glycocalyx through high fucosidase and sialidase activities. bioRxiv, 2024.2001. 2009.574844 (2024).","DOI":"10.1101\/2024.01.09.574844"},{"key":"747_CR48","doi-asserted-by":"publisher","first-page":"676114","DOI":"10.3389\/fcimb.2021.676114","volume":"11","author":"S Vagios","year":"2021","unstructured":"Vagios, S. & Mitchell, C. M. Mutual preservation: a review of interactions between cervicovaginal mucus and microbiota. Front. cell. infect. microbiol. 11, 676114 (2021).","journal-title":"Front. cell. infect. microbiol."},{"key":"747_CR49","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-022-02635-9","volume":"23","author":"MT France","year":"2022","unstructured":"France, M. T. et al. Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data. Genome Biol. 23, 66 (2022).","journal-title":"Genome Biol."},{"key":"747_CR50","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-40719-7","volume":"14","author":"J Liao","year":"2023","unstructured":"Liao, J. et al. Microdiversity of the vaginal microbiome is associated with preterm birth. Nat. Commun. 14, 4997 (2023).","journal-title":"Nat. Commun."},{"key":"747_CR51","doi-asserted-by":"publisher","first-page":"S38","DOI":"10.1111\/j.1753-4887.2012.00493.x","volume":"70","author":"LK Ursell","year":"2012","unstructured":"Ursell, L. K., Metcalf, J. L., Parfrey, L. W. & Knight, R. Defining the human microbiome. Nutr. Rev. 70, S38\u2013S44 (2012).","journal-title":"Nutr. Rev."},{"key":"747_CR52","doi-asserted-by":"publisher","first-page":"2147","DOI":"10.1007\/s00203-020-01931-x","volume":"202","author":"E Dekaboruah","year":"2020","unstructured":"Dekaboruah, E., Suryavanshi, M. V., Chettri, D. & Verma, A. K. Human microbiome: an academic update on human body site specific surveillance and its possible role. Arch. Microbiol. 202, 2147\u20132167 (2020).","journal-title":"Arch. Microbiol."},{"key":"747_CR53","doi-asserted-by":"publisher","first-page":"860589","DOI":"10.3389\/fcimb.2022.860589","volume":"12","author":"B Xiao","year":"2022","unstructured":"Xiao, B., Qin, H., Mi, L. & Zhang, D. Correlation analysis of vaginal microbiome changes and bacterial vaginosis plus vulvovaginal candidiasis mixed vaginitis prognosis. Front. cell. infect. microbiol. 12, 860589 (2022).","journal-title":"Front. cell. infect. microbiol."},{"key":"747_CR54","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/gix120","volume":"7","author":"Y Chen","year":"2018","unstructured":"Chen, Y. et al. SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. GigaScience 7, gix120 (2018).","journal-title":"GigaScience"},{"key":"747_CR55","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357\u2013359 (2012).","journal-title":"Nat. Methods"},{"key":"747_CR56","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-019-1891-0","volume":"20","author":"DE Wood","year":"2019","unstructured":"Wood, D. E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol. 20, 1\u201313 (2019).","journal-title":"Genome Biol."},{"key":"747_CR57","doi-asserted-by":"publisher","DOI":"10.7717\/peerj-cs.104","volume":"3","author":"J Lu","year":"2017","unstructured":"Lu, J., Breitwieser, F. P., Thielen, P. & Salzberg, S. L. Bracken: estimating species abundance in metagenomics data. PeerJ Comput. Sci. 3, e104 (2017).","journal-title":"PeerJ Comput. Sci."},{"key":"747_CR58","doi-asserted-by":"publisher","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","volume":"31","author":"D Li","year":"2015","unstructured":"Li, D., Liu, C.-M., Luo, R., Sadakane, K. & Lam, T.-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674\u20131676 (2015).","journal-title":"Bioinformatics"},{"key":"747_CR59","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-11-119","volume":"11","author":"D Hyatt","year":"2010","unstructured":"Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinf. 11, 1\u201311 (2010).","journal-title":"BMC Bioinf."},{"key":"747_CR60","doi-asserted-by":"publisher","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","volume":"28","author":"L Fu","year":"2012","unstructured":"Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150\u20133152 (2012).","journal-title":"Bioinformatics"},{"key":"747_CR61","doi-asserted-by":"publisher","first-page":"726","DOI":"10.1016\/j.jmb.2015.11.006","volume":"428","author":"M Kanehisa","year":"2016","unstructured":"Kanehisa, M., Sato, Y. & Morishima, K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J. Mol. Biol. 428, 726\u2013731 (2016).","journal-title":"J. Mol. Biol."},{"key":"747_CR62","doi-asserted-by":"publisher","first-page":"W115","DOI":"10.1093\/nar\/gkad328","volume":"51","author":"J Zheng","year":"2023","unstructured":"Zheng, J. et al. dbCAN3: automated carbohydrate-active enzyme and substrate annotation. Nucleic Acids Res. 51, W115\u2013W121 (2023).","journal-title":"Nucleic Acids Res."},{"key":"747_CR63","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s40168-018-0541-1","volume":"6","author":"GV Uritskiy","year":"2018","unstructured":"Uritskiy, G. V., DiRuggiero, J. & Taylor, J. MetaWRAP\u2014a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome 6, 1\u201313 (2018).","journal-title":"Microbiome"},{"key":"747_CR64","doi-asserted-by":"publisher","first-page":"5315","DOI":"10.1093\/bioinformatics\/btac672","volume":"38","author":"P-A Chaumeil","year":"2022","unstructured":"Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics 38, 5315\u20135316 (2022).","journal-title":"Bioinformatics"},{"key":"747_CR65","doi-asserted-by":"publisher","first-page":"W293","DOI":"10.1093\/nar\/gkab301","volume":"49","author":"I Letunic","year":"2021","unstructured":"Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293\u2013W296 (2021).","journal-title":"Nucleic Acids Res."},{"key":"747_CR66","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-07641-9","volume":"9","author":"C Jain","year":"2018","unstructured":"Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T. & Aluru, S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat. Commun. 9, 5114 (2018).","journal-title":"Nat. Commun."}],"container-title":["npj Biofilms and Microbiomes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41522-025-00747-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41522-025-00747-1","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41522-025-00747-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,12]],"date-time":"2025-06-12T20:02:15Z","timestamp":1749758535000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41522-025-00747-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,6,12]]},"references-count":66,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["747"],"URL":"https:\/\/doi.org\/10.1038\/s41522-025-00747-1","relation":{},"ISSN":["2055-5008"],"issn-type":[{"value":"2055-5008","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,6,12]]},"assertion":[{"value":"31 May 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 June 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 June 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"The study was approved by the Institutional Review Board (IRB) of Kyungpook National University Chilgok Hospital (IRB: KNUCH 2023-08-054-001). All participants signed a consent form.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}}],"article-number":"105"}}