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Here, 258 vaginal and 92 paired endocervical samples from women of diverse ethnicities in Fiji were analyzed using metagenomic shotgun sequencing. Using VALENCIA, a sub-community state type (subCST) classifier, 93 (36.04%) vaginal and 38 (41.30%) endocervical microbiomes did not match reference subCSTs. We, therefore, designed four unique subCSTs, IV-D0, IV-D1, IV-D2, and IV-E\u2014differentially dominated by\n            <jats:italic>Gardnerella vaginalis<\/jats:italic>\n            ,\n            <jats:italic>Prevotella<\/jats:italic>\n            spp., and\n            <jats:italic>Lactobacillus iners<\/jats:italic>\n            \u2014to improve microbiome classifications.\n            <jats:italic>Ct<\/jats:italic>\n            -infected paired endocervical and vaginal microbiomes were significantly more likely to have differential species relative abundance (81.58%) than uninfected pairs (35.84%; adjusted odds ratio, 7.93; 95% confidence interval, 2.93\u201321.93;\n            <jats:italic>P<\/jats:italic>\n            &lt; 0.0001). Among paired microbiomes, the endocervix had a significantly higher alpha diversity and independently a higher alpha diversity for high-risk human papilloma virus (HPV) types compared to low-risk and no HPV. The\n            <jats:italic>Ct-<\/jats:italic>\n            infected endocervical network compared to all others had smaller clusters\u2014indicating lower species abundance and decreased weight of interactions among bacterial groups within clusters\u2014and no interactions with potentially beneficial\n            <jats:italic>Lactobacillus<\/jats:italic>\n            spp. These data suggest a distinct influence on this network from\n            <jats:italic>Ct<\/jats:italic>\n            -infected endocervical cells. Furthermore, the high relative abundance of\n            <jats:italic>G. vaginalis<\/jats:italic>\n            and\n            <jats:italic>Prevotella<\/jats:italic>\n            spp. may generate polymicrobial biofilms that predispose to and\/or promote\n            <jats:italic>Ct<\/jats:italic>\n            and possibly HPV persistence and pathogenicity. While these data expand on the existing repertoire of endocervical and vaginal microbiomes and fill in knowledge gaps regarding PIs, prospective studies are needed to define causal associations to develop successful interventions.\n          <\/jats:p>\n          <jats:sec>\n            <jats:title>IMPORTANCE<\/jats:title>\n            <jats:p>\n              <jats:italic>Chlamydia trachomatis<\/jats:italic>\n              (\n              <jats:italic>Ct<\/jats:italic>\n              ) is the most common sexually transmitted bacterium globally. Endocervical and vaginal microbiome interactions are rarely examined within the context of\n              <jats:italic>Ct<\/jats:italic>\n              or among vulnerable populations. We evaluated 258 vaginal and 92 paired endocervical samples from Fijian women using metagenomic shotgun sequencing. Over 37% of the microbiomes could not be classified into sub-community state types (subCSTs). We, therefore, developed subCSTs IV-D0, IV-D1, IV-D2, and IV-E\u2014dominated primarily by\n              <jats:italic>Gardnerella vaginalis<\/jats:italic>\n              \u2014to improve classification. Among paired microbiomes, the endocervix had a significantly higher alpha diversity and, independently, higher diversity for high-risk human papilloma virus (HPV) genotypes compared to low-risk and no HPV.\n              <jats:italic>Ct-<\/jats:italic>\n              infected endocervical networks had smaller clusters without interactions with potentially beneficial\n              <jats:italic>Lactobacillus<\/jats:italic>\n              spp. Overall, these data suggest that\n              <jats:italic>G. vaginalis<\/jats:italic>\n              may generate polymicrobial biofilms that predispose to and\/or promote\n              <jats:italic>Ct<\/jats:italic>\n              and possibly HPV persistence and pathogenicity. Our findings expand on the existing repertoire of endocervical and vaginal microbiomes and fill in knowledge gaps regarding Pacific Islanders.\n            <\/jats:p>\n          <\/jats:sec>","DOI":"10.1128\/mbio.03063-23","type":"journal-article","created":{"date-parts":[[2023,12,20]],"date-time":"2023-12-20T14:01:32Z","timestamp":1703080892000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":7,"title":["Unique microbial diversity, community composition, and networks among Pacific Islander endocervical and vaginal microbiomes with and without\n            <i>Chlamydia trachomatis<\/i>\n            infection in Fiji"],"prefix":"10.1128","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4469-7925","authenticated-orcid":false,"given":"Sankhya","family":"Bommana","sequence":"first","affiliation":[{"name":"Department of Pediatrics, University of California San Francisco, Oakland, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi-Juan","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mike","family":"Kama","sequence":"additional","affiliation":[{"name":"Ministry of Health and Medical Services, Suva, Fiji"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruohong","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Francisco, Oakland, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reshma","family":"Kodimerla","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Francisco, Oakland, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kenan","family":"Jijakli","sequence":"additional","affiliation":[{"name":"Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8966-9680","authenticated-orcid":false,"given":"Timothy D.","family":"Read","sequence":"additional","affiliation":[{"name":"Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4490-1746","authenticated-orcid":false,"given":"Deborah","family":"Dean","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Francisco, Oakland, California, USA"},{"name":"Department of Medicine, University of California San Francisco, San Francisco, California, USA"},{"name":"Department of Bioengineering, Joint Graduate Program, University of California San Francisco and University of California Berkeley, San Francisco, California, USA"},{"name":"Bixby Center for Global Reproductive Health, University of California San Francisco, San Francisco, California, USA"},{"name":"University of California San Francisco, Benioff Center for Microbiome Medicine, San Francisco, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_5_2_2","volume-title":"Global health sector strategy on sexually transmitted infections","author":"World Health Organization","year":"2016","unstructured":"World Health Organization. 2016. 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