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In this study, 57 cervical swab samples from 19 HIV\/HPV co-infected women were analyzed for both virome and bacteriome composition. Virome analysis focused on circular DNA viruses through rolling circle amplification followed by next-generation sequencing (NGS). Data were assigned to virus families and genera, and HPV types were identified. NGS data of bacterial 16S from a subset of 24 samples were assigned to operational taxonomic units and classified according to vaginal microbiome community state types (CSTs). Four viral families were found: Papillomaviridae, Anelloviridae, Genomoviridae, and Herpesviridae. Papillomavirus reads were more abundant in women with premalignant cervical lesions, which were also strongly associated with multiple (\u22653) high-risk HPV infection. Anellovirus read abundance was negatively correlated with host CD4+ T-cell counts. The bacteriome revealed the presence of CST III and CST IV, and women with \u22651% frequency of genomovirus or herpesvirus reads displayed an increased risk of carrying CST IV. By characterizing the composition of the cervical circular DNA viruses and the bacteriome of HIV\/HPV co-infected women, we identified putative interactions between these two microorganism communities and their associations with patients\u2019 clinical characteristics, notably immunodeficiency status.<\/jats:p>","DOI":"10.3390\/v11050422","type":"journal-article","created":{"date-parts":[[2019,5,9]],"date-time":"2019-05-09T11:22:35Z","timestamp":1557400955000},"page":"422","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":45,"title":["Composite Analysis of the Virome and Bacteriome of HIV\/HPV Co-Infected Women Reveals Proxies for Immunodeficiency"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4266-9795","authenticated-orcid":false,"given":"Juliana","family":"Siqueira","sequence":"first","affiliation":[{"name":"Programa de Oncovirologia, Instituto Nacional de C\u00e2ncer, Rio de Janeiro 20231-050, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gislaine","family":"Curty","sequence":"additional","affiliation":[{"name":"Programa de Oncovirologia, Instituto Nacional de C\u00e2ncer, Rio de Janeiro 20231-050, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deng","family":"Xutao","sequence":"additional","affiliation":[{"name":"Vitalant Research Institute, San Francisco, CA 94118, USA"},{"name":"Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8633-0913","authenticated-orcid":false,"given":"Cristina","family":"Hofer","sequence":"additional","affiliation":[{"name":"Instituto de Ginecologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 20211-340, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth","family":"Machado","sequence":"additional","affiliation":[{"name":"Instituto de Puericultura e Pediatria Martag\u00e3o Gesteira, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-912, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"H\u00e9ctor","family":"Seu\u00e1nez","sequence":"additional","affiliation":[{"name":"Programa de Gen\u00e9tica, Instituto Nacional de C\u00e2ncer, Rio de Janeiro 20231-050, Brazil"},{"name":"Departamento de Gen\u00e9tica, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21944-970, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9013-2570","authenticated-orcid":false,"given":"Marcelo","family":"Soares","sequence":"additional","affiliation":[{"name":"Programa de Oncovirologia, Instituto Nacional de C\u00e2ncer, Rio de Janeiro 20231-050, Brazil"},{"name":"Departamento de Gen\u00e9tica, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21944-970, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6296-4484","authenticated-orcid":false,"given":"Eric","family":"Delwart","sequence":"additional","affiliation":[{"name":"Vitalant Research Institute, San Francisco, CA 94118, USA"},{"name":"Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Esmeralda","family":"Soares","sequence":"additional","affiliation":[{"name":"Programa de Oncovirologia, Instituto Nacional de C\u00e2ncer, Rio de Janeiro 20231-050, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2019,5,7]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Wylie, K.M., Mihindukulasuriya, K.A., Zhou, Y., Sodergren, E., Storch, G.A., and Weinstock, G.M. 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