{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T10:25:55Z","timestamp":1776421555966,"version":"3.51.2"},"reference-count":68,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2025,9,11]],"date-time":"2025-09-11T00:00:00Z","timestamp":1757548800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Secretar\u00eda de Salud (SSA), Direcci\u00f3n General de Pol\u00edticas de Investigaci\u00f3n en Salud (DGPIS), \u201cFinanciamiento de Proyectos de Investigaci\u00f3n en Salud\u201d","award":["FPIS2024-HJM-6460"],"award-info":[{"award-number":["FPIS2024-HJM-6460"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Progressive immune damage associated with Human Immunodeficiency Virus (HIV) alters mucosal homeostasis, favouring oral microbial imbalance and the development of opportunistic infections. The aim of this study was to characterize the composition and structure of the oral microbiota in different clinical conditions of HIV infection. A cross-sectional study was conducted in 99 Mexican men divided into five groups: HIV-negative controls, newly diagnosed without antiretroviral treatment, virally suppressed, with oral candidiasis, and with HPV infection. Metagenomic DNA was obtained from salivary samples, and the V1\u2013V3 region of the 16S rRNA gene was massively sequenced. Taxonomic profiles, alpha\/beta diversity, differential abundance, microbial co-occurrence networks and degree of dysbiosis were analysed. The results showed distinctive profiles between the groups. Alpha and beta diversity was significantly higher in the groups with oral Candida and HPV lesions, reflecting a disturbance of microbial balance. Differential abundance analysis revealed an increase in Streptococcus, Veillonella, Lactobacillus and Actinomyces genera in HIV patients, while healthy subjects showed higher abundance of Neisseria, Treponema, and Rothia, associated with a eubiotico state. The group of patients with HPV lesions had the highest number of taxa with differential abundance, suggesting an ecological environment altered by the lesion. Analysis of co-occurrence networks revealed a progressive pattern of microbial complexity: controls presented simple networks with weak positive correlations, while HIV groups showed increased connection density and appearance of structured nuclei. The group of patients with HPV lesions presented the highest connectivity, with multiple strongly correlated cores and core nodes such as Prevotella melaninogenica and Shuttleworthia. The dysbiosis score increased progressively from healthy subjects to those with HPV lesions, indicating a gradient of oral microbial disruption. These findings suggest that HIV immunosuppression and the presence of oral lesions are associated with enhanced dysbiosis, although their individual contributions could not be independently assessed due to the absence of non-HIV lesion controls. The integration of microbial networks and dysbiosis scores could be useful for assessing mucosal and immune health in people with HIV and used as biomarkers of clinical progression.<\/jats:p>","DOI":"10.3390\/microorganisms13092121","type":"journal-article","created":{"date-parts":[[2025,9,11]],"date-time":"2025-09-11T07:51:46Z","timestamp":1757577106000},"page":"2121","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Oral Microbiota Dysbiosis in Male HIV Patients: Comparative Analysis of Candidiasis and HPV-Associated Lesions"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-9304-7047","authenticated-orcid":false,"given":"Magnolia del Carmen","family":"Ram\u00edrez-Hern\u00e1ndez","sequence":"first","affiliation":[{"name":"Hospital Ju\u00e1rez de M\u00e9xico, Mexico City 07760, Mexico"},{"name":"Secci\u00f3n de Estudios de Posgrado e Investigaci\u00f3n, Escuela Superior de Medicina, Instituto Polit\u00e9cnico Nacional, Mexico City 11340, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Javier","family":"Gayt\u00e1n-Cervantes","sequence":"additional","affiliation":[{"name":"Divisi\u00f3n de Desarrollo de la Investigaci\u00f3n, Centro M\u00e9dico Nacional Siglo XXI, Mexico City 06720, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carolina","family":"Gonz\u00e1lez-Torres","sequence":"additional","affiliation":[{"name":"Divisi\u00f3n de Desarrollo de la Investigaci\u00f3n, Centro M\u00e9dico Nacional Siglo XXI, Mexico City 06720, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5383-8737","authenticated-orcid":false,"given":"Miguel \u00c1ngel","family":"Loyola-Cruz","sequence":"additional","affiliation":[{"name":"Hospital Ju\u00e1rez de M\u00e9xico, Mexico City 07760, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rebeca Eunice","family":"Garc\u00eda-Mendiola","sequence":"additional","affiliation":[{"name":"Cl\u00ednica Especializada Condesa Iztapalapa, Mexico City 09730, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1555-3102","authenticated-orcid":false,"given":"Clemente","family":"Cruz-Cruz","sequence":"additional","affiliation":[{"name":"Hospital Ju\u00e1rez de M\u00e9xico, Mexico City 07760, Mexico"},{"name":"Secci\u00f3n de Estudios de Posgrado e Investigaci\u00f3n, Escuela Superior de Medicina, Instituto Polit\u00e9cnico Nacional, Mexico City 11340, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9409-5896","authenticated-orcid":false,"given":"Iliana Alejandra","family":"Cort\u00e9s-Ort\u00edz","sequence":"additional","affiliation":[{"name":"Hospital Ju\u00e1rez de M\u00e9xico, Mexico City 07760, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9817-6183","authenticated-orcid":false,"given":"Eduardo","family":"Garc\u00eda-Moncada","sequence":"additional","affiliation":[{"name":"Hospital Ju\u00e1rez de M\u00e9xico, Mexico City 07760, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Teresa","family":"L\u00f3pez-Flores","sequence":"additional","affiliation":[{"name":"Cl\u00ednica Especializada Condesa Iztapalapa, Mexico City 09730, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8985-486X","authenticated-orcid":false,"given":"Emilio Mariano","family":"Dur\u00e1n-Manuel","sequence":"additional","affiliation":[{"name":"Hospital Ju\u00e1rez de M\u00e9xico, Mexico City 07760, Mexico"},{"name":"Secci\u00f3n de Estudios de Posgrado e Investigaci\u00f3n, Escuela Superior de Medicina, Instituto Polit\u00e9cnico Nacional, Mexico City 11340, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nancy","family":"G\u00f3mez-Mancilla","sequence":"additional","affiliation":[{"name":"Cl\u00ednica Especializada Condesa Iztapalapa, Mexico City 09730, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mar\u00eda Fernanda","family":"Oviedo-L\u00f3pez","sequence":"additional","affiliation":[{"name":"Cl\u00ednica Especializada Condesa Iztapalapa, Mexico City 09730, Mexico"},{"name":"Posgrado en Patolog\u00eda y Medicina Bucal, Universidad Aut\u00f3noma Metropolitana, Mexico City 04960, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9195-746X","authenticated-orcid":false,"given":"Carlos Alberto","family":"Jim\u00e9nez-Zamarripa","sequence":"additional","affiliation":[{"name":"Secci\u00f3n de Estudios de Posgrado e Investigaci\u00f3n, Escuela Superior de Medicina, Instituto Polit\u00e9cnico Nacional, Mexico City 11340, Mexico"},{"name":"Hospital Psiqui\u00e1trico Dr. Samuel Ram\u00edrez Moreno, Valle de Chalco Solidaridad 56619, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3851-5881","authenticated-orcid":false,"given":"Araceli","family":"Rojas-Bernab\u00e9","sequence":"additional","affiliation":[{"name":"Secci\u00f3n de Estudios de Posgrado e Investigaci\u00f3n, Escuela Superior de Medicina, Instituto Polit\u00e9cnico Nacional, Mexico City 11340, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8807-1353","authenticated-orcid":false,"given":"Omar Agni","family":"Garc\u00eda-Hern\u00e1ndez","sequence":"additional","affiliation":[{"name":"Facultad de Medicina, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City 54090, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6941-6248","authenticated-orcid":false,"given":"Jonathan","family":"Puente-Rivera","sequence":"additional","affiliation":[{"name":"Hospital Ju\u00e1rez de M\u00e9xico, Mexico City 07760, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adolfo","family":"L\u00f3pez-Ornelas","sequence":"additional","affiliation":[{"name":"Hospital Ju\u00e1rez de M\u00e9xico, Mexico City 07760, Mexico"},{"name":"Hospital Nacional Homeop\u00e1tico, Hospitales Federales de Referencia, Mexico City 06800, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5354-9900","authenticated-orcid":false,"given":"Nayeli Goreti","family":"Nieto-Vel\u00e1zquez","sequence":"additional","affiliation":[{"name":"Hospital Ju\u00e1rez de M\u00e9xico, Mexico City 07760, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dulce Milagros Razo","family":"Blanco-Hern\u00e1ndez","sequence":"additional","affiliation":[{"name":"Hospital Ju\u00e1rez de M\u00e9xico, Mexico City 07760, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2663-9155","authenticated-orcid":false,"given":"Julio C\u00e9sar","family":"Casta\u00f1eda-Ortega","sequence":"additional","affiliation":[{"name":"Facultad de Biolog\u00eda, Universidad Veracruzana, Xalapa 91090, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Benito","family":"Hern\u00e1ndez-Castellanos","sequence":"additional","affiliation":[{"name":"Facultad de Biolog\u00eda, Universidad Veracruzana, Xalapa 91090, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8881-867X","authenticated-orcid":false,"given":"Gabriela","family":"Anaya-Saavedra","sequence":"additional","affiliation":[{"name":"Posgrado en Patolog\u00eda y Medicina Bucal, Universidad Aut\u00f3noma Metropolitana, Mexico City 04960, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5893-8566","authenticated-orcid":false,"given":"Claudia Camelia","family":"Calzada-Mendoza","sequence":"additional","affiliation":[{"name":"Secci\u00f3n de Estudios de Posgrado e Investigaci\u00f3n, Escuela Superior de Medicina, Instituto Polit\u00e9cnico Nacional, Mexico City 11340, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9957-3807","authenticated-orcid":false,"given":"Juan Manuel","family":"Bello-L\u00f3pez","sequence":"additional","affiliation":[{"name":"Hospital Ju\u00e1rez de M\u00e9xico, Mexico City 07760, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,9,11]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Lindegger, D.J. (2024). Advanced Therapies for Human Immunodeficiency Virus. Med. Sci., 12.","DOI":"10.3390\/medsci12030033"},{"key":"ref_2","unstructured":"GBD 2021 HIV Collaborators (2024). Global, regional, and national burden of HIV\/AIDS, 1990\u20132021, and forecasts to 2050, for 204 countries and territories: The Global Burden of Disease Study 2021. Lancet HIV, 11, e807\u2013e822."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"106","DOI":"10.7861\/clinmed.ed.23.2.harv","article-title":"Pandemic HIV and its legacy for medicine and global health","volume":"23","author":"Johnson","year":"2023","journal-title":"Clin. Med."},{"key":"ref_4","unstructured":"Organizaci\u00f3n Panamericana de la Salud (2025, August 11). Lanzan Red de Respuesta al VIH en M\u00e9xico. PAHO, Available online: https:\/\/www.paho.org\/es\/noticias\/5-6-2025-lanzan-red-respuesta-al-vih-mexico."},{"key":"ref_5","unstructured":"Escand\u00f3n, P. (2025, August 11). VIH en M\u00e9xico: 202 mil Casos Activos y un Repunte Preocupante en J\u00f3venes. Exc\u00e9lsior. Available online: https:\/\/www.excelsior.com.mx\/trending\/vih-mexico-2025-panorama-general\/1722311."},{"key":"ref_6","unstructured":"Proceso (2025, August 11). Organizaci\u00f3n VIHVE LIBRE Alerta Sobre Aumento de Casos de VIH. Proceso. Available online: https:\/\/www.proceso.com.mx\/nacional\/2025\/6\/28\/organizacion-vihve-libre-alerta-sobre-aumento-de-casos-de-vih-353866.html."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1104423","DOI":"10.3389\/fimmu.2023.1104423","article-title":"The initial interplay between HIV and mucosal innate immunity","volume":"14","author":"Caputo","year":"2023","journal-title":"Front. Immunol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1038\/s41579-018-0089-x","article-title":"The oral microbiota: Dynamic communities and host interactions","volume":"16","author":"Lamont","year":"2018","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1186\/s12967-023-03995-x","article-title":"The oral microbiome in autoimmune diseases: Friend or foe?","volume":"21","author":"Huang","year":"2023","journal-title":"J. Transl. Med."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"2788","DOI":"10.1097\/CM9.0000000000001825","article-title":"Alterations in the oral microbiome in HIV infection: Causes, effects and potential interventions","volume":"134","author":"Li","year":"2021","journal-title":"Chin. Med. J."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1111\/odi.13515","article-title":"Interplay between oral immunity in HIV and the microbiome","volume":"26","author":"Fidel","year":"2020","journal-title":"Oral Dis."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e112901","DOI":"10.1371\/journal.pone.0112901","article-title":"Design aspects of a case-control clinical investigation of the effect of HIV on oral and gastrointestinal soluble innate factors and microbes","volume":"9","author":"Phelan","year":"2014","journal-title":"PLoS ONE"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"7106","DOI":"10.4103\/jfmpc.jfmpc_940_22","article-title":"Assessment of oral mucosal lesions among HIV positive transgenders residing in Odisha with and without Antiretroviral therapy","volume":"11","author":"Rai","year":"2022","journal-title":"J. Fam. Med. Prim. Care"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Lomel\u00ed-Mart\u00ednez, S.M., Gonz\u00e1lez-Hern\u00e1ndez, L.A., Ruiz-Anaya, A.J., Lomel\u00ed-Mart\u00ednez, M.A., Mart\u00ednez-Salazar, S.Y., Mercado Gonz\u00e1lez, A.E., Andrade-Villanueva, J.F., and Varela-Hern\u00e1ndez, J.J. (2022). Oral Manifestations Associated with HIV\/AIDS Patients. Medicina, 58.","DOI":"10.3390\/medicina58091214"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1016\/j.bjorl.2023.01.001","article-title":"Associated oral manifestations with HIV southeastern Brazilian patients on antiretroviral therapy","volume":"89","author":"Lemos","year":"2023","journal-title":"Braz. J. Otorhinolaryngol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1186\/1471-2180-12-153","article-title":"Evidence of an increased pathogenic footprint in the lingual microbiome of untreated HIV infected patients","volume":"12","author":"Dang","year":"2012","journal-title":"BMC Microbiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"695515","DOI":"10.3389\/fcimb.2021.695515","article-title":"Alteration in Oral Microbiome Among Men Who Have Sex Whit Men with Acute and Chronic HIV Infection on Antiretroviral Therapy","volume":"11","author":"Li","year":"2021","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1089\/aid.2017.0200","article-title":"Oral Microbiome in HIV-Infected Women: Shifts in the Abundance of Pathogenic and Beneficial Bacteria Are Associated with Aging, HIV Load, CD4 Count, and Antiretroviral Therapy","volume":"35","author":"Lewy","year":"2019","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"960","DOI":"10.1038\/s41598-020-80247-8","article-title":"Impact of long-term antiretroviral therapy on gut and oral microbiotas in HIV-1-infected patients","volume":"11","author":"Imahashi","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1364002","DOI":"10.3389\/fcimb.2024.1364002","article-title":"Human immunodeficiency virus and oral microbiota: Mutual influence on the establishment of a viral gingival reservoir in individuals under antiretroviral therapy","volume":"14","author":"Pillet","year":"2024","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"676669","DOI":"10.3389\/fimmu.2021.676669","article-title":"HIV-Associated Interactions Between Oral Microbiota and Mucosal Immune Cells: Knowledge Gaps and Future Directions","volume":"12","author":"Coker","year":"2021","journal-title":"Front. Immunol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"895537","DOI":"10.3389\/fmicb.2022.895537","article-title":"The Oral Microbiota: Community Composition, Influencing Factors, Pathogenesis, and Interventions","volume":"13","author":"Li","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Xia, Q., and Pierson, S. (2025). HPV Infection and Oral Microbiota: Interactions and Future Implications. Int. J. Mol. Sci., 26.","DOI":"10.20944\/preprints202501.0193.v1"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"995423","DOI":"10.3389\/fdmed.2022.995423","article-title":"Oral dysbiosis and systemic diseases","volume":"3","author":"Georges","year":"2022","journal-title":"Front. Dent. Med."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1038\/s41522-023-00413-4","article-title":"Oral and anal microbiome from HIV-exposed individuals: Role of host-associated factors in taxa composition and metabolic pathways","volume":"9","author":"Lacunza","year":"2023","journal-title":"npj Biofilms Microbiomes"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Ponce, P.N.O., Chaves, L.B., Perce-da-Silva, D.S., Carneiro-Alencar, A.L., Rodolphi, C.M., Soares, I.F., Rodrigues-da-Silva, R.N., Alves-da-Silva, A.C., Marques, F.V., and Peres, R.V. (2025). Periodontal Health in Individuals Living with HIV: An Exploratory and Descriptive Molecular Approach of Microbial Interspecific and Intraspecific Diversity in Brazilian Patients. Microorganisms, 13.","DOI":"10.3390\/microorganisms13040867"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1007\/s00248-006-9134-9","article-title":"High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment","volume":"53","author":"DeSantis","year":"2007","journal-title":"Microb. Ecol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1128\/aem.59.3.695-700.1993","article-title":"Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA","volume":"59","author":"Muyzer","year":"1993","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"5112","DOI":"10.1128\/AEM.01043-13","article-title":"Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform","volume":"79","author":"Kozich","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Na, H.S., Song, Y., Yu, Y., and Chung, J. (2023). Comparative Analysis of Primers Used for 16S rRNA Gene Sequencing in Oral Microbiome Studies. Methods Protoc., 6.","DOI":"10.3390\/mps6040071"},{"key":"ref_31","unstructured":"Andrews Simon FASTQC (2025, May 15). A Quality Control Tool for High Throughput Sequence Data. Available online: https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: High-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"D590","DOI":"10.1093\/nar\/gks1219","article-title":"The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools","volume":"41","author":"Quast","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"e61217","DOI":"10.1371\/journal.pone.0061217","article-title":"phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data","volume":"8","author":"McMurdie","year":"2013","journal-title":"PLoS ONE"},{"key":"ref_36","unstructured":"Anderson, M.J. (2014). Permutational Multivariate Analysis of Variance (PERMANOVA). Wiley StatsRef: Statistics Reference Online, John Wiley & Sons."},{"key":"ref_37","unstructured":"Caret Package Team (2025, May 10). A Short Introduction to the Caret Package. Available online: https:\/\/cran.r-project.org\/web\/packages\/caret\/vignettes\/caret.html."},{"key":"ref_38","unstructured":"MLeval Package Team (2025, May 10). MLeval: Machine Learning Model Evaluation. Available online: https:\/\/cran.r-project.org\/web\/packages\/MLeval\/MLeval.pdf."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1038\/s41596-019-0264-1","article-title":"Using microbiomeanalyst for comprehensive statistical, functional, and meta-analysis of microbiome data","volume":"15","author":"Chong","year":"2020","journal-title":"Nat. Protoc."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"4027","DOI":"10.1093\/bioinformatics\/btac438","article-title":"MicrobiomeMarker: An R\/Bioconductor package for microbiome marker identification and visualization","volume":"38","author":"Cao","year":"2022","journal-title":"Bioinformatics"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"ref_42","unstructured":"Lewis, K.B.S.R. (2025, May 15). EnhancedVolcano: Publication-Ready Volcano Plots with Enhanced Colouring and Labeling. GitHub. Available online: https:\/\/github.com\/kevinblighe\/EnhancedVolcano."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1093\/bib\/bbaa290","article-title":"NetCoMi: Network construction and comparison for microbiome data in R","volume":"22","author":"Peschel","year":"2021","journal-title":"Brief. Bioinform."},{"key":"ref_44","unstructured":"Shetty, S.A., and de Steenhuijsen Piters, W.A.A. (2025, May 15). dysbiosisR: An R Package for Calculating Microbiome Dysbiosis Measures. GitHub Repository. Available online: https:\/\/github.com\/microsud\/dysbiosisR."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1016\/j.immuni.2015.04.019","article-title":"Cervicovaginal bacteria are a major modulator of host inflammatory responses in the female genital tract","volume":"42","author":"Anahtar","year":"2015","journal-title":"Immunity."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1080\/14787210.2016.1206469","article-title":"The respiratory microbiome of HIV-infected individuals","volume":"14","author":"Lawani","year":"2016","journal-title":"Expert Rev. Anti-Infect. Ther."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"3080969","DOI":"10.1155\/2023\/3080969","article-title":"Intestinal Microbiota Dysbiosis Promotes Mucosal Barrier Damage and Immune Injury in HIV-Infected Patients","volume":"28","author":"Pan","year":"2023","journal-title":"Can. J. Infect. Dis. Med. Microbiol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1568352","DOI":"10.3389\/fcimb.2025.1568352","article-title":"Gut microbiota differences linked to weight gain and ART in people living with HIV are enterotype specific and minor compared to the large differences linked to sexual behavior","volume":"15","author":"Kehrmann","year":"2025","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1016\/j.phrs.2012.11.006","article-title":"The oral microbiome in health and disease","volume":"69","author":"Wade","year":"2013","journal-title":"Pharmacol. Res."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"R1","DOI":"10.1186\/gb-2013-14-1-r1","article-title":"Biogeography of the ecosystems of the healthy human body","volume":"14","author":"Zhou","year":"2013","journal-title":"Genome Biol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"e0087123","DOI":"10.1128\/spectrum.00871-23","article-title":"Impact of HIV on the Oral Microbiome of Children Living in Sub-Saharan Africa, Determined by Using an rpoC Gene Fragment Metataxonomic Approach","volume":"11","author":"Mann","year":"2023","journal-title":"Microbiol. Spectr."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"e5821","DOI":"10.1097\/MD.0000000000005821","article-title":"Oral microbiome in HIV-associated periodontitis","volume":"96","author":"Peterson","year":"2017","journal-title":"Medicine"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"937039","DOI":"10.3389\/fcimb.2022.937039","article-title":"Clinical Oral Condition Analysis and the Influence of Highly Active Antiretroviral Therapy on Human Salivary Microbial Community Diversity in HIV-Infected\/AIDS Patients","volume":"12","author":"Cao","year":"2022","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1098","DOI":"10.1093\/infdis\/jiac010","article-title":"Oral Human Papillomavirus Associated with Differences in Oral Microbiota Beta Diversity and Microbiota Abundance","volume":"226","author":"Zhang","year":"2022","journal-title":"J. Infect. Dis."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"5002","DOI":"10.1128\/JB.00542-10","article-title":"The human oral microbiome","volume":"192","author":"Dewhirst","year":"2010","journal-title":"J. Bacteriol."},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Human Microbiome Project Consortium (2012). Structure, function and diversity of the healthy human microbiome. Nature, 486, 207\u2013214.","DOI":"10.1038\/nature11234"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"S12","DOI":"10.1111\/jcpe.12679","article-title":"Dental biofilm: Ecological interactions in health and disease","volume":"44","author":"Marsh","year":"2017","journal-title":"J. Clin. Periodontol."},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Rajasekaran, J.J., Krishnamurthy, H.K., Bosco, J., Jayaraman, V., Krishna, K., Wang, T., and Bei, K. (2024). Oral Microbiome: A Review of Its Impact on Oral and Systemic Health. Microorganisms, 12.","DOI":"10.20944\/preprints202406.1923.v1"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"1602962","DOI":"10.3389\/fmicb.2025.1602962","article-title":"Formation, architecture, and persistence of oral biofilms: Recent scientific discoveries and new strategies for their regulation","volume":"16","author":"Lv","year":"2025","journal-title":"Front. Microbiol."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"1400","DOI":"10.1128\/JCM.02954-13","article-title":"HIV infection and microbial diversity in saliva","volume":"52","author":"Li","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1001\/archoto.2012.873","article-title":"Local inflammation and human papillomavirus status of head and neck cancers","volume":"138","author":"Tezal","year":"2012","journal-title":"Arch. Otolaryngol. Head Neck Surg."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1016\/j.virol.2013.06.007","article-title":"Diseases associated with human papillomavirus infection","volume":"445","author":"Cubie","year":"2013","journal-title":"Virology"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1007\/s12070-011-0370-z","article-title":"Oral Microflora: A Comparative Study in HIV and Normal Patients","volume":"66","author":"Hegde","year":"2014","journal-title":"Indian J. Otolaryngol. Head Neck Surg."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1093\/infdis\/jiu409","article-title":"Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection","volume":"211","author":"Dinh","year":"2015","journal-title":"J. Infect. Dis."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"905653","DOI":"10.3389\/fcimb.2022.905653","article-title":"Characteristics of Microbial Distribution in Different Oral Niches of Oral Squamous Cell Carcinoma","volume":"12","author":"Nie","year":"2022","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"e00395-21","DOI":"10.1128\/AEM.00395-21","article-title":"Determining Gut Microbial Dysbiosis: A Review of Applied Indexes for Assessment of Intestinal Microbiota Imbalances","volume":"87","author":"Wei","year":"2021","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1038\/nature07540","article-title":"A core gut microbiome in obese and lean twins","volume":"457","author":"Turnbaugh","year":"2009","journal-title":"Nature"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1136\/gut.2003.025403","article-title":"Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease","volume":"53","author":"Ott","year":"2004","journal-title":"Gut"}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/13\/9\/2121\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:43:35Z","timestamp":1760035415000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/13\/9\/2121"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9,11]]},"references-count":68,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2025,9]]}},"alternative-id":["microorganisms13092121"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms13092121","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,9,11]]}}}