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      Altered Vaginal Microbiota Composition Correlates With Human Papillomavirus and Mucosal Immune Responses in Women With Symptomatic Cervical Ectopy

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          Abstract

          Cervical ectopy is a benign condition of the lower genital tract that is frequently detected in women of reproductive age. Although cervical ectopy is regarded as a physiological condition, some women experience symptoms such as leucorrhoea, persistent bleeding and recurrent vaginal infections that require medical intervention. Cervical ectopy has not been linked to cervical cancer, but it is thought to facilitate the acquisition of sexually transmitted diseases (STDs), like Human Papillomavirus (HPV) infection, as it provides a favorable microenvironment for virus infection and dissemination. We and others have described the presence of oncogenic HPV types in women with symptomatic cervical ectopy. The relevance of this finding and the impact of symptomatic cervical ectopy on the cervicovaginal microenvironment (vaginal microbiota, immune and inflammatory responses) are currently unknown. To shed some light into the interplay between HPV, the vaginal microbiota and mucosal immune and inflammatory responses in the context of this condition, we enrolled 156 women with symptomatic cervical ectopy and determined the presence of HPV using a type-specific multiplex genotyping assay. Overall, HPV was detected in 54.48% women, oncogenic HPV types were found in more than 90% of HPV-positive cases. The most prevalent HPV types were HPV16 (29.4%), HPV31 (21.17%) and HPV18 (15.29%). Next, we evaluated the vaginal microbial composition and diversity by 16S rDNA sequencing, and quantified levels of cytokines and chemokines by flow cytometry using bead-based multiplex assays in a sub-cohort of 63 women. IL-21 and CXCL9 were significantly upregulated in HPV-positive women ( p=0.0002 and p=0.013, respectively). Women with symptomatic cervical ectopy and HPV infection had increased diversity ( p<0.001), and their vaginal microbiota was enriched in bacterial vaginosis-associated anaerobes ( Sneathia, Shuttleworthia, Prevotella, and Atopobium) and depleted in Lactobacillus spp. Furthermore, the vaginal microbiota of women with symptomatic cervical ectopy and HPV infection correlated with vaginal inflammation (IL-1β, rho=0.56, p=0.0004) and increased mucosal homeostatic response (IL-22, rho=0.60, p=0.0001). Taken together, our results suggest that HPV infection and dysbiotic vaginal communities could favor a vaginal microenvironment that might delay the recovery of the cervical epithelium in women with symptomatic cervical ectopy and favor STDs acquisition.

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          DADA2: High resolution sample inference from Illumina amplicon data

          We present DADA2, a software package that models and corrects Illumina-sequenced amplicon errors. DADA2 infers sample sequences exactly, without coarse-graining into OTUs, and resolves differences of as little as one nucleotide. In several mock communities DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.
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            Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

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              phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

              Background The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data. Results Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research. Conclusions The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.
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                Author and article information

                Contributors
                URI : https://loop.frontiersin.org/people/1696431
                URI : https://loop.frontiersin.org/people/527499
                URI : https://loop.frontiersin.org/people/531487
                URI : https://loop.frontiersin.org/people/1017117
                URI : https://loop.frontiersin.org/people/499545
                URI : https://loop.frontiersin.org/people/1765167
                URI : https://loop.frontiersin.org/people/854389
                Journal
                Front Cell Infect Microbiol
                Front Cell Infect Microbiol
                Front. Cell. Infect. Microbiol.
                Frontiers in Cellular and Infection Microbiology
                Frontiers Media S.A.
                2235-2988
                17 May 2022
                2022
                : 12
                : 884272
                Affiliations
                [1] 1Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM) , Ciudad de México, Mexico
                [2] 2International Agency for Research on Cancer , Lyon, France
                [3] 3Clínica de Colposcopia Fundación “Cruz Talonia” , Ciudad de Mexico, Mexico
                [4] 4Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas , Ciudad de México, Mexico
                [5] 5Deparatamento de Oncología, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes , Ciudad de México, Mexico
                [6] 6Departamento de Infectología e Inmunología, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes , Ciudad de México, Mexico
                [7] 7Mesenchymal Stem Cells Laboratory, Oncology Research Unit, Oncology Hospital, National Medical Center, Instituto Mexicano del Seguro Social (IMSS) , Mexico City, Mexico
                Author notes

                Edited by: Leticia Reyes, University of Wisconsin-Madison, United States

                Reviewed by: Martin James Holland, University of London, United Kingdom; Jose Eleuterio Junior, Federal University of Ceara, Brazil

                *Correspondence: Leticia Rocha-Zavaleta, lrochaz@ 123456iibiomedicas.unam.mx ; Sandra Pinto-Cardoso, sandra.pintocardoso.cieni@ 123456gmail.com

                †Present address: Massimo Tommasino, Dipartimento di Farmacia - Scienze del Farmaco, University of Bari, Bari, Italy

                ‡These authors have contributed equally to this work

                This article was submitted to Microbiome in Health and Disease, a section of the journal Frontiers in Cellular and Infection Microbiology

                Article
                10.3389/fcimb.2022.884272
                9152460
                35656032
                e58b41f6-3c0e-49b0-b281-4457b3439291
                Copyright © 2022 López-Filloy, Cortez, Gheit, Cruz y Cruz, Cruz-Talonia, Chávez-Torres, Arteaga-Gómez, Mancilla-Herrera, Montesinos, Cortés-Morales, Aguilar, Tommasino, Pinto-Cardoso and Rocha-Zavaleta

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 26 February 2022
                : 19 April 2022
                Page count
                Figures: 5, Tables: 3, Equations: 0, References: 61, Pages: 15, Words: 7517
                Funding
                Funded by: Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México , doi 10.13039/501100020704;
                Categories
                Cellular and Infection Microbiology
                Original Research

                Infectious disease & Microbiology
                human papillomavirus,vaginal microbiota,mucosal immune responses,genital inflammation,cervicovaginal mucus,cervical ectopy

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