VMAP: Vaginal Microbiome Atlas during Pregnancy

Autors de IIS La Fe

• Antonio Parraga Leo

  Autor

• Patricia Díaz Gimeno

  Autor

Autors aliens a IIS La Fe

• Oskotsky, Tomiko T.
• Oskotsky, Boris
• Wibrand, Camilla
• Roldan, Alennie
• Tang, Alice S.
• Ha, Connie W. Y.
• Wong, Ronald J.
• Minot, Samuel S.
• Andreoletti, Gaia
• Kosti, Idit
• Theis, Kevin R.
• Ng, Sherrianne
• Lee, Yun S.
• Bennett, Phillip R.
• Macintyre, David A.
• Lynch, Susan, V
• Romero, Roberto
• Tarca, Adi L.
• Stevenson, David K.
• Aghaeepour, Nima
• Golob, Jonathan L.
• Sirota, Marina

Grups d'Investigació

• Biomarcadores, Medicina Genómica, Estadística y Análisis masivo de datos en Reproducción humana asistida

  

  Investigador Principal

  Marcos Meseguer Escrivá

Abstract

Objectives To enable interactive visualization of the vaginal microbiome across the pregnancy and facilitate discovery of novel insights and generation of new hypotheses.Material and Methods Vaginal Microbiome Atlas during Pregnancy (VMAP) was created with R shiny to generate visualizations of structured vaginal microbiome data from multiple studies.Results VMAP (http://vmapapp.org) visualizes 3880 vaginal microbiome samples of 1402 pregnant individuals from 11 studies, aggregated via open-source tool MaLiAmPi. Visualized features include diversity measures, VALENCIA community state types, and composition (phylotypes, taxonomy) that can be filtered by various categories.Discussion This work represents one of the largest and most geographically diverse aggregations of the vaginal microbiome in pregnancy to date and serves as a user-friendly resource to further analyze vaginal microbiome data and better understand pregnancies and associated outcomes.Conclusion VMAP can be obtained from https://github.com/msirota/vmap.git and is currently deployed as an online app for non-R users. The vaginal microbiome plays a significant role in birth outcomes, including preterm and spontaneous labor. Despite the increasing number of microbiome studies being performed, the information remains separated and difficult to compare due to technical challenges in its aggregation. This fact hinders analyses of large and widely-representative data. To address this drawback, we present the Vaginal Microbiome Atlas during Pregnancy (VMAP), a web application that enables the visualization of 11 different microbiome studies, including a total of 3880 vaginal microbiome samples aggregated leveraging an open-source tool, MaLiAmPi. VMAP offers an online platform for exploring robust vaginal microbiome data in the context of pregnancy from multiple studies, providing interactive visualization of diverse microbiome features, allowing a better understanding of the role of the vaginal microbiome in preterm birth, and facilitating the generation of new research hypotheses.

© The Author(s) 2024. Published by Oxford University Press on behalf of the American Medical Informatics Association.

Keywords

• 16S rRNA sequencing; bioinformatics; data integration; microbiome; visualization