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VMAP: Vaginal Microbiome Atlas during Pregnancy.

Antonio Parraga-Leo1,2,3,4,5, Tomiko T Oskotsky1,2,3, Boris Oskotsky1,2

  • 1Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA 94143, United States.

JAMIA Open
|September 30, 2024
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Summary
This summary is machine-generated.

The Vaginal Microbiome Atlas during Pregnancy (VMAP) offers interactive visualization of vaginal microbiome data from over 3,800 samples. This resource aids researchers in understanding pregnancy and its outcomes.

Keywords:
16S rRNA sequencingbioinformaticsdata integrationmicrobiomevisualization

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Area of Science:

  • Microbiome research
  • Reproductive health
  • Data visualization

Background:

  • The vaginal microbiome plays a crucial role in pregnancy outcomes.
  • Understanding its dynamics is essential for maternal and infant health.
  • Previous studies have generated fragmented data, limiting comprehensive analysis.

Purpose of the Study:

  • To create an interactive visualization tool for the vaginal microbiome during pregnancy.
  • To facilitate the discovery of novel insights and hypothesis generation.
  • To aggregate and standardize data from multiple studies.

Main Methods:

  • Developed the Vaginal Microbiome Atlas during Pregnancy (VMAP) using R shiny.
  • Aggregated data from 11 studies comprising 3880 samples from 1402 pregnant individuals.
  • Utilized the open-source tool MaLiAmPi for data aggregation.

Main Results:

  • VMAP visualizes diversity measures, VALENCIA community state types, and microbial composition (phylotypes, taxonomy).
  • Data can be filtered by various categories for detailed analysis.
  • Represents one of the largest and most geographically diverse aggregations of vaginal microbiome data in pregnancy.

Conclusions:

  • VMAP serves as a user-friendly resource for analyzing vaginal microbiome data.
  • It enhances understanding of pregnancies and associated outcomes.
  • The tool is accessible online for researchers and non-R users.