Related Experiment Video
Updated: Jun 11, 2025

Author Spotlight: Revolutionizing Research on Vaginal Microbiome Interactions Using a Vaginal Chip
Published on: February 16, 2024
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.
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.
Related Concept Videos
Surface Membrane Barriers
The outer layer of the skin, the epidermis, is a robust barrier comprising layers of closely packed keratinized cells. This dense arrangement prevents microbes from penetrating the body. The periodic shedding of epidermal cells...
Anatomy of the Intestines
Small Intestines
The small intestine is an ~7 meter-long tube with an inner diameter of just 2.5 cm. Since most nutrients are absorbed here, the inner lining of the...
Bacterial Flora of the Large Intestine
The normal gut flora of the colon plays a critical role in generating essential vitamins such as vitamins K, B5, and B7.
Defense Mechanism Against Infection
In addition, many body organ systems have unique defenses against infection. The skin is an intact, multilayered surface preventing invasion by microorganisms unless impaired. Mucous membranes lining the mouth, nose, and eyelids are barriers...
Disorders of the Female Reproductive System

