VMAP: Vaginal Microbiome Atlas during Pregnancy

Antonio Parraga-Leo; Tomiko T Oskotsky; Boris Oskotsky; Camilla Wibrand; Alennie Roldan; Alice S Tang; Connie W Y Ha; Ronald J Wong; Samuel S Minot; Gaia Andreoletti; Idit Kosti; Kevin R Theis; Sherrianne Ng; Yun S Lee; Patricia Diaz-Gimeno; Phillip R Bennett; David A MacIntyre; Susan V Lynch; Roberto Romero; Adi L Tarca; David K Stevenson; Nima Aghaeepour; Jonathan L Golob; Marina Sirota

doi:10.1093/jamiaopen/ooae099

VMAP: Vaginal Microbiome Atlas during Pregnancy

JAMIA Open. 2024 Sep 27;7(3):ooae099. doi: 10.1093/jamiaopen/ooae099. eCollection 2024 Oct.

Authors

Antonio Parraga-Leo^{1

2

3

4

5}, Tomiko T Oskotsky^{1

2

3}, Boris Oskotsky^{1

2}, Camilla Wibrand^{1

2

3

6}, Alennie Roldan^{1

2

3}, Alice S Tang^{1

2

3}, Connie W Y Ha^{7

8}, Ronald J Wong⁹, Samuel S Minot¹⁰, Gaia Andreoletti^{1

2

3}, Idit Kosti^{1

2

3}, Kevin R Theis¹¹, Sherrianne Ng^{12

13}, Yun S Lee^{12

13}, Patricia Diaz-Gimeno⁵, Phillip R Bennett^{12

13}, David A MacIntyre^{12

13}, Susan V Lynch^{7

8}, Roberto Romero^{14

15

16}, Adi L Tarca^{14

17

18

19}, David K Stevenson^{9

20}, Nima Aghaeepour^{9

21

22}, Jonathan L Golob^{3

23}, Marina Sirota^{1

2

3}

Affiliations

¹ Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA 94143, United States.
² Department of Pediatrics, University of California San Francisco, San Francisco, CA 94158, United States.
³ March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA 94143, United States.
⁴ Department of Pediatrics, Obstetrics and Gynaecology, Universidad de Valencia, Valencia 46010, Spain.
⁵ IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia 28023, Spain.
⁶ Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus 8200, Denmark.
⁷ Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA 94143, United States.
⁸ Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, United States.
⁹ Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, United States.
¹⁰ Data Core, Fred Hutchinson Cancer Center, Seattle, WA 98109, United States.
¹¹ Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI 48201, United States.
¹² Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, United Kingdom.
¹³ March of Dimes Prematurity Research Centre at Imperial College London, London W12 0NN, United Kingdom.
¹⁴ Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD 20892, United States.
¹⁵ Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI 48109, United States.
¹⁶ Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI 48824, United States.
¹⁷ Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, United States.
¹⁸ Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201, United States.
¹⁹ Department of Computer Science, Wayne State University College of Engineering, Detroit, MI 48202, United States.
²⁰ Center for Academic Medicine, Stanford University School of Medicine, Stanford, CA 94304, United States.
²¹ Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305, United States.
²² Department of Biomedical Data Sciences, Stanford University School of Medicine, Stanford, CA 94305, United States.
²³ Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, United States.

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.

Keywords: 16S rRNA sequencing; bioinformatics; data integration; microbiome; visualization.

Grants and funding

R01 AG058417/AG/NIA NIH HHS/United States