VMAP: Vaginal Microbiome Atlas During Pregnancy

Antonio Parraga-Leo; Tomiko T Oskotsky; Boris Oskotsky; Camilla Wibrand; Alennie Roldan; Alice 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 Golob; Marina Sirota

doi:10.1101/2023.03.21.23286947

VMAP: Vaginal Microbiome Atlas During Pregnancy

medRxiv [Preprint]. 2023 Apr 5:2023.03.21.23286947. doi: 10.1101/2023.03.21.23286947.

Authors

Antonio Parraga-Leo^{1

2

3

4

5}, Tomiko T Oskotsky^{1

2

3}, Boris Oskotsky^{1

2}, Camilla Wibrand^{1

2

3

4}, Alennie Roldan^{1

2

3}, Alice Tang^{1

2

3}, Connie W Y Ha^{6

7}, Ronald J Wong⁸, Samuel S Minot⁹, Gaia Andreoletti^{1

2

3}, Idit Kosti^{1

2

3}, Kevin R Theis¹⁰, Sherrianne Ng^{10

11}, Yun S Lee^{10

11}, Patricia Diaz-Gimeno⁵, Phillip R Bennett^{10

11}, David A MacIntyre^{10

11}, Susan V Lynch^{6

7}, Roberto Romero^{12

13

14

15

16}, Adi L Tarca^{12

15

17

18}, David K Stevenson^{8

19}, Nima Aghaeepour^{8

20

21}, Jonathan Golob^{3

22}, Marina Sirota^{1

2

3}

Affiliations

¹ Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA.
² Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA.
³ March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA.
⁴ Department of Pediatrics, Obstetrics and Gynaecology, Universidad de Valencia, Valencia, Spain.
⁵ Instituto de Investigación Sanitaria La Fe (IIS La Fe), IVI Foundation, Valencia, Spain.
⁶ Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA.
⁷ Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, California. USA.
⁸ Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA.
⁹ Data Core, Fred Hutchinson Cancer Center. Seattle, WA. USA.
¹⁰ Imperial College Parturition Research Group, Division of the Institute of Reproduction and Developmental Biology, Imperial College London, UK.
¹¹ March of Dimes Prematurity Research Centre at Imperial College London, London, UK.
¹² Perinatology 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, Detroit, MI. USA.
¹³ Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI. USA.
¹⁴ Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI. USA.
¹⁵ Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI. USA; Detroit Medical Center, Detroit, MI. USA.
¹⁶ Department of Obstetrics and Gynecology, Florida International University, Miami, FL. USA.
¹⁷ Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI. USA.
¹⁸ Department of Computer Science, Wayne State University College of Engineering, Detroit, MI. USA.
¹⁹ Center for Academic Medicine, Stanford University School of Medicine, Stanford, California.
²⁰ Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University School of Medicine, Stanford, CA. USA.
²¹ Department of Biomedical Data Sciences, Stanford University School of Medicine, Stanford, CA. USA.
²² Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA.

Abstract

The vaginal microbiome has been shown to be associated with pregnancy outcomes including preterm birth (PTB) risk. Here we present VMAP: Vaginal Microbiome Atlas during Pregnancy (http://vmapapp.org), an application to visualize features of 3,909 vaginal microbiome samples of 1,416 pregnant individuals from 11 studies, aggregated from raw public and newly generated sequences via an open-source tool, MaLiAmPi. Our visualization tool (http://vmapapp.org) includes microbial features such as various measures of diversity, VALENCIA community state types (CST), and composition (via phylotypes and taxonomy). This work serves as a resource for the research community to further analyze and visualize vaginal microbiome data in order to better understand both healthy term pregnancies and those associated with adverse outcomes.

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Abstract

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