VMAP: Vaginal Microbiome Atlas during Pregnancy

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.

PMID: 39345789
PMCID: PMC11430916
DOI: 10.1093/jamiaopen/ooae099

VMAP: Vaginal Microbiome Atlas during Pregnancy

Antonio Parraga-Leo et al. JAMIA Open. 2024.

. 2024 Sep 27;7(3):ooae099.

doi: 10.1093/jamiaopen/ooae099. eCollection 2024 Oct.

Authors

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.

PMID: 39345789
PMCID: PMC11430916
DOI: 10.1093/jamiaopen/ooae099

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.

PubMed Disclaimer

Conflict of interest statement

Antonio Parraga-Leo and Patricia Diaz-Gimeno are receiving hononaria from the IVI Foundation. All other authors declare no financial or non-financial competing interests.

Figures

**Figure 1.**
VMAP RShiny App. VMAP encompasses information from different microbiome studies gathering demographic information, birth outcomes, diversity measures, CST, and phylogeny (left). A user can visualize demographic features of the cohort, diversity measures (including correlations between them) by outcome of interest, alluvial plots of CSTs, dimensionality reduction plots of phylogeny, and heatmaps of taxonomical features (right). The visualizations are customizable by the filters in the bar on the left, allowing one to choose which projects and samples to visualize. Abbreviation: CST = community state types. Created with BioRender.com.

See this image and copyright information in PMC

Update of

VMAP: Vaginal Microbiome Atlas During Pregnancy.
Parraga-Leo A, Oskotsky TT, Oskotsky B, Wibrand C, Roldan A, Tang A, Ha CWY, Wong RJ, Minot SS, Andreoletti G, Kosti I, Theis KR, Ng S, Lee YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Lynch SV, Romero R, Tarca AL, Stevenson DK, Aghaeepour N, Golob J, Sirota M. Parraga-Leo A, et al. medRxiv [Preprint]. 2023 Apr 5:2023.03.21.23286947. doi: 10.1101/2023.03.21.23286947. medRxiv. 2023. Update in: JAMIA Open. 2024 Sep 27;7(3):ooae099. doi: 10.1093/jamiaopen/ooae099. PMID: 36993193 Free PMC article. Updated. Preprint.

References

1. Hyman RW, Fukushima M, Jiang H, et al.Diversity of the vaginal microbiome correlates with preterm birth. Reprod Sci. 2014;21:32-40. 10.1177/1933719113488838 - DOI - PMC - PubMed
1. DiGiulio DB, Callahan BJ, McMurdie PJ, et al.Temporal and spatial variation of the human microbiota during pregnancy. Proc Natl Acad Sci USA. 2015;112:11060-11065. 10.1073/pnas.1502875112 - DOI - PMC - PubMed
1. Callahan BJ, DiGiulio DB, Goltsman DSA, et al.Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women. Proc Natl Acad Sci USA. 2017;114:9966-9971. 10.1073/pnas.1705899114 - DOI - PMC - PubMed
1. Kindinger LM, Bennett PR, Lee YS, et al.The interaction between vaginal microbiota, cervical length, and vaginal progesterone treatment for preterm birth risk. Microbiome. 2017;5:6. 10.1186/s40168-016-0223-9 - DOI - PMC - PubMed
1. Kindinger LM, MacIntyre DA, Lee YS, et al.Relationship between vaginal microbial dysbiosis, inflammation, and pregnancy outcomes in cervical cerclage. Sci Transl Med. 2016;8:350ra102. 10.1126/scitranslmed.aag1026 - DOI - PubMed

Grants and funding

R01 AG058417/AG/NIA NIH HHS/United States

LinkOut - more resources

Full Text Sources
- PubMed Central
- eScholarship, University of California - Access Free Full Text

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

VMAP: Vaginal Microbiome Atlas during Pregnancy

Affiliations

VMAP: Vaginal Microbiome Atlas during Pregnancy

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

Update of

References

Grants and funding

LinkOut - more resources

Full Text Sources