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[Preprint]. 2023 Apr 5:2023.03.21.23286947.

doi: 10.1101/2023.03.21.23286947.

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

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.

PMID: 36993193
PMCID: PMC10055588
DOI: 10.1101/2023.03.21.23286947

VMAP: Vaginal Microbiome Atlas During Pregnancy

Antonio Parraga-Leo et al. medRxiv. 2023.

[Preprint]. 2023 Apr 5:2023.03.21.23286947.

doi: 10.1101/2023.03.21.23286947.

Authors

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.

PMID: 36993193
PMCID: PMC10055588
DOI: 10.1101/2023.03.21.23286947

Update in

VMAP: Vaginal Microbiome Atlas during Pregnancy.
Parraga-Leo A, Oskotsky TT, Oskotsky B, Wibrand C, Roldan A, Tang AS, 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 JL, Sirota M. Parraga-Leo A, et al. JAMIA Open. 2024 Sep 27;7(3):ooae099. doi: 10.1093/jamiaopen/ooae099. eCollection 2024 Oct. JAMIA Open. 2024. PMID: 39345789 Free PMC article.

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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Conflict of interest statement

Conflict of Interest 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 RShinv App Screenshot.**
A user can visualize demographic features of the cohort, diversity measures (both correlation between them) and each one by outcome of interest, CSTs as alluvial plots, dimensionality reduction plots of phylogeny and heatmaps of taxonomical features. The visualizations are customizable by the bar on the left allowing one to choose which projects and samples to visualize. A) visualized by age B) visualized by outcome

See this image and copyright information in PMC

References

1. Hyman R. W. et al. Diversity of the Vaginal Microbiome Correlates With Preterm Birth. Reprod. Sci. 21, 32–40 (2014). - PMC - PubMed
1. DiGiulio D. B. et al. Temporal and spatial variation of the human microbiota during pregnancy. Proc. Natl. Acad. Sci. U. S. A. 112, 11060–11065 (2015). - PMC - PubMed
1. Callahan B. J. 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. U. S. A. 114, 9966–9971 (2017). - PMC - PubMed
1. Kindinger L. M. et al. The interaction between vaginal microbiota, cervical length, and vaginal progesterone treatment for preterm birth risk. Microbiome 5, 6 (2017). - PMC - PubMed
1. Kindinger L. M. et al. Relationship between vaginal microbial dysbiosis, inflammation, and pregnancy outcomes in cervical cerclage. Sci. Transl. Med. 8, 350ra102 (2016). - PubMed

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This is a preprint.

VMAP: Vaginal Microbiome Atlas During Pregnancy

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VMAP: Vaginal Microbiome Atlas During Pregnancy

Authors

Affiliations

Update in

Abstract

Conflict of interest statement

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