VMAP: Vaginal Microbiome Atlas During Pregnancy.

Journal

medRxiv : the preprint server for health sciences
Titre abrégé: medRxiv
Pays: United States
ID NLM: 101767986

Informations de publication

Date de publication:
05 Apr 2023
Historique:
pubmed: 31 3 2023
medline: 31 3 2023
entrez: 30 3 2023
Statut: epublish

Résumé

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.

Identifiants

DOI: 10.1101/2023.03.21.23286947 PMID: 36993193 PMC: PMC10055588
pubmed: 36993193
doi: 10.1101/2023.03.21.23286947
pmc: PMC10055588
pii:
doi:

Types de publication

Preprint

Langues

eng

Déclaration de conflit d'intérêts

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.

Auteurs

Antonio Parraga-Leo (A)

Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA.
Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA.
March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA.
Department of Pediatrics, Obstetrics and Gynaecology, Universidad de Valencia, Valencia, Spain.
Instituto de Investigación Sanitaria La Fe (IIS La Fe), IVI Foundation, Valencia, Spain.

Tomiko T Oskotsky (TT)

Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA.
Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA.
March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA.

Boris Oskotsky (B)

Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA.
Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA.

Camilla Wibrand (C)

Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA.
Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA.
March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA.
Department of Pediatrics, Obstetrics and Gynaecology, Universidad de Valencia, Valencia, Spain.

Alennie Roldan (A)

Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA.
Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA.
March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA.

Alice Tang (A)

Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA.
Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA.
March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA.

Connie W Y Ha (CWY)

Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA.
Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, California. USA.

Ronald J Wong (RJ)

Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA.

Samuel S Minot (SS)

Data Core, Fred Hutchinson Cancer Center. Seattle, WA. USA.

Gaia Andreoletti (G)

Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA.
Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA.
March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA.

Idit Kosti (I)

Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA.
Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA.
March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA.

Kevin R Theis (KR)

Imperial College Parturition Research Group, Division of the Institute of Reproduction and Developmental Biology, Imperial College London, UK.

Sherrianne Ng (S)

Imperial College Parturition Research Group, Division of the Institute of Reproduction and Developmental Biology, Imperial College London, UK.
March of Dimes Prematurity Research Centre at Imperial College London, London, UK.

Yun S Lee (YS)

Imperial College Parturition Research Group, Division of the Institute of Reproduction and Developmental Biology, Imperial College London, UK.
March of Dimes Prematurity Research Centre at Imperial College London, London, UK.

Patricia Diaz-Gimeno (P)

Instituto de Investigación Sanitaria La Fe (IIS La Fe), IVI Foundation, Valencia, Spain.

Phillip R Bennett (PR)

Imperial College Parturition Research Group, Division of the Institute of Reproduction and Developmental Biology, Imperial College London, UK.
March of Dimes Prematurity Research Centre at Imperial College London, London, UK.

David A MacIntyre (DA)

Imperial College Parturition Research Group, Division of the Institute of Reproduction and Developmental Biology, Imperial College London, UK.
March of Dimes Prematurity Research Centre at Imperial College London, London, UK.

Susan V Lynch (SV)

Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA.
Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, California. USA.

Roberto Romero (R)

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.
Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI. USA.
Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI. USA.
Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI. USA; Detroit Medical Center, Detroit, MI. USA.
Department of Obstetrics and Gynecology, Florida International University, Miami, FL. USA.

Adi L Tarca (AL)

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.
Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI. USA; Detroit Medical Center, Detroit, MI. USA.
Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI. USA.
Department of Computer Science, Wayne State University College of Engineering, Detroit, MI. USA.

David K Stevenson (DK)

Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA.
Center for Academic Medicine, Stanford University School of Medicine, Stanford, California.

Nima Aghaeepour (N)

Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA.
Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University School of Medicine, Stanford, CA. USA.
Department of Biomedical Data Sciences, Stanford University School of Medicine, Stanford, CA. USA.

Jonathan Golob (J)

March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA.
Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA.

Marina Sirota (M)

Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA.
Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA.
March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA.

Classifications MeSH