VMAP: Vaginal Microbiome Atlas during Pregnancy
Year: 2024
Type: article
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.
Source: JAMIA Open
Authors: 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
Institutions: Universitat de València, University of California, San Francisco, Instituto de Investigación Sanitaria La Fe, IVIRMA Global, Fundación IVI, Aarhus University Hospital, Stanford Medicine, Stanford University, Fred Hutch Cancer Center, Wayne State University, Imperial College London, National Institutes of Health, University of Michigan, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Michigan State University, Michigan Medicine
Language: English
Subfield: Microbiology
Field: Immunology and Microbiology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,950
Funders: U.S. Department of Health and Human Services, March of Dimes Foundation, Wayne State University, Robertson Foundation, Ministerio de Ciencia, Innovación y Universidades, Australian Government, European Commission, Ministerio de Ciencia e Innovación, National Institutes of Health, University of California, San Francisco, Instituto de Salud Carlos III, National Institute on Aging, National Heart, Lung, and Blood Institute, National Institute of General Medical Sciences, National Institute of Neurological Disorders and Stroke, National Institute of Child Health and Human Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NHLBI Division of Intramural Research
Awards: G1284009618, G1348649281, Machine Learning for Integrative Modeling of the Immune System in Clinical Settings, G2671377752, SPRINT: Signature for Pain Recovery IN Teens, G3388402394, Dietary Modulation of Neuroinflammation in Age-Related Memory Disorders, G5750123646, G7105508972, Preeclampsia to cardiovascular disease: Life course analysis of biomarkers and risk, G8751880874, UCSF Stanford Endometriosis Center for Discovery, Innovation, Training and Community Engagement, Trio Analysis of Recurrent Pregnancy Loss Integrated Bioinformatics Genomics Study (TRIOS), Stanford Alzheimer's Disease Research Center
OpenAlex ID: W4402903644