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mSystems. 2019 Oct 8;4(5). pii: e00392-19. doi: 10.1128/mSystems.00392-19.

Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019.

Author information

1
Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA.
2
Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA.
3
Molecular and Comparative Pathobiology, Johns Hopkins University, Baltimore, Maryland, USA.
4
Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, Maryland, USA.
5
Department of Population Health and Pathobiology, North Carolina State University, Raleigh, North Carolina, USA.
6
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.
7
American Society for Engineering Education, Washington, DC, USA.
8
Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
9
University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, Maryland, USA.
10
Department of Computer Science, George Mason University, Fairfax, Virginia, USA.
11
Department of Ecology and Evolutionary Biology, Yale University, New Haven Connecticut, USA.
12
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA.
13
Department of Civil and Environmental Engineering, Howard University, Washington, DC, USA.
14
Center for Conservation Genomics, Smithsonian National Zoological Park & Conservation Biology Institute, Washington, DC, USA.
15
Department of Pathology and Laboratory Medicine, University of Pennsylvania and Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.
16
School of Public Health, University of Maryland, College Park, Maryland, USA.
17
Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA.
18
Department of Biology, Morgan State University, Baltimore, Maryland, USA.
19
National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA.
20
University of Maryland School of Nursing, Baltimore, Maryland, USA.
21
Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA jdiruggiero@jhu.edu sprehei1@jhu.edu.
22
Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA jdiruggiero@jhu.edu sprehei1@jhu.edu.
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Contributed equally

Abstract

Accurate predictions across multiple fields of microbiome research have far-reaching benefits to society, but there are few widely accepted quantitative tools to make accurate predictions about microbial communities and their functions. More discussion is needed about the current state of microbiome analysis and the tools required to overcome the hurdles preventing development and implementation of predictive analyses. We summarize the ideas generated by participants of the Mid-Atlantic Microbiome Meet-up in January 2019. While it was clear from the presentations that most fields have advanced beyond simple associative and descriptive analyses, most fields lack essential elements needed for the development and application of accurate microbiome predictions. Participants stressed the need for standardization, reproducibility, and accessibility of quantitative tools as key to advancing predictions in microbiome analysis. We highlight hurdles that participants identified and propose directions for future efforts that will advance the use of prediction in microbiome research.

KEYWORDS:

bioinformatics; conceptual models; machine learning; metagenomics; microbiome; prediction; quantitative models

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