mSystems (Oct 2019)
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
- Eric Sakowski,
- Gherman Uritskiy,
- Rachel Cooper,
- Maya Gomes,
- Michael R. McLaren,
- Jacquelyn S. Meisel,
- Rebecca L. Mickol,
- C. David Mintz,
- Emmanuel F. Mongodin,
- Mihai Pop,
- Mohammad Arifur Rahman,
- Alvaro Sanchez,
- Winston Timp,
- Jeseth Delgado Vela,
- Carly Muletz Wolz,
- Joseph P. Zackular,
- Jessica Chopyk,
- Seth Commichaux,
- Meghan Davis,
- Douglas Dluzen,
- Sukirth M. Ganesan,
- Muyideen Haruna,
- Dan Nasko,
- Mary J. Regan,
- Saul Sarria,
- Nidhi Shah,
- Brook Stacy,
- Dylan Taylor,
- Jocelyne DiRuggiero,
- Sarah P. Preheim
Affiliations
- Eric Sakowski
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
- Gherman Uritskiy
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
- Rachel Cooper
- Molecular and Comparative Pathobiology, Johns Hopkins University, Baltimore, Maryland, USA
- Maya Gomes
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, Maryland, USA
- Michael R. McLaren
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, North Carolina, USA
- Jacquelyn S. Meisel
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
- Rebecca L. Mickol
- American Society for Engineering Education, Washington, DC, USA
- C. David Mintz
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Emmanuel F. Mongodin
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, Maryland, USA
- Mihai Pop
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
- Mohammad Arifur Rahman
- Department of Computer Science, George Mason University, Fairfax, Virginia, USA
- Alvaro Sanchez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven Connecticut, USA
- Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
- Jeseth Delgado Vela
- Department of Civil and Environmental Engineering, Howard University, Washington, DC, USA
- Carly Muletz Wolz
- Center for Conservation Genomics, Smithsonian National Zoological Park & Conservation Biology Institute, Washington, DC, USA
- Joseph P. Zackular
- Department of Pathology and Laboratory Medicine, University of Pennsylvania and Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Jessica Chopyk
- School of Public Health, University of Maryland, College Park, Maryland, USA
- Seth Commichaux
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
- Meghan Davis
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Douglas Dluzen
- Department of Biology, Morgan State University, Baltimore, Maryland, USA
- Sukirth M. Ganesan
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
- Muyideen Haruna
- Department of Biology, Morgan State University, Baltimore, Maryland, USA
- Dan Nasko
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
- Mary J. Regan
- University of Maryland School of Nursing, Baltimore, Maryland, USA
- Saul Sarria
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
- Nidhi Shah
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
- Brook Stacy
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
- Dylan Taylor
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
- Jocelyne DiRuggiero
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
- Sarah P. Preheim
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
- DOI
- https://doi.org/10.1128/mSystems.00392-19
- Journal volume & issue
-
Vol. 4,
no. 5
Abstract
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
