Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: Report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018

Jacquelyn S. Meisel, Daniel J. Nasko, Brian Brubach, Victoria Cepeda-Espinoza, Jessica Chopyk, Héctor Corrada-Bravo, Marcus Fedarko, Jay Ghurye, Kiran Javkar, Nathan D. Olson, Nidhi Shah, Sarah M. Allard, Adam L. Bazinet, Nicholas H. Bergman, Alexis Brown, James G Caporaso, Sean Conlan, Jocelyne Diruggiero, Samuel P. Forry, Nur A. HasanJason Kralj, Paul M. Luethy, Donald K. Milton, Brian D. Ondov, Sarah Preheim, Shashikala Ratnayake, Stephanie M. Rogers, M. J. Rosovitz, Eric G. Sakowski, Nils Oliver Schliebs, Daniel D. Sommer, Krista L. Ternus, Gherman Uritskiy, Sean X. Zhang, Mihai Pop, Todd J. Treangen

Research output: Contribution to journalArticle

1 Scopus citations

Abstract

The Mid-Atlantic Microbiome Meet-up (M 3 ) organization brings together academic, government, and industry groups to share ideas and develop best practices for microbiome research. In January of 2018, M 3 held its fourth meeting, which focused on recent advances in biodefense, specifically those relating to infectious disease, and the use of metagenomic methods for pathogen detection. Presentations highlighted the utility of next-generation sequencing technologies for identifying and tracking microbial community members across space and time. However, they also stressed the current limitations of genomic approaches for biodefense, including insufficient sensitivity to detect low-abundance pathogens and the inability to quantify viable organisms. Participants discussed ways in which the community can improve software usability and shared new computational tools for metagenomic processing, assembly, annotation, and visualization. Looking to the future, they identified the need for better bioinformatics toolkits for longitudinal analyses, improved sample processing approaches for characterizing viruses and fungi, and more consistent maintenance of database resources. Finally, they addressed the necessity of improving data standards to incentivize data sharing. Here, we summarize the presentations and discussions from the meeting, identifying the areas where microbiome analyses have improved our ability to detect and manage biological threats and infectious disease, as well as gaps of knowledge in the field that require future funding and focus.

Original languageEnglish (US)
Article number197
JournalMicrobiome
Volume6
Issue number1
DOIs
StatePublished - Nov 5 2018

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Keywords

  • Biodefense
  • Bioinformatics
  • Biothreats
  • Longitudinal analysis
  • Metagenomics
  • Microbiome
  • Pathogen detection

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)

Cite this

Meisel, J. S., Nasko, D. J., Brubach, B., Cepeda-Espinoza, V., Chopyk, J., Corrada-Bravo, H., Fedarko, M., Ghurye, J., Javkar, K., Olson, N. D., Shah, N., Allard, S. M., Bazinet, A. L., Bergman, N. H., Brown, A., Caporaso, J. G., Conlan, S., Diruggiero, J., Forry, S. P., ... Treangen, T. J. (2018). Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: Report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018. Microbiome, 6(1), [197]. https://doi.org/10.1186/s40168-018-0582-5