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Microbiome. 2018 Nov 5;6(1):197. doi: 10.1186/s40168-018-0582-5.

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.

Author information

1
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA.
2
School of Public Health, University of Maryland, College Park, College Park, MD, USA.
3
Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
4
National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA.
5
Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
6
The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
7
National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
8
Department of Biology, Johns Hopkins University, Baltimore, MD, USA.
9
CosmosID, Inc., Rockville, MD, USA.
10
Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA.
11
Maryland Institute for Applied Environmental Health, School of Public Health, University of Maryland, College Park, College Park, MD, USA.
12
Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD, USA.
13
B.Next, In-Q-Tel, Inc., Arlington, VA, USA.
14
Department of Computer Science, University of Tübingen, Tübingen, Germany.
15
Signature Science, LLC, Arlington, VA, USA.
16
Division of Medical Microbiology, Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
17
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA. treangen@rice.edu.
18
Present address: Department of Computer Science - MS-132, Rice University, P.O. Box 1892, Houston, TX, 77005-1892, USA. treangen@rice.edu.

Abstract

The Mid-Atlantic Microbiome Meet-up (M3) organization brings together academic, government, and industry groups to share ideas and develop best practices for microbiome research. In January of 2018, M3 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.

KEYWORDS:

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

PMID:
30396371
PMCID:
PMC6219074
DOI:
10.1186/s40168-018-0582-5
[Indexed for MEDLINE]
Free PMC Article

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