TY - JOUR
T1 - Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection
T2 - Report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018
AU - Meisel, Jacquelyn S.
AU - Nasko, Daniel J.
AU - Brubach, Brian
AU - Cepeda-Espinoza, Victoria
AU - Chopyk, Jessica
AU - Corrada-Bravo, Héctor
AU - Fedarko, Marcus
AU - Ghurye, Jay
AU - Javkar, Kiran
AU - Olson, Nathan D.
AU - Shah, Nidhi
AU - Allard, Sarah M.
AU - Bazinet, Adam L.
AU - Bergman, Nicholas H.
AU - Brown, Alexis
AU - Caporaso, J. Gregory
AU - Conlan, Sean
AU - Diruggiero, Jocelyne
AU - Forry, Samuel P.
AU - Hasan, Nur A.
AU - Kralj, Jason
AU - Luethy, Paul M.
AU - Milton, Donald K.
AU - Ondov, Brian D.
AU - Preheim, Sarah
AU - Ratnayake, Shashikala
AU - Rogers, Stephanie M.
AU - Rosovitz, M. J.
AU - Sakowski, Eric G.
AU - Schliebs, Nils Oliver
AU - Sommer, Daniel D.
AU - Ternus, Krista L.
AU - Uritskiy, Gherman
AU - Zhang, Sean X.
AU - Pop, Mihai
AU - Treangen, Todd J.
N1 - Publisher Copyright:
© 2018 The Author(s).
PY - 2018/11/5
Y1 - 2018/11/5
N2 - 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.
AB - 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.
KW - Biodefense
KW - Bioinformatics
KW - Biothreats
KW - Longitudinal analysis
KW - Metagenomics
KW - Microbiome
KW - Pathogen detection
UR - http://www.scopus.com/inward/record.url?scp=85056099496&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85056099496&partnerID=8YFLogxK
U2 - 10.1186/s40168-018-0582-5
DO - 10.1186/s40168-018-0582-5
M3 - Article
C2 - 30396371
AN - SCOPUS:85056099496
SN - 2049-2618
VL - 6
JO - Microbiome
JF - Microbiome
IS - 1
M1 - 197
ER -