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 - Funding Information:
We would like to thank all those who helped make this meeting a success, especially Barbara Lewis (UMD) who organized the administrative aspects of the program, and CosmosID, Inc. for funding the event. We would also like to thank Dr. Jayne Morrow and Dr. Robert Hanisch for providing helpful feedback on the manuscript. Opinions expressed in this paper are the authors’ and do not necessarily reflect the policies and views of NIST or affiliated venues. Certain commercial equipment, instruments, or materials are identified in this paper in order to specify the experimental procedure adequately. Such identification is not intended to imply recommendations or endorsement by NIST nor is it intended to imply that the materials or equipment identified are necessarily the best available for the purpose. Official contribution of NIST; not subject to copyrights in the USA.
Funding Information:
The meeting was supported in part by the Center for Health-related Informatics and Bioimaging, a Center organized under the MPowering the State Partnership between the University of Maryland Baltimore and College Park campuses. JSM, BB, VCE, MF, JG, KJ, NS, and MP were supported in part by grants to MP, including grant R01-AI-100947 from the NIH and grant IIS-1513615 from the NSF. DJN and TJT were supported in part by the FunGCAT program from the Office of the Director of National Intelligence (ODNI), Intelligence Advanced Research Projects Activity (IARPA), via the Army Research Office (ARO) under Federal Award No. W911NF-17-2-0089. HC was supported by the NIH, R01 grant GM114267. The views and conclusions contained herein are those of the authors and should not be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of the ODNI, IARPA, ARO, or the US Government. The contributions of ALB, NHB, MJR, DDS, and SR were funded under Contract No. HSHQDC-15-C-00064 awarded by the Department of Homeland Security (DHS) Science and Technology Directorate (S&T) for the operation and management of the National Biodefense Analysis and Countermeasures Center (NBACC), a Federally Funded Research and Development Center. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the DHS or S&T. In no event shall DHS, NBACC, S&T, or Battelle National Biodefense Institute have any responsibility or liability for any use, misuse, inability to use, or reliance upon the information contained herein. DHS does not endorse any products or commercial services mentioned in this publication. JGC was supported in part by the National Cancer Institute of the National Institutes of Health under the awards for the Partnership of Native American Cancer Prevention U54CA143924 (UACC) and U54CA143925 (NAU) and by the National Science Foundation award 1565100. SC was supported by NIH Intramural Research. JD and GU were supported in part by the NSF, grant DEB1556574 to JD. BDO was supported by the Intramural Research Program of the National Human Genome Research Institute and National Institutes of Health and utilized the computational resources of the NIH HPC Biowulf cluster (https://hpc.nih.gov).
Funding Information:
The conference was partly supported through funding from CosmosID, Inc. The sponsor did not participate in the organization of the event or the selection of speakers and topics.
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
VL - 6
JO - Microbiome
JF - Microbiome
SN - 2049-2618
IS - 1
M1 - 197
ER -