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.

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PubMed ID: 30396371

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Meisel JS, Nasko DJ, Brubach B, Cepeda-Espinoza V, Chopyk J, Corrada-Bravo H, Fedarko M, Ghurye J, Javkar K, Olson ND, Shah N, Allard SM, Bazinet AL, Bergman NH, Brown A, Caporaso JG, Conlan S, DiRuggiero J, Forry SP, Hasan NA, Kralj J, Luethy PM, Milton DK, Ondov BD, Preheim S, Ratnayake S, Rogers SM, Rosovitz MJ, Sakowski EG, Schliebs NO, Sommer DD, Ternus KL, Uritskiy G, Zhang SX, Pop M, Treangen TJ

Microbiome. Nov 2018. doi: 10.1186/s40168-018-0582-5

COMMENT: In January of 2018, The Mid-Atlantic Microbiome Meet-up had their fourth meeting. The meeting was about recent advances in biodefense, focused on infectious disease and metagenomic methods for pathogen detection.

They discussed how the community could improve the existing biological and computational technologies and also how to manage the obtained and existing information, like datasets that are subject to privacy regulations. As well, it is essential to define quality data standards for genomic datasets.

Next-generation sequencing (NGS) technologies have contributed to the advance in biodefense research although it is necessary to improve the speed, accuracy, precision, sensitivity, and cost of the analysis. It is also necessary to conduct more microbiome studies focus on viral, fungal and eukaryotic organisms due to their important role in pathogenesis.

Scientists must evaluate if they are using the best method of analysis to address their specific problem. Another aspect that was treated was the importance of creating user-friendly and adaptable resources with complete, clear and comprehensive documentation. 

Open-source software for sequence processing and quality control, taxonomic annotation, metagenomic assembly, and binning, and data visualization have been essential for growth. Continued development of these resources will result in significant scientific advances

The participants also remarked about the importance of careful evaluation and interpretation of results to prevent panic and execute appropriate plans of action.

Because the version of software and databases used can significantly affect the findings, this information should be reported more consistently in the literature. 


Carmen Martín