New Technologies Open New Career Opportunities
“One of the paradigm shifts I see is that it’s now possible to generate data faster than you can analyze it as an individual,” says Errol Strain, the Director of the Biostatistics and Bioinformatics Staff in the Office of Analytics and Outreach at the FDA Center for Food Safety and Applied Nutrition. He has worked closely with Eric Brown, Director of the Division of Microbiology in the Office of Regulatory Science, to introduce microbial genomics to the FDA. The FDA now applies whole-genome sequencing (WGS) to many microbial isolates, which means that each experiment generates large amounts of data that must be analyzed for nucleotide-level differences to pinpoint contamination sources.
The increasing applications of sequencing technologies have led to the development of new job titles, descriptions, and skill sets required for microbiologists on their team at the FDA. Strong bench skills such as sterile technique remain imperative for accurate microbial identification, but one must also master computer-based skills like programming and knowledge of statistical software. No longer are biochemical or genetic assays the basis of most of their microbial investigations; in the future, he envisions “microbiologists will be working at the computer, based on genomics,” says Brown.
No scientist works in isolation, and this is especially true in large facilities like the FDA. Teams of experts with specialties in different areas work together to solve a common problem, with teams consisting of both basic lab technicians and large data set analysts, so no one member is expected to know everything. But to build a bridge between the bench and the computer, microbiology students will need to gain at least a basic familiarity with genomics and bioinformatics tools. This basic understanding allows microbiologists to determine when to perform the initial bioinformatics analysis and when to turn to collaborators for help with complex or voluminous data sets.
Classical microbiology training will continue to be the cornerstone of a career in microbial genomics. “Remember, genomics provides tools,” says Brown, “and it’s still going to take very skilled microbiologists to know how and when to apply those tools appropriately to get the job done.” The large amount of information WGS provides for each isolate means a strong grounding in pathogenesis, genetics, and biochemistry is still necessary to channel the information through the right path to answer the right questions.
Those with interests other than microbial surveillance will also apply the wealth of information provided by the thousands of genomes publicly available in databases such as GenomeTrakr. For example, virulence determinant sequences can be tracked and traced back to their origin, including transfers between species. Large datasets can be hypothesis generators, too: by pulling information about metabolism genes from genomes of clinical isolates, scientists can predict the importance of particular pathways in pathogenesis, which can then be tested using standard genetic methods.
The culmination of new computer-based skills in microbiology is the creation of new opportunities. At the FDA, Maria Hoffman was recently hired for the newly created position of Research Microbial Genomicist. Her training in both genomic data analysis and food microbiology made her a natural fit for the FDA. Says Brown: “The educational background that fuses these two fields is going to be absolutely critical for any up-and-coming microbiologist.”
“These are the types of positions we’re going to be going after in the future.” Microbiologists in training, take note.