Feature Stories

Food Safety

Researching the genomics and community ecology of bacteria
  • Image of DNA sequencing green, red and blue
Biochemistry major Johan Einson is characterzing microbial communities to predict outcomes such as pathogenic risk.
Identifying and understanding interactions of environmental bacteria in food facilities is critically important for food safety. Utilizing cutting-edge DNA sequencing technologies, UMass Amherst undergraduate Jonah Einson–a rising biochemistry major–is working to expand this knowledge base.

Einson has been awarded an undergraduate summer research fellowship from the American Society for Microbiology (ASM) to study and identify environmental bacteria in food processing facilities.

Einson is planning procedures to identify bacteria found at a local fermented-foods processing facility. His goal is to study the community ecology of bacteria that inhabit the plant, and to characterize their working relationships. He is conducting his research project using cutting-edge DNA sequencing and data processing technology.

“In a food processing plant like this, you should have a good understanding of the bacteria, first for pathogenic safety and second to classify the ones responsible for vegetable fermentation,” Einson explains.

"Sometimes the plant has batches that don't ferment, and we would like to gather quantitative evidence as to why. At the facility being studied, live cultures are not added to the vegetables that are to be fermented. The bacteria that naturally inhabit the skins do it sufficiently under controlled conditions, given that the proper microbes are present. Few studies have really taken the care and time to study this ancient process using modern technology in a real-world setting.”

Einson draws upon microbiology, biochemistry, ecology and computer science in the research project, which relies heavily on computational programming and next-generation DNA sequencing. Einson is calibrating his methods and equipment to make sure the sample collection techniques for both facility and vegetable surfaces can be done efficiently without contamination.

UMass Amherst food microbiologist David Sela–Einson’s faculty advisor–explains that Einson is studying the microbial ecology of various systems including animal experimental models and the microbiology of the built environment, for which he was awarded the fellowship.

Sela, who was awarded the same ASM fellowship in 2001, says, “Opportunities to do undergraduate research really propelled me forward. This is a tremendous program to help young scientists cement their scientific training.”

“Specifically, under my mentorship Jonah will characterize the microbial communities that are established on various surfaces of food production facilities and attempt to predict outcomes such as pathogenic risk. This is a rich cross-disciplinary training,” says Sela.

Based on this work, Einson will also present a poster at the ASM general meeting in Boston in summer 2016, which is an important conference in microbiology, Sela adds.

At the plant, Einson will collect bacterial samples using cotton swabs, from which he will extract DNA. He will then sequence the DNA using an instrument that can process millions of base pairs in a single run. These data will then help him to identify what genus and sometimes species of bacteria are present. The faster speed and lower cost of DNA sequencing in recent years has opened the door to these types of studies, he points out.

“In a previous experiment we detected 100 different taxa of bacteria at varying concentrations from a single sample. With older, culture-based approaches this would not have been possible,” Einson says. Einson is on target tp receive his B.S. degree from UMass Amherst in spring 2017 and is considering graduate research work in the growing field of bioinformatics. 

UMass Amherst News Office