Imagine this: You are standing at the precipice of the Grand Canyon, a vast landscape teeming with rock formations, water features, and desert plants and animals. Instead of taking in the entire view, however, you are forced to look at it through the opening of a drinking straw.

You can view any small part of the landscape, such as a single tree, or rock, or lizard—just not at the same time. Squinting through the small opening, it becomes apparent to you that what could have been a sweeping gaze across an amazing vista has become a long and tedious undertaking.

In the past, this was the scenario for genomic scientists. Instead of being able to view a whole cell and all of its features, they could only view a small part at one time. Utah State University researcher Bart Weimer is working to make the “big picture” that will enable scientists to view an entire cell all at once.

The science of creating a cell’s big picture is called metabolomics, or functional genomics. Instead of just looking at and decoding a few cell genes, functional genomics strives to create an overall view of how all genes affect the functions that occur in a cell, including regulatory networks, biochemical pathways, and protein-protein interactions.

“The goal of genomics at USU is to engineer good organisms to have broader uses towards improving our quality of life,” says Weimer, professor in the Department of Nutrition and Food Sciences, Director of the Center for Microbe Detection & Physiology, and Director of the Center for Integrated BioSystems. “Our aim is to understand how different organisms express specific genes in a variety of situations. Genomics impacts many fields and industries, including agriculture, nutrition, and medicine.”

Weimer is using genomics to study the millions and millions of microbes that exist in food and the environment. Not only will this big-picture research help food manufacturers create better-tasting, longer-lasting food, but it will also provide knowledge needed to make food safer from threats, ranging from simple food poisoning to large-scale contamination.

Looking at an organism’s entire genetic structure takes a huge amount of computing power. Weimer and his colleagues have designed their own computer programs to design gene expression arrays for analysis of the full genome of two bacteria, which allows them to study a cell’s entire gene expression and regulation in a variety of environments—with changes in temperature, moisture, and pH—and manipulate how the cells react in those environments. Production of microbial genomes also require computing power that is beginning to be harnessed for the over 1500 finished microbial genomes.

For the past three years, Weimer has been working with the Lactic Acid Bacteria Genome Consortium to complete the genome sequencing of 11 lactic acid bacteria and other microbes that are used in the production of dairy products and fermented food, which is the basis for building arrays. The team has just finished closing these 11 genomes and now can examine how genes are regulated for growth, production of chemicals, and production of flavors.

“Understanding and predicting how cells respond to changes in the environment aids food scientists in being able to control the response in order to enhance flavor, consistency, and safety in food,” says Weimer.

Weimer is also using a specialized field of functional genomics, called proteomics, which studies a cell’s proteins to determine how cells will respond to changes in the environment. Using a method called two-dimensional gel electrophoresis, Weimer separates the proteins in a cell at a specific point in their growth. These proteomic studies are helping scientists manipulate what bacteria can survive in food and how long food can be stored.

“We’re looking at the bacteria’s genetic structure to figure out how we can make products like Cheddar cheese taste better,” says Weimer. “Better-tasting cheese is a huge economic impact of our research, especially in a state like Utah, which has a strong dairy industry.”

In addition to using genomics to study what he calls “good bugs,” Weimer is using metabolomics and proteomics to understand the “bad bugs,” or dangerous microbes in food that can make people sick, such as E. coli, Listeria, Bacillus, and Salmonella.

Weimer and his colleague Marie Walsh, associate professor in the Department of Nutrition and Food Sciences, established the Center for Rapid Microbe Detection and Physiology, which creates technology that can quickly detect pathogens in food.

“The Center began as a response to the dairy industry’s need to remove antibiotics in milk,” says Weimer. “We now have four technologies that capture and concentrate bacteria for subsequent detection; some of them are very large-scale, and others are made to be able to sit on a bench or table.”

In the past, running microbial tests on food could take as long as a couple of days, says Weimer. Detectors being developed by the Center can identify microbial threats in as little as 15 minutes, and can be adjusted to test water and soil, not just food.

“To date, the Center has licensed technology for use in the food industry, acquired patents and is continually working to provide biotechnology solutions,” says Weimer.

Two of those technologies developed by the center is ImmunoFlow and GlycoBind, which has many uses, ranging from water to food, and has the potential to detect many types of bacteria in less than 30 minutes, even if less than 100 dangerous cells are in the entire sample.

“It’s so important for us to be able to look at a whole cell or a whole microbe and get the big picture,” says Weimer. “That’s the best way for us to really learn about how we can use microbes to improve our lives.”

- Rachel von Niederhausern and Anna McEntire