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Biotechnology Program (BIT)

What Will Eat Your Carbon Source? Bioprospecting with Dr. Crook

April 17, 2025

What is one thing in common between products such as pharmaceuticals, cosmetics, and agricultural chemicals like pesticides and fertilizers? They are often developed through a biotechnology technique known as bioprospecting. Bioprospecting allows scientists and researchers to understand microbial metabolism and use it to synthesize valuable products from nature. How does understanding microbial metabolism help us achieve such developments?

For his postdoctoral fellowship, Dr. Nathan Crook joined the Dantas Lab at Washington University in St. Louis. In the Dantas Lab, he researched antibiotic resistance genes, their impact on the gut microbiome, and how to minimize resistance. In January 2018, Dr. Crook joined the Department of Chemical and Biomolecular Engineering at NC State as an assistant professor and ended up opening the Crook Lab. The Crook Lab focuses on applying genetic engineering techniques to help discover new biological phenomena and develop technologies to help convert food into energy, nutrients, and therapeutics with the help of the human gut microbiota. In 2023, Dr. Crook received the prestigious NSF CAREER Award, through which he decided to develop his new course on bioprospecting. 

“I want to use this technique in my lab to discover new proteins myself and decided that the best way to learn something is to teach a course about it.”
Dr. Nathan Crook
Students in Dr. Crook’s class working in teams of two to find microbes consuming their carbon source.
Students in Dr. Crook’s class working in teams of two to find microbes consuming their carbon source.

The course structure follows the students bringing in their own sample of microbes, which is “usually soil but is not limited to that, it could be mud under a lake, biofilm growing on a dumpster, or just anything that is likely to not contain pathogens.” After settling on their sample, students extract all the DNA and then chop them up into small fragments, usually about four kilobases in size each. In one instance where one soil sample had a high clay content that made it difficult for the student to extract the DNA, Dr. Crook provided an alternative sample that the student could work on. Once the DNA has been cleaved into small fragments, they are placed in a bacterial expression vector. The gene-containing DNA fragments are then inserted into the host Escherichia coli, commonly known as E. coli, provided by Dr. Crook to create a genomic library. Students then look for a carbon source that E. coli can’t normally metabolize, such as sucrose and cellobiose. After identifying a carbon source, students plate their microbes on it and observe whether a new colony forms, indicating presence of a gene that allows the E. coli to eat the carbon source that it originally wasn’t able to. Sequencing and annotating the colony in an in silico lab then allows them to identify where the gene is and why it allows the E. coli to eat the carbon source. Nearing the end of the course, students are able to present their findings to each other.

Students presenting their findings to the class.
Students presenting their findings to the class.
“Bioprospecting is like peering into the unknown and seeing what we find.”
Dr. Nathan Crook

Through this course, Dr. Crook hopes that students develop a “better appreciation and understanding of microbial metabolism in microbiomes.” Spring 2025 marked a successful first semester of BIT 495/595 Special Topics in Microbial Prospecting, with future offerings in following spring semesters. Make sure to leave room in your shopping cart for Spring 2026 to see what genes you can find!