RESEARCH SPOTLIGHT: IDing of food spoilage organisms for dairy manufacturers
This research spotlight highlights the work that Lab Technician Tim DeMarsh is doing to help prevent spoilage microbes from causing issues in the dairy industry. Contamination with spoilage microbes can result in food waste and loss of revenue for dairy producers. Remediating spoilage issues can be difficult, especially when producers don’t know which microbe is responsible. It’s much easier to create solutions when manufacturers can specifically target the organism that is causing the problem. Producers can send their contaminated food samples to the Alcaine Research Group where Tim identifies the offending species. Using this information, the manufacturer can develop strategies to mitigate this specific species and prevent future instances of spoilage.
To identify the organism, it must first be isolated from the food sample. The microbe is grown up on a petri dish for isolation and then its cells are split open, exposing its DNA for extraction. Tim then uses a technique called Polymerase Chain Reaction (a.k.a. PCR; the same process used for COVID-19 tests!) to make billions of copies of the organism’s DNA. The PCR product is loaded into an agarose gel, a scientific version of your favorite Jell-O dessert. Then, the gel is exposed to an electrical field. Since DNA is a negatively charged molecule, it migrates through the gel to the positively charged side, creating bands of DNA.
To make these bands really stand out, the gel is stained with ethidium bromide, a chemical that binds to DNA and fluoresces under UV light. When the gel is exposed to UV light, colorful bands of DNA aggregates are visible, verifying that Tim’s PCR process was successful. He now has billions of copies of the pesky spoilage microbe’s DNA! The DNA is purified and sent to another lab at Cornell that sequences the DNA for him, creating a genetic fingerprint for the organism.
When Tim receives the DNA sequence data, it must be cleaned up a little, and then he compares the sequence to an NCBI database that contains over 1.3 billion unique DNA sequences. The database identifies close matches to the DNA sequence and provides names of organisms that are similar. If the fidelity of the match is 99% or higher, he can be relatively confident that his organism matches the organism in the database, and he has found the name of the species causing the spoilage issues!
The name of the microbe is then given to the dairy processor, and they can create a targeted approach to remediating the issue. This service provided by the Alcaine Research Group helps manufacturers ensure that they are producing high-quality, spoilage free products that consumers everywhere will enjoy!
Agarose Gel 
The group cleaning up the DNA sequence Sequence in the database