In 2001, Allen-Vercoe moved to Canada, where she joined the University of Calgary. Allen-Vercoe worked on Escherichia coli. In 2004, she was awarded a Canadian Association of Gastroenterology Fellow-to-Faculty Transition Award.[1][2] She moved to the University of Guelph in 2007.[1] Her research considers the gut microbiome.[3][4] She worked with the biotechnology company Infors to create a bioreactor that can maintain biological samples in specific anaerobic atmospheres whilst her research team studying the constituents microbes.[4]
Allen-Vercoe isolates bacteria from human stool samples, places them in the so-called robo-gut and monitors their behaviour in precise conditions.[5][6] For example, the robo-gut (or mechanical colon) can recreate environments that allow for particular genes and bacteria to thrive, which allows Allen-Vercoe to study the microbiobes associated with certain medical conditions.[4][7] Allen-Vercoe has identified the general bacteria that exist in all microbiomes, as well as monitoring the microbiome's metabolomics.[8] She has worked on microbial therapeutics to treat various diseases, including Clostridioides difficile infection and cancer.[9][10]
Allen-Vercoe launched the NuBiyota in 2013, a biotechnology company that looks to grow microbes in a controlled environment.[11] She was awarded a Tier 1 Canada Research Chair in 2019, which allowed her to study the influence of the gut microbiome on health and disease.[12]