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Computational and biochemical analysis of Lake Mac microbes

Project Full Title:

Computational and biochemical analysis of microbial sources within the Lake Macatawa watershed

Project Mentor(s):

Best,Aaron; Krueger,Brent; Pikaart,Michael

Project Mentor(s) EMail:

best@hope.edu; kruegerb@hope.edu; pikaart@hope.edu

Project Start Date:

5/13/2020

Project End Date:

7/24/2020

Project Description:

This project blends computer science, math, biology, and chemistry. Our research efforts have resulted in the compilation of a large multi-year dataset that includes DNA sequences for many thousands of microbes, as well as individually isolated E. coli strains, from hundreds of samples acquired under a variety of environmental conditions. We hope to understand how the variation in the different microbial species that are present and their relative abundance depends on environmental conditions and other factors. To accomplish this we will combine sophisticated computational methods (e.g.  machine learning) with more traditional PCR and biochemical analyses. Using these tools, we are posing several questions: If we find evidence of fecal contamination, can we tell whether that contamination is from humans versus nonhuman origin (domestic or wildlife)?  Can we identify the specific location from which such contamination is originating? We anticipate that identifying and predicting possible sources of contamination in the watershed will serve as a means to understand risk and aid in remediation of potentially harmful microbial contamination. Students are likely to focus on either biochemical or computational methods, though it is possible for a student to work in both areas if they desire.

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