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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:;;

Project Start Date:


Project End Date:


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 such as antimicrobial resistance genes present within the microbes themselves. To accomplish this we will combine sophisticated computational methods (e.g.  machine learning) with more next-generation sequencing, 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) and can we identify the specific location from which such contamination is originating? Do we identify antimicrobial resistance genes in E. coli that are living in the watershed? 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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