General Microbiology Laboratory: Adaptation of E. coli to Non Host-Associated Environments

Project Location

This research experience is embedded in a semester long project in a general microbiology laboratory for undergraduates. It is designed to meet the American Society for Microbiology guidelines for introductory labs while addressing the open question of whether environmental isolates of Escherichia exhibit characteristics consistent with adaption to a non-host assocatied environment.

Student Audience

Advanced, Major

Scientific Domain

  • Bioinformatics/Computational biology
  • Environmental science
  • Evolution
  • Genetics/Genomics
  • Microbiology

Nature of the Research

  • Wet lab/bench research
  • Informatics/computational research
  • Basic research

Core Concepts

  • Evolution: The diversity of life evolved over time by process of mutation, selection, and genetic change.
  • Structure and Function: Basic units of structure define the function of all living things.
  • Information Flow and Exchange: The growth and behavior of organisms are activated through the expression of genetic information in context.
  • Pathways and Transformation of Energy: Biological systems grow and change by processes based on chemical transformation pathways and are governed by the laws of thermodynamics.
  • Systems: Living systems are interconnected and interacting.

Core Competencies

  • Applying the process of science
  • Using quantitative reasoning
  • Tapping into the interdisciplinary nature of science
  • Communicating and collaborating
  • Understanding the relationship between science and society

Guiding Questions

  • What are the levels of presumptive E. coli found in different parts of a watershed over time?
  • Is there evidence for environmental adaptation of E. coli strains to non host-associated environments at both physiological and genetic levels?
  • Are there correlations between physiological characteristics and genotype (e.g., antibiotic resistance patterns and genes present in the genome)?
  • What are the phylogenetic relationships of watershed strains to each other and laboratory, commensal, and pathogenic strains of E. coli?

Learning Objectives

  • Relate fundamental concepts in the discipline of microbiology, including basic and applied aspects of microbiology, to experimental techniques and observation
  • Become exposed to and proficient in basic and advanced experimental methods used in the field of microbiology
  • Engage in experimental design, implementation, data analysis and interpretation of microbiology research questions
  • Come to appreciate the impact of microbes upon our daily lives
  • Explore the future of microbiology as a scientific field of inquiry and application


This project is a full redesign of an existing general microbiology laboratory for undergraduate biology majors. Typically, junior or senior level students are in the course, although sophomore level courses could employ this approach. The redesign incorporates an authentic research project that spans the entirety of the semester. The research focuses on characterizing microbial populations of fecal indicator bacteria (FIB) in the Macatawa Watershed, specifically E. coli isolates; the levels of FIB are often used by local, state and federal agencies to make decisions about the safety and accessibility of recreational waters. The research gives students the opportunity to consider open scientific questions with relevance to the local community, learn standard microbiological concepts and techniques recommended by the American Society of Microbiology (ASM) guidelines for undergraduate microbiology courses, and introduces modern microbial genomics and comparative analyses into the course. Students design and perform a series of physiological experiments on different strains, draft genome sequences are produced, and students analyze genome sequence data in context with physiological experiment results.

Getting Started

Much of the laboratory can be conducted using standard general microbiology lab materials and supplies. Additional supplies include water filtration equipment, mTEC agar, genomic DNA isolation kits, genome sequencing materials/facility (can be sent out for sequencing), and web based genome analysis tools. 


1-2 hours per class period

Member Contact

Class time

2-4 hours per week