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We Are Not Alone

The Unseen World of the Human Microbiome

By Joan-Beth Gow

We Are Not Alone



This interrupted case study for the flipped classroom introduces the human microbiome from the perspective of one of its occupants, Heidi Helicobacter (Helicobacter pylori).  Heidi lives in the gut of Kristen, a college student, and discusses her fellow microbial inhabitants, functions of these various microbes, and alludes to factors that can disrupt the healthy human microbiome. Students prepare for class by viewing several brief videos and then discuss in class whether Kristen should undergo a fecal microbiota transplant to treat her Clostridium difficile infection.  A lab component has students model, using colored beads, how antibiotics can act as a selective agent for drug-resistant microbes such as C. difficile. The case concludes with Kristen about to give birth to a new baby several years later.  Students listen in as Kristen's microbes discuss the formation of the new baby's microbiome. The case has been used successfully in a general biology class and could easily be adapted for a microbiology, human physiology, ecology, or evolution course.


Date Posted




  • Define the term microbiome and provide examples of the types of microorganisms that comprise it.
  • Differentiate prokaryotic organisms, eukaryotic organisms, and viruses, and describe typical features of each.
  • Describe the complex relationship of humans with their microbes using Helicobacter pylori as an example.
  • Enumerate factors that determine the makeup of the microbiome.
  • Summarize the rationale for using fecal transplant as a treatment for Clostridium difficile infection (C. diff; CDI) and evaluate its potential effectiveness for treatment of other conditions.
  • Define the term dysbiosis and perform a simulation to model how overuse or misuse of antibiotics can lead to disease.
  • Cite specific examples of the role of the human microbiome in health and disease.


CDI; Clostridium difficile; C. difficile; Helicobacter pylori; antibiotic resistance; normal microbiota; fecal microbiota transplant; FMT; Human Microbiome project; virome; prokaryote; eukaryote; archaea; dysbiosis


Subject Headings

Biology (General)
Medicine (General)
Science (General)


High school, Undergraduate lower division, Undergraduate upper division












N/A, Directed, Flipped, Interrupted, Laboratory



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