Skip to Content

We Are Not Alone

The Unseen World of the Human Microbiome

Joan-Beth Gow
School of Professional Studies
Anna Maria College


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.


  • 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

Educational Level

High school, Undergraduate lower division, Undergraduate upper division



Type Methods

N/A, Directed, Flipped, Interrupted, Laboratory



Subject Headings

Biology (General) Medicine (General) Microbiology Physiology Science (General)

Date Posted


Teaching Notes

Case teaching notes are password-protected and access to them is limited to paid subscribed instructors. To become a paid subscriber, begin the process by registering.

Teaching notes are intended to help teachers select and adopt a case. They typically include a summary of the case, teaching objectives, information about the intended audience, details about how the case may be taught, and a list of references and resources.

Answer Key

Answer keys for the cases in our collection are password-protected and access to them is limited to paid subscribed instructors. To become a paid subscriber, begin the process by registering.


The following video(s) are recommended for use in association with this case study.

  • The Human Ecosystem
    This video explores the microbiome as a human ecosystem and describes adaptations that different microbes need to survive in different areas of the body. Running time: 3:56 min. Produced by Genetic Science Learning Center, 2014.
  • We Are Not Alone: The Unseen World of the Human Microbiome
    This video is an integral part of the case study and introduces students to the human microbiome, the diversity of the microbial world, and that our complicated association with microbes involves both positive and negative effects. Running time: 10:45 min. Created by Joan-Beth Gow for the National Center for Case Study Teaching in Science, 2017.
  • Fecal Microbiota Transplantation
    This video presents a discussion between two physicians at the Mayo Clinic on the use of fecal microbiota transplantation (FMT) for treatment of CDI (Clostridium difficile infection). This video will help students respond to questions for Part I of the in-class portion of the case. Running time: 4:30 min. Produced by the Mayo Clinic, 2014.
  • Your Very Special Microbial Cloud “Science
    SUPPLEMENTAL VIDEO: It’s floating all around you, all the time—a wafting cloud formed by billions of bacteria that slough off your body with every movement you make. At the Biology and the Built Environment Center at the University of Oregon, researchers have revealed that not only can they detect and catalog this personal microbial cloud, but each person’s cloud is unique. Created by: Science Friday. Produced by: Luke Groskin. Running Time: 5:32 min. Date: January 25, 2016.


Deborah Harbour

Biological Sciences
College of Southern Nevada
Las Vegas, NV
This is a wonderful introduction to the microbiome. I have videos and lectures of each of these as my classes move through the microbiome. But this case has it all. Thanks and great job.