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Microbiome Balance

Run the Microbiome Balance MicroSim Fullscreen

About This MicroSim

Your colon is home to a crowded community of bacteria, the gut microbiota. A healthy community is diverse, and its normal residents (commensal bacteria) keep potentially harmful opportunists in check, a protection called colonization resistance. Antibiotics save lives, but they also knock down commensals. Human studies show that gut diversity drops quickly during an antibiotic course and that most of the community regrows within weeks, though recovery is not always complete and differs from person to person.

This MicroSim is a cartoon community of 24 made-up species in five groups: fiber fermenters, butyrate producers, Bifidobacteria, other commensals, and opportunists (tomato red). Each group has a few abundant species and several rare ones.

  • The dot field shows the community; each dot is a small share of it.
  • The bar shows each group's share, with percentages.
  • The chart tracks a diversity index (the Shannon index: higher means more kinds of bacteria, more evenly mixed). Antibiotic days are shaded.
  • The panel shows the day, the diversity index, and how many of the 24 species are still present.

How to Use

  1. Press Start and watch the community stay roughly stable.
  2. Predict what an antibiotic course will do to diversity, then press Give antibiotic course. Watch the opportunists bloom while commensals shrink.
  3. Keep the sim running and watch the commensals regrow and push the opportunists back down. When the diversity line levels off, check Species present. Did any species disappear for good?
  4. Press New person and repeat the antibiotic course. Compare how many species this person loses.
  5. Press Reset, then switch the Diet to Low-fiber, high-sugar for a couple of months of simulated time. Watch the makeup and the diversity index, then switch back to fiber-rich.

Learning Objective

Bloom level: Apply. The learner will predict how an antibiotic course and a change in diet shift the diversity and makeup of a gut bacterial community, and explain why recovery is often partial and differs between people.

Iframe Embed Code

<iframe src="https://aaryavvatts-lab.github.io/gut-brain-textbook/sims/ch03-microbiome-balance/main.html" height="682px" width="100%" scrolling="no"></iframe>

Lesson Plan

Grade level: 9 to 12 (biology, ecology, or health science)

Duration: 25 to 30 minutes

Activity:

  1. Warm-up (3 minutes). Ask: "If you take an antibiotic, what happens to the bacteria in your gut, and do they come back?" Students write a prediction.
  2. Explore (8 minutes). In pairs, students run one antibiotic course and record the starting diversity index, the lowest value, the value about 100 days later, and the number of species lost.
  3. Compare people (6 minutes). Each pair presses New person twice and repeats the course. The class pools results and discusses why responses differ.
  4. Diet test (5 minutes). Students switch to the low-fiber diet for about 60 simulated days, then back, and describe what changed and whether it reversed.
  5. Limits (3 minutes). Read the "What this model leaves out" box in Chapter 3 and name one way real gut communities differ from the sim.

Assessment questions:

  1. Why do the opportunists bloom during the antibiotic course, and why do they shrink again afterward?
  2. Why doesn't diversity always return to exactly where it started?
  3. Two "people" got the same antibiotic course but lost different numbers of species. What in the sim explains this, and what might explain it in real people?
  4. Why can't this sim predict what an antibiotic will do to your own microbiome?

Chapter 3: Meet the Microbiome