Four different activities help educators from K-12 and undergraduate teach students about the importance of the human microbiome.

Want to teach about the importance of the human microbiome, but don’t really know where to start? The ASM education blog just released a post – Bring the Magic of the Microbiome to Your Classroom – pulling together four of the microbiome exercises that have been published in JMBE recently. Take a look at these different classroom microbiome activities. I especially, love that there’s one – Microbe Motels – for K-8 and am looking forward to trying it out! Check out the Journal of Microbiology and Biology Education (JMBE) published by the American Society for Microbiology (ASM). JMBE is the educational journal of the society and features excellent classroom activities. It’s open access and even FREE for members to publish in! WIN WIN!

Microbiome Modeling with Bag ‘o Beans

I was thrilled that ASM included my “Modeling the Digestive System Microbiome” beans and pasta exercise. In my original exercise, participants are given a premade “gut microbiome” (a resealable snack bag filled with beans and pasta) and a key to the “bacterial identity” of the beans and pasta. They use this key to determine what their gut “feed upon”. We compare bacterial diversity and types in guts fed on a meat and dairy diet, a plant diet, and a mixed, plant, animal, dairy diet. This exercise was inspired by this paper by David et al. on diet effects on the gut microbiome [1]. Then participants are asked to remove certain “antibiotic sensitive” bacteria for 3 minutes to represent a 3 day course of antibiotics. This antibiotic treatment then opens up space in the gut for new bacteria to enter the gut. Participants are then asked to add “environmental” bacteria to the gut to refill the gut habitat. Finally, I ask students to look and see how many guts contain more than 5 or 10 yellow or green lentils. These lentils represent Clostridium difficile bacteria and the person now has C. diff-induced diarrhea. These participants should now expect to need to go to the bathroom every 15 minutes all day. The groans throughout the classroom are always a hoot.

I’ve uploaded the slides I use along with this exercise to Slide Share –

Since publishing that manuscript, I’ve modified the exercise to talk about resident vs transient microbes. Resident microbes are those that are native to your gut, while transient are ones that come through the gut usually on food, but do not live in the gut. They pass through.

Beans Model Breast Fed and Formula Fed Microbiome

Most recently, and maybe now my favorite version of the exercise,  I revised the pasta and beans activity to talk about the different microbes found in the gut of infants fed breast milk, formula, or mixed breast milk and formula. A colleague and I presented the beans exercise at the 6th National Breastfeeding Coalition Conference of the US Breastfeeding Committee in August, 2016. The exercise is based on several papers, mostly from David Mills’ lab out of the University of California at Davis [2-4], that focus on how the sugars in human breast milk influence the infant gut microbiome. See my  post “It’s All About the Breast Milk Sugars, Baby” for more about milk sugars and bacterial communities. I also modified the exercise to use only beans (instead of beans and pasta) so that a recipe for 15-bean soup could be given to participants. Many of the participants at USBC’s meeting were lactation consultants and often worked with women on WIC (The Women, Infants, and Children program – a government program to aid low income women and their families). I want to train these ladies to communicate that the microbiome is important AND include a cheap, easy, and microbiome-friendly recipe for families.


mixed_fed_bag formula_fed_bag

I’d love to hear if you use any of these exercises and what the reactions are. Also would love to hear if you have suggestions to modify the activities! Finally, if YOU have a great activity – think about submitting to JMBE. I had a great experience submitting my first manuscript there and have another in the works.


  1. David L, Maurice C, Carmody R, Gootenberg D, Button J, Wolfe B: Diet rapidly and reproducibly alters the human gut microbiome. Nature 2014, 505:559 – 563.
  2. Underwood MA, German JB, Lebrilla CB, Mills DA: Bifidobacterium longum subspecies infantis: champion colonizer of the infant gut. Pediatr Res 2015, 77(1-2):229-235.
  3. Zivkovic AM, German JB, Lebrilla CB, Mills DA: Human milk glycobiome and its impact on the infant gastrointestinal microbiota. Proc Natl Acad Sci U S A 2011, 108.
  4. Zivkovic AM, Lewis ZT, German JB, Mills DA: Establishment of a Milk-Oriented Microbiota (MOM) in Early Life: How Babies Meet Their Moms. Functional Food Reviews 2013, 5(1):3-12.

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