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Modeling the Dynamic Digestive System Microbiome

    Author: Anne M. Estes1
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    Affiliations: 1: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Supplemental materials available at http://jmbe.asm.org
    • Corresponding author. Mailing address: Institute for Genome Sciences, University of Maryland School of Medicine, 801 W. Baltimore Street, BioPark II, Baltimore, MD 21201. Phone: 410-706-0790. E-mail: anneestes@gmail.com.
    • ©2015 Author(s). Published by the American Society for Microbiology.
    Source: J. Microbiol. Biol. Educ. December 2015 vol. 16 no. 2 271-273. doi:10.1128/jmbe.v16i2.908
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    Abstract:

    “Modeling the Dynamic Digestive System Microbiome” is a hands-on activity designed to demonstrate the dynamics of microbiome ecology using dried pasta and beans to model disturbance events in the human digestive system microbiome. This exercise demonstrates how microbiome diversity is influenced by: 1) niche availability and habitat space and 2) a major disturbance event, such as antibiotic use. Students use a pictorial key to examine prepared models of digestive system microbiomes to determine what the person with the microbiome “ate.” Students then model the effect of taking antibiotics by removing certain “antibiotic sensitive” pasta. Finally, they add in “environmental microbes” or “native microbes” to recolonize the digestive system, determine how resilient their model microbome community is to disturbance, and discuss the implications. Throughout the exercise, students discuss differences in the habitat space available and microbiome community diversity. This exercise can be modified to discuss changes in the microbiome due to diet shifts and the emergence of antibiotic resistance in more depth.

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2015-12-01
2017-11-18

Abstract:

“Modeling the Dynamic Digestive System Microbiome” is a hands-on activity designed to demonstrate the dynamics of microbiome ecology using dried pasta and beans to model disturbance events in the human digestive system microbiome. This exercise demonstrates how microbiome diversity is influenced by: 1) niche availability and habitat space and 2) a major disturbance event, such as antibiotic use. Students use a pictorial key to examine prepared models of digestive system microbiomes to determine what the person with the microbiome “ate.” Students then model the effect of taking antibiotics by removing certain “antibiotic sensitive” pasta. Finally, they add in “environmental microbes” or “native microbes” to recolonize the digestive system, determine how resilient their model microbome community is to disturbance, and discuss the implications. Throughout the exercise, students discuss differences in the habitat space available and microbiome community diversity. This exercise can be modified to discuss changes in the microbiome due to diet shifts and the emergence of antibiotic resistance in more depth.

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Figures

Image of FIGURE 1

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FIGURE 1

Example of digestive system microbiome of omnivore. Note the presence of a few green and orange lentils and that the smallest pasta falls to the bottom of the bag.

Source: J. Microbiol. Biol. Educ. December 2015 vol. 16 no. 2 271-273. doi:10.1128/jmbe.v16i2.908
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Image of FIGURE 2

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FIGURE 2

Key to the pasta types that represent bacteria with the ability to feed on meat, dairy, and plant-based diets.

Source: J. Microbiol. Biol. Educ. December 2015 vol. 16 no. 2 271-273. doi:10.1128/jmbe.v16i2.908
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Image of FIGURE 3

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FIGURE 3

“Antibiotic-sensitive” pasta shapes (yellow and green fusilli, ditalini, macaroni, rotelle, and ziti) that should be removed during the antibiotic treatment portion of the activity.

Source: J. Microbiol. Biol. Educ. December 2015 vol. 16 no. 2 271-273. doi:10.1128/jmbe.v16i2.908
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Image of FIGURE 4

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FIGURE 4

Example of bag of environmental bacteria, including both green and orange lentils.

Source: J. Microbiol. Biol. Educ. December 2015 vol. 16 no. 2 271-273. doi:10.1128/jmbe.v16i2.908
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