The impact of diet and antibiotics on the gut microbiome

Abstract

The goal of this article is to describe an active learning exercise that can be used in a variety of advanced microbiology courses, including bacterial physiology, ecology, or systems biology. The gut microbiome is a multi-species bacterial community that is impacted by outside factors, such as the food we consume or treatments with antibiotics, and impacts our health. In this active learning experience; students start with a simple 'pasta' simulation of a gut microbiome, adapted from a previously published lesson, where different types of pasta in a plastic bag simulate different bacteria in the gut and the composition of the pasta types is representative of diet related differences in the microbiome. Students will then mimic an antibiotic treatment by removing certain pasta/bacteria and replacing them with beans/different bacteria. Next, students will analyze the gut microbiome at the level of phylum, genus, or species. With the help of assigned scientific literature, students will learn how the composition of the gut microbiome responds to diet, a process that is accompanied by the synthesis of bacterial fermentation and other bacterial metabolic products that elicit a molecular response in the host intestinal cells. Students will gain an initial understanding of how these changes impact human health. Through this experience, students will increase their knowledge of bacterial metabolic pathways and products, improve their understanding of the complex community that constitutes the microbiome, analyze the microbiome at multiple systematic levels, and apply their knowledge in a context that is relevant to human health.