Gut Check: Exploring Your Microbiome

About this course: Imagine if there were an organ in your body that weighed as much as your brain, that affected your health, your weight, and even your behavior. Wouldn’t you want to know more about it? There is such an organ — the collection of microbes in and on your body, your human microbiome.

Created by:  University of Colorado Boulder, University of Colorado System, University of California, San Diego

• Taught by:  Rob Knight, Professor

  Pediatrics and Computer Science & Engineering. Director, Center for Microbiome Innovation, University of California, San Diego

• Taught by:  Dr. Jessica L. Metcalf, Senior Research Associate

  BioFrontiers Institute

• Taught by:  Dr. Katherine R. Amato, Postdoctoral Research Associate

  Department of Anthropology, BioFrontiers Institute

Language English, Subtitles: Catalan How To Pass Pass all graded assignments to complete the course. User Ratings 4.7 stars Average User Rating 4.7See what learners said Coursework

Each course is like an interactive textbook, featuring pre-recorded videos, quizzes and projects.

Help from your peers

Connect with thousands of other learners and debate ideas, discuss course material, and get help mastering concepts.

Certificates

Earn official recognition for your work, and share your success with friends, colleagues, and employers.

University of Colorado Boulder CU-Boulder is a dynamic community of scholars and learners on one of the most spectacular college campuses in the country. As one of 34 U.S. public institutions in the prestigious Association of American Universities (AAU), we have a proud tradition of academic excellence, with five Nobel laureates and more than 50 members of prestigious academic academies. University of Colorado System The University of Colorado is a recognized leader in higher education on the national and global stage. We collaborate to meet the diverse needs of our students and communities. We promote innovation, encourage discovery and support the extension of knowledge in ways unique to the state of Colorado and beyond. University of California, San Diego UC San Diego is an academic powerhouse and economic engine, recognized as one of the top 10 public universities by U.S. News and World Report. Innovation is central to who we are and what we do. Here, students learn that knowledge isn't just acquired in the classroom—life is their laboratory.

Syllabus


WEEK 1


Introduction to Microbes and the Human Microbiome



Welcome Citizen Scientists! We're very pleased to have you join us on an exploration of the human microbiome. This is a fascinating area of study, and we hope you will find this six-module course worthwhile. Each module's content will be presented in similar fashion; our team will introduce topics by way of pre-recorded video lectures interspersed with guest interviews by subject matter experts. Module 1 will provide a broad overview about microbes and their diversity on earth and in the human body.


10 videos, 3 readings expand

1. Video: Introduction
2. Reading: About This Course
3. Video: Welcome to the Course
4. Video: What are Microbes?
5. Video: Interview: Jack Gilbert
6. Video: Interview: Valerie McKenzie
7. Video: The Human Microbiome
8. Video: Where Do You Get Your Microbes?
9. Video: Web interview: Maria Gloria Dominguez-Bello
10. Video: Web interview: Elizabeth Costello
11. Video: Rob's Module 1 wrap-up
12. Reading: Assignments
13. Reading: Part 1: You and Your Gut

Graded: Introduction to Microbes and the Human Microbiome
Graded: Personal Microbiome Project Part I: Brainstorming

WEEK 2


Studying the Microbiome



In this module, we will dive into the fundamentals of how we study the human microbiome. We highlight recent advances in microbiome research methods and take you on a tour of the Knight lab. Please keep in mind, that Modules 2 and 3 are meant to provide a glimpse into our world of data generation and analysis. Modules 4, 5, and 6 will be less technical and provide a broad overview of fascinating research on the human microbiome. Stick with us!


9 videos, 2 readings expand

1. Video: How we study the microbiome: Introduction
2. Video: The history of studying microbes with Norm Pace
3. Video: Basics of high-throughput DNA sequencing
4. Video: Demo: Tour of the Knight Lab
5. Video: 'Omics' and other useful technologies
6. Video: Interview: Luke Thompson
7. Video: Web interview: Janet Jansson
8. Video: Web interview: Pieter Dorrestein
9. Video: Rob's Module 2 wrap-up
10. Reading: Assignments
11. Reading: Part 1: You and Your Gut (continued)

Graded: Studying the Microbiome

WEEK 3


Making Sense Out of Microbial Data



This module highlights the basics of generating and analyzing microbiome data. We will also discuss how computational scientists are revolutionizing the development of tools for analyzing large, complex biological data sets and show you some of the cool ways that we visualize data! This module will help you understand data plots in later modules, but do not get discouraged if the material here is too technical, a full understanding is not required to complete the course!


7 videos, 2 readings expand

1. Video: How do we identify a microbe?
2. Video: Web interview: Philip Hugenholtz
3. Video: Basics of alpha-diversity with fuzzy microbe demo
4. Video: Beta-diversity, and visualizing differences
5. Video: Demo: EMPeror, a QIIME visualization tool
6. Video: Web interview: Gregory Caporaso
7. Video: Rob's Week 3 wrap-up
8. Reading: Assignments
9. Reading: Part 1: You and Your Gut (continued)

Graded: Making Sense Out of Microbial Data

WEEK 4


The Human Gut Microbiome and Your Health



Now that we've given you some background about the methods we use to analyze microbial data, it's time for us to talk more about recent discoveries in microbiome research. This module will focus on the main factors impacting the gut microbiota as well as the influence of the gut microbiota on nutrition and gut health. This is the fun part, so get excited!


8 videos, 1 reading expand

1. Video: Impact of diet and age on the gut microbiota
2. Video: Obesity and the gut microbiota
3. Video: Human microbiome and gut disease
4. Video: Interview: On location in Tanzania with Martin Blaser
5. Video: Interview: On location in Tanzania with Jeff Leach
6. Video: Interview: On location in Tanzania with Maria Gloria Dominguez-Bello
7. Video: Manipulating the microbiome through fecal transplants
8. Video: Rob's Module 4 wrap-up
9. Reading: Assignments

Graded: The Human Gut Microbiome and Your Health
Graded: Personal Microbiome Project Part I: Reflection Questions

WEEK 5


Gut Microbe-Host Interactions: Beyond Nutrition



You're more than halfway through the course! We hope you've been learning lots of new, exciting things about the human gut microbiota! In this module, we'll shift the focus from nutrition and gut health to the rest of your body. How do your gut microbes and your immune system interact? What about your nervous system? Does the gut microbiota play a role in allergies and stress?


11 videos, 1 reading expand

1. Video: Gut microbiota interactions with the immune system
2. Video: Gut microbiota, autoimmune diseases, and allergies
3. Video: Web interview: Sarkis Mazmanian
4. Video: Interview: Cathy Lozupone
5. Video: The gut-brain axis
6. Video: Post-mortem human microbiome
7. Video: Zech on machine learning
8. Video: Web interview: Sibyl Bucheli
9. Video: Web interview: David Carter
10. Video: Web interview: Charlotte Carter
11. Video: Rob's Module 5 wrap-up
12. Reading: Assignments

Graded: Gut Microbe-Host Interactions: Beyond Nutrition

WEEK 6


What's in the American Gut



We will wrap up the course in this module by discussing what's in the American Gut. Rob will walk us through results from the American Gut Project and compare results from Jeff Leach and Michael Pollan. We will also hear from Michael Pollan on the importance of microbiome research and how it has changed the way he thinks about his health and what he eats.


8 videos, 4 readings expand

1. Video: The American Gut Project and crowd-funding
2. Video: Interview: Tom Cech
3. Video: Collecting samples
4. Video: Interview: Daniel McDonald
5. Video: Michael Pollan vs. Jeff Leach: American Gut results explained
6. Video: Web interview: Michael Pollan
7. Video: Comparing the American Gut to other populations
8. Video: Rob's Module 6 wrap-up and thank you's
9. Reading: Assignments
10. Reading: Closing Remarks
11. Reading: Acknowledgements
12. Reading: Post-Course Survey

Graded: What's in the American Gut
Graded: Personal Microbiome Project Part II