Course Meeting Times

Lectures: 1 session / week, 2 hours / session


A general knowledge of molecular biology, biochemistry or cell biology will be helpful. This includes courses such as:

7.05 Biological Chemistry

7.06 Cell Biology

7.28 Molecular Biology

or their equivalents. Chemistry, Chemical Engineering, and Bioengineering students are highly encouraged to attend.

Course Description

There are more microbes permanently living in our gut than there are cells in the human body. This rich community of bacteria, fungi and viruses, called the microbiome, plays a central role in human health and disease. Recent research has linked this passenger community to nutrition, circadian rhythms, infectious disease, inflammatory disease, cancer, diabetes, arthritis and even immune system and nervous system development. The connections seem to be so far-reaching that some scientists are starting to consider this human-microbiome system as a “holobiont” or “superorganism.”

Why are we realizing this situation only now? Are microbes actually interacting with us so fundamentally? What are the mechanisms by which effects of the microbiome are mediated? Can we survive without our microbiome? How can we analyze such a complex system? Can we exploit the microbiome to improve human health? Can interactions with microbes be harnessed for drug delivery?

In this course, we will explore the primary scientific literature to find the answers to these questions and learn to critically assess observational and experimental data and to distinguish between correlation and causality. We will discuss several of the key signaling molecules that mediate the interactions between humans and their microbiomes, such as human-produced antimicrobial peptides, microbial pheromones, bacterial peptide toxins and neuroactive microbial metabolites. We will learn about recent methods that make possible the analysis of these interactions. In particular, we will consider microfluidics, the technology of manipulating fluid in micro to pico liter scales in networks of tiny channels, as an emerging tool for the investigation of microbiome signaling. We will learn about other cutting-edge technologies, such as next-generation DNA and RNA sequencing and the use of germ-free mice.

Finally, we will discuss how a large reduction in the cost of DNA synthesis is enabling the development of synthetic microbes that can be used to interrogate and manipulate the microbiome. Together these mechanistic insights and emerging tools are transforming microbiome research and might lead to new types of therapeutics and drug delivery for improving human health.


This course will introduce students to the primary scientific literature surrounding the exciting field of microbiome biology and therapeutics. Students will learn:

  • how to critically assess the results and impacts of key experiments,
  • how to distinguish between correlative and mechanistic studies, and
  • learn about the role each plays in developing therapies to improve human health.


The class will meet weekly for two hours. Each week, students will read two papers from the primary research literature and critically evaluate these papers focusing on experimental design, control experiments, methods and interpretation of the data. At the end of each class, the instructors will give a short introduction to the papers for the following week.

Field Trip

Students will visit Gingko Bioworks, a company that is at the forefront of designing and building microbes for diverse applications.


Students will complete one written assignment, due in Week 7, and one final presentation, due on the last session of the course.


The course will be graded as “pass” or “fail.” A passing grade will be given to students who attend the class, participate in discussions, and complete both assignments in a satisfactory manner.


1 Introduction to the human microbiome  
Small-molecule Signals, Microfluidics and Synthetic Biology
2 Microbes use small molecules to communicate  
3 Microfluidics technology to study the human microbiome  
4 Field trip to Ginkgo Bioworks, the organism company Field Trip to Ginko Bioworks
5 Microbes engineered to detect and potentially kill pathogens  
Peptide Signals for Defense, Therapeutics and Competence
6 Microbes use peptides as a defense and as signals  
7 Drug delivery using microbes engineered to secrete peptides Written Assignment due
8 Competence-stimulating peptides as cross-species signals  
The Future of the Microbiome for Human Health
9 Using seminars and talks for sharing scientific discoveries  
10 Advance culturing techniques to study microbiomes Paper Distributed for Final Presentation
11 Host-generated peptides shape their microbiomes  
12 Microbes as neuromodulators  
13 Microbes as cancer therapeutics  
14 Oral presentations, conclusion and closing remarks Final Presentations Due

Course Info

As Taught In
Spring 2018
Learning Resource Types
Presentation Assignments
Written Assignments
Instructor Insights