IID 209: Microbial Communities and the Human Microbiome

IID 209: Microbial Communities and the Human Microbiome

Microbial Communities and the Human Microbiome
IID209, Spring II, 2019
Time: MW 2:00-3:30
Location of Class: Kresge 201


Dr. Wendy Garrett, Professor, IID and GCD, Harvard Chan School
Office: SPH1 909
Email: wgarrett@hsph.harvard.edu
Phone: 617-432-3243

Dr. Curtis Huttenhower, Professor, Biostatistics and IID, Harvard Chan School
Office: SPH1 413
Email: chuttenh@hsph.harvard.edu
Phone: 617-432-4912

Office Hours and Location:
Curtis                                      F 11:00-12:00, SPH1 413
Wendy                                    By appointment wgarrett@hsph.harvard.edu

Teaching Assistant:          Sydney Lavoie, BPH G6
Office Hours:                     By appointment: sydneylavoie@fas.harvard.edu
Office Address:                  SPH 1 - 9th floor


Course Description
This course introduces students to the human microbiome and other microbial community concepts, including survey topics on relevant components of immunology, microbiology, ecology, health practice, and bioinformatics. It includes examples of the human microbiome's relevance to public health, such as chronic disease (e.g. cancer, inflammatory bowel disease). It also introduces study design considerations, model systems, and technologies for studying the microbiome in public health.


Learning Objectives
Students completing the course will be able to:

  • Identify translational, basic biological, and population health topics relevant to the microbiome.
  • Read and discuss current research literature on microbial community studies.
  • Employ animal, molecular, and computational tools for microbial community research.
  • Propose and execute introductory studies incorporating microbiome components and molecular technologies.


This course has no formal prerequisites; familiarity with basic molecular biology and introductory quantitative analysis environments is encouraged.



  • Required: Bacteriology of Humans: An Ecological Perspective, Michael Wilson


Course Structure
This course assumes substantial and informed student participation.  General discussion of theory and practice is encouraged and expected of all students.  At a minimum, being informed requires class attendance, completion of assigned readings and homework, and good performance on tests and other assessments.  Class attendance and thoughtful participation are important and will be reflected in part in the final grade.  Please notify the instructor of an absence before the class.

The final grade for this course will be based on:

  • Homework, three problem sets (60%)
  • Final project (30%)
  • Participation, based on lecture attendance and participation (10%)

All assignments are to be completed individually except for the final project, for which small groups will be formed. The maximum score for late work will fall exponentially: 90% if one day late, 75% if two, 40% if three, and all credit lost if four or more days late. Extensions may be granted with reason if requested at least 24 hours in advance of the assignment deadline. Final letter grades will be curved based on the percentiles of total scores received by students in the class.

Homework, three problem sets (60%)
Problem sets will be assigned roughly biweekly through the first two-thirds of the course. They will consist of written take-home assignments including questions on assigned readings and reasoning around microbial community research topics. Empirical questions will also be included to assess students' ability to analyze example microbial community data.

Final project (30%)
Final projects will be assigned three weeks before the end of the course, to be carried out in small groups (2-5 students, 3-4 recommended, self-organized with moderation by the instructors if requested). These will consist of designing and carrying out a microbial community research task of moderate scope, using either public data or data from students' current research. Research questions will be suggested for groups that do not have their own available research or analysis interests. Tasks will be signed off by the instructor at the time of group formation, with implementations to be completed by finals week. Grading will be based on an in-class group presentation in addition to individually submitted extended abstract writeups.

Participation (10%)
Class participation will be included in the final grade based on a combination of active participation during lectures (questions posed by students, and answers provided by students to those posed during lecture) and attendance. Students should arrive to class prepared to ask and answer questions, share their viewpoints in constructive and respectful ways, and otherwise actively engage with other students and the course instructor. Notification of class absences should be provided by email to the instructional team at least 24 hours in advance. Otherwise, class participation will be graded as follows:

  • 10%: Always contributes to discussions by asking thoughtful questions; relates diverse topics from lecture sessions; reads and discusses all assigned literature; attends all sessions.
  • 5-9%: Sometimes contributes to discussions as above; interaction during only a subset of topic areas over the course of the semester; reads most but not all assigned literature; more than one lecture or lab absences without notice.
  • 0-4%: Rarely contributes to discussions as above; more than three lecture absences without notice.

Course Website and Communication
All course communication will be through the course Canvas site.


Harvard Chan Policies and Expectations

Inclusivity Statement
Diversity and inclusiveness are fundamental to public health education and practice. It is a requirement that you have an open mind and respect differences of all kinds. I share responsibility with you for creating a learning climate that is hospitable to all perspectives and cultures; please contact me if you have any concerns or suggestions.

Bias Related Incident Reporting
The Harvard Chan School believes all members of our community should be able to study and work in an environment where they feel safe and respected. As a mechanism to promote an inclusive community, we have created an anonymous bias-related incident reporting system. If you have experienced bias, please submit a report here so that the administration can track and address concerns as they arise and to better support members of the Harvard Chan community.

Title IX
The following policy applies to all Harvard University students, faculty, staff, appointees, or third parties: Harvard University Sexual and Gender-Based Harassment Policy. Procedures For Complaints Against a Faculty Member. Procedures For Complaints Against Non-Faculty Academic Appointees 

Academic Integrity
Each student in this course is expected to abide by the Harvard University and the Harvard. T.H. Chan School of Public Health Codes of Academic Integrity.  All work submitted to meet course requirements is expected to be a student’s own work.  In the preparation of work submitted to meet course requirements, students should always take great care to distinguish their own ideas and knowledge from information derived from sources. 

Students must assume that collaboration in the completion of assignments is prohibited unless explicitly specified.  Students must acknowledge any collaboration and its extent in all submitted work. This requirement applies to collaboration on editing as well as collaboration on substance.

Should academic misconduct occur, the student(s) may be subject to disciplinary action as outlined in the Student Handbook. See the Student Handbook for additional policies related to academic integrity and disciplinary actions.

Accommodations for Students with Disabilities
Harvard University provides academic accommodations to students with disabilities. Any requests for academic accommodations should ideally be made before the first week of the semester, except for unusual circumstances, so arrangements can be made. Students must register with the Local Disability Coordinator in the Office for Student Affairs to verify their eligibility for appropriate accommodations. Contact Colleen Cronin ccronin@hsph.harvard.edu in all cases, including temporary disabilities.

Religious Holidays, Absence Due to
According to Chapter 151c, Section 2B, of the General Laws of Massachusetts, any student in an educational or vocational training institution, other than a religious or denominational training institution, who is unable, because of his or her religious beliefs, to attend classes or to participate in any examination, study, or work requirement on a particular day shall be excused from any such examination or requirement which he or she may have missed because of such absence on any particular day, provided that such makeup examination or work shall not create an unreasonable burden upon the School. See the student handbook for more information.

Grade of Absence from Examination
A student who cannot attend a regularly scheduled examination must request permission for an alternate examination from the instructor in advance of the examination. See the student handbook for more information. 

Final Examination Policy
No student should be required to take more than two examinations during any one day of finals week. Students who have more than two examinations scheduled during a particular day during the final examination period may take their class schedules to the director for student affairs for assistance in arranging for an alternate time for all exams in excess of two. Please refer to the student handbook for the policy.

Course Evaluations
Constructive feedback from students is a valuable resource for improving teaching. The feedback should be specific, focused and respectful. It should also address aspects of the course and teaching that are positive as well as those which need improvement. 

Completion of the evaluation is a requirement for each course. Your grade will not be available until you submit the evaluation. In addition, registration for future terms will be blocked until you have completed evaluations for courses in prior terms.

Course Summary:

Date Details