BIO534: Human Microbiome Ecology (Spring 2021)

• Professor: Dr. Emily Cope (Emily.Cope@nau.edu)
• Course time: Tu/Th 11:10-12:25
• Course Location: Zoom and Physical Sciences RM 321
• Office Hours: Tuesday and Wednesday 1-2pm via Zoom (link in BBL) or by appointment
• Office Location: ARD Building #56, Suite 220, Room 222. COVID office location: Zoom

• Course schedule: Access via BBL or here

Course Prerequisites: BIO205

Recommended: BIO375 and BIO401C

OR - Graduate student standing or instructor consent

Course Description. This course will cover the ecology of the microbial inhabitants of the human body, how the host depends on these microorganisms to maintain health, and what happens when our microbial communities are perturbed. This course will be project-oriented, with in-class presentations (journal club), small take-home assignments, and a large final project. We will cover topics such as current techniques in microbial community profiling, microbial diversity analyses, microbial interactions with the host immune system and other microorganisms, and potential for microbiome-directed therapeutics to impact human disease.  Journal Club presentations will cover primary scientific literature. The final project will involve writing and presenting grant proposal based on what you’ve learned in this course.

Student Learning Expectations/Outcomes for this Course. After taking this course, students should be comfortable with microbial community profiling technologies, measures of microbial diversity, and should understand the relationships of the human microbiota to each other and the host. Students will gain experience reading, digesting, and communicating results and conclusions from primary literature. Students will also understand how to design and carry out a project aimed at interrogating the human microbiome. Graduate students are expected to critically read scientific papers, and provide peer-review level feedback including constructive criticism on experimental design, hypotheses, and whether the evidence presented in a paper supports the conclusions drawn by the authors. Finally, graduate students are expected to design a project that aims to interrogate the human microbiota diversity, composition, or function and develop an NIH-style grant with a reasonable budget.

Course Structure/Approach. This course will be lecture-based with both instructor and student-led presentations focused on discussing primary literature. Short in-class quizzes, take-home assignments (Problem Sets), Peer-review assessments, a Journal Club-style presentation, and a final project consisting of a grant proposal and presentation will count toward your grade. In-class time will be focused on lectures and thoughtful discussion of emerging topics. Take-home assignments (Problem Sets) should be completed by the due date provided on the course schedule. Assignments not completed by the due date will be docked 5 points for each late day (assignments will be worth 20 points total).

There will be regular quizzes throughout the semester. These will cover recently presented material and are not designed to be difficult for students who attend class and keep up with the readings.

This course covers a lot of diverse material that are currently active areas of research. Thus, in class discussions are highly encouraged. In addition, office hours are your chance to directly interact with the instructor to ensure that you understand the concepts being covered in class.

Required Materials.

• Much of the material covered in this course is new and thus the primary material will be review papers and scientific literature, which I will assign and post on the course schedule. Examples include:

1.            Goodrich JK, Di Rienzi SC, Poole AC, Koren O, Walters WA, Caporaso JG, Knight R, Ley RE. 2014. Conducting a microbiome study. Cell 158:250–262.

2.            Atarashi K, Tanoue T, Shima T, Imaoka A, Kuwahara T, Momose Y, Cheng G, Yamasaki S, Saito T, Ohba Y, Taniguchi T, Takeda K, Hori S, Ivanov II, Umesaki Y, Itoh K, Honda K. 2011. Induction of colonic regulatory T cells by indigenous Clostridium species. Science 331:337–41.

3.            Trompette A, Gollwitzer ES, Yadava K, Sichelstiel AK, Sprenger N, Ngom-Bru C, Blanchard C, Junt T, Nicod LP, Harris NL, Marsland BJ. 2014. Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med 20:159–66.

4.            Byrd BAL, Segre JA. 2016. Adapting Koch’s postulates. Science (80- ) 351:224–226.

5.            Woese CR, Fox GE. 1977. Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proc Natl Acad Sci 74:5088–5090.

6.            Pace NR, Stahl DA, Lane DJ, Olsen GJ. 1986. The Analysis of Natural Microbial Populations by Ribosomal RNA Sequences, p. 1–55. In . Springer US.

Course Schedule. A tentative schedule is provided at the link at the top of the syllabus and here. I reserve the right to change the schedule as the needs of the course dictate. As such, the schedule will change over the course of the semester as we identify areas that we want to expand our discussion upon. The spreadsheet linked above will be kept up to date and will be where you find current due dates, quiz dates, reading materials, and lecture information. Check this link regularly!

Assessment of Student Learning Outcomes. You will be primarily assessed through graded material. See grading system, below. Problem Sets are generally conceptual, requiring students to think through problems; there may not be a single correct answer. Graduate students will be asked 1-2 additional conceptual questions compared to the undergraduate assessment.  A small portion of your grade will be participation-based. This will allow me to assess whether you are grasping the course material, as we will be discussing complex concepts and primary literature. Specifically, I expect you to participate in at least 50% of the course discussions by contributing to paper discussions via Perusall, asking questions, providing critiques of scientific papers, or through respectful interaction with fellow students or myself. As a graduate student, you will be expected to read additional journal articles as indicated on the course schedule and provide a short summary of each article. This will be counted toward your participation points. Check with me any time during the semester on your current participation score or grade. Rubrics for presentations and papers will be distributed at least one week prior to the due date.

Grading System.

• Participation = 50 Points
• Problem sets = 100 Points
• Short quizzes (lowest score will be dropped) = 100 Points
• Graduate Student Reviewer Assignments (2 total) = 40 Points (20 points each)
• Student-led journal Club presentation = 50 Points
• Final project: NIH-style Grant Proposal (6 page) = 100 Points
• Final project: Grant Presentation (15 minutes) = 75 Points

Grading Scale: A: 90-100; B: 80-89; C: 70-79; D: 60-69; F: 0-59

 Course Policy.

• If you have a legitimate (e.g. institutional excuse) reason why you cannot make one of the quiz times or presentation days, come talk to me or e-mail me as soon as the conflict is identified and something can be arranged. Routine medical appointments that you schedule do not count as legitimate excuses, and all absences for illness must be accompanied by a doctor’s note or other evidence. Students who do not show up for quizzes without making prior arrangements will get a zero. There will be no make-up quizzes. If you miss a quiz day without making prior arrangements, it will count as your dropped quiz score.
• Students will not be graded on attendance, but participation in class counts as 10% of your grade. Come talk to me if you want to know where you stand on participation points. The majority of these points will come from participation on Perusall.
• Some projects will be group based. I expect that all students will contribute equally to their group. Come talk to me if there are legitimate issues with the workload distribution.
• The primary reading for this course will be from the literature; I will provide PDFs of each assigned reading. Computers may be used during class to access these articles – you do not need to print each one. However, you may not use computers in class for non-course-related work such as checking e-mail or Facebook. If I notice you doing this, I will document it and deduct participation points.
• No computers, cell phones, headphones, books, or papers may be used during the quizzes. If a student is observed using or looking at any of these items, it will be considered cheating and handled accordingly with NAU published policies on academic integrity, found here https://policy.nau.edu/policy/policy.aspx?num=100601#_ftn1. To be safe, I recommend keeping your phone off during quizzes.
• Plagiarism and cheating will not be tolerated. Any students found guilty of each will receive a failing grade in the class. We will go over what is considered plagiarism on the first day of class. If plagiarism is suspected, I will check the document using Safeassign.
• I expect you to check the course schedule at least 24h prior to class. I will e-mail when I add a reading assignment or change a due date.
• COVID-19 policies:

• Masks are required if you choose to attend class in-person. Proper mask wearing will also be required (covering the mouth and nose). Any person not complying to proper mask wearing will be asked to leave and attend class remotely.
• I understand that COVID-19 has placed undue stress on students. Please reach out to me if you have any questions or concerns regarding COVID-19 or otherwise and I will do my best to accommodate.

University Policies. The Safe Environment, Students with Disabilities, Institutional Review Board, Academic Integrity, Academic Contact Hour, Classroom Management and Professional Ethics and Code of Conduct policies are available at https://policy.nau.edu/policy/policy.aspx?num=100601#_ftn1. Students are responsible for reviewing and und