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BIO499: Human Microbiome Ecology (Spring 2021)

3 Credit Hours

• 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 Purpose. 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 consequences when 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 are group based and will cover primary scientific literature. The final project will involve writing and presenting a review paper.  This course integrates concepts from other Biology Department course offerings (Microbiology, Immunology, Ecology) in the context of the human system. BIO 434 students will interact with Biology Graduate students in this course (BIO 534) by observing graduate student presentations on primary literature and grant proposal development.

Student Learning Expectations/Outcomes for this Course. After taking this course, students should be able to explain and contrast different microbial community profiling technologies, measures of microbial diversity, and should describe the relationships of the human microbiota to each other and the host through written work and presentations. Students should be able to describe different clinical study designs and identify the study design used in primary research articles, as demonstrated through contrasting clinical study designs in their final review paper. Students will be able to critically read scientific papers and communicate results and conclusions from primary literature as demonstrated through oral presentations and written evaluations. Students will also describe how to design and carry out a project aimed at interrogating the human microbiome through journal club style presentations and take-home problem sets.

 Course Structure/Approach. This course will be lecture-based with presentations focused on discussing primary literature. Short in-class quizzes, take-home assignments (Problem Sets), a group journal club presentation, and a final project consisting of a literature review and presentation will count toward your grade. In-class time will be focused on lectures and thoughtful discussion of emerging topics. Take-home 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 and discussions via Perusall are critical. 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: http://bit.ly/499-599_Sp18. 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. Discussion of primary literature via Perusall, short in-class quizzes, take-home assignments (Problem Sets), a group journal club presentation, and a final project consisting of a literature review and presentation will count toward your grade (see grading breakdown, below). Problem Sets are generally conceptual, requiring students to think through problems; there may not be a single correct answer. Multiple answers, if well justified, will be marked correct. Detailed instructions of your review paper assignment will be provided along with a rubric (example here). 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. 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.

Breakdown:

• Participation = 45 Points
• Problem sets = 100 Points
• Short quizzes (lowest score will be dropped) = 100 Points
• Group Journal Club presentation = 50 Points
• Final project: Review paper (3 page) = 100 Points
• Final project: Poster presentation (5-8 min on your Review subject) = 50 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 http://nau.edu/Curriculum-and-Assessment/_Forms/Curricular-Policy/Syllabus_Policy_Statements/  Students are responsible for reviewing and understanding these policies.