Course Overview
Microbiomes and Health
11:680:475
Spring Semester
Meeting times TBD
Meeting Location: TBD
Contact Information
Instructor: Dr. Liping Zhao
Lipman Hall, Room 326
848-932--5675
iping.zhao@rutgers.edu
Office Hours: By appointment
Instructor: Dr. Maria G Dominguez-Bello
Lipman Hall, Room 326
917-565-1142
mg.dominguez-bello@rutgers.edu
Office Hours: By appointment
Invited Speakers
Course Website, Resources, and Materials
Reading assignments include selected sections from:
- Cox, L.M., et al., Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences. Cell, 2014. 158(4): p. 705-21.
- Douglas, A., Fundamentals of Microbiome Science: How Microbes Shape Animal Biology. 2018, 41 William Street, Princeton, New Jersey 08540: Princeton University Press.
- HMP, C., Structure, function and diversity of the healthy human microbiome. Nature, 2012. 486(7402): p. 207-14.
- Diaz Heijtz, R., et al., Normal gut microbiota modulates brain development and behavior. Proc Natl Acad Sci U S A, 2011. 108(7): p. 3047-52.
- Sonnenburg, E.D. and J.L. Sonnenburg, Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates. Cell Metab, 2014. 20(5): p. 779-86.
- Sonnenburg, E.D., et al., Diet-induced extinctions in the gut microbiota compound over generations. Nature, 2016. 529(7585): p. 212-5.
- Zou, J., et al., Fiber-Mediated Nourishment of Gut Microbiota Protects against Diet-Induced Obesity by Restoring IL-22-Mediated Colonic Health. Cell Host Microbe, 2018. 23(1): p. 41-53 e4.
- Azad, M.B., et al., Infant Feeding and Weight Gain: Separating Breast Milk From Breastfeeding and Formula From Food. Pediatrics, 2018. 142(4).
- Yassour, M., et al., Strain-level analysis of mother-to-child bacterial transmission during the first few months of life. Cell Host Microbe, 2018. 24(1): p. 146-154 e4.
- Dominguez-Bello, M.G., et al., Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nat Med, 2016. 22(3): p. 250-3.
- Moeller, A.H., et al., Rapid changes in the gut microbiome during human evolution. Proc Natl Acad Sci U S A, 2014. 111(46): p. 16431-5.
Course Description
This course provides an overview on the role of microbiome in human health and disease. It focuses on conceptual framework and technologies for understanding how microbiome, particularly gut microbiome impact human health and well-being.
Topics covered include the concept of human superorganism; Microbiome and human adaptation/evolution; Ecological principles of microbiomes; Systems thinking and approaches for working on human microbiome; Bioinformatics and statistics tool kits for human microbiome research; Research strategy and experimental/trial design in microbiome study; From correlation to causality of human microbiome in chronic diseases; Nutrition and gut microbiome; Food processing and gut microbiome; Microbiome in pharmacology; Intergenerational, vertical transmission of human microbiomes; Horizontal transfer of human microbiomes; Microbiome and human society; Microbiome and Human-Nature relationship.
Learning Goals
Course Learning Goals
By the end of the course, students will be able to:
- Illustrate ecological principles of the human microbiome, and the importance of conservation of the global microbiomes of peoples from different human populations
- Examine how microbiome may impact human health
- Summarize the tools and strategies for studying the microbiome
- Evaluate new developments reported in scientific journals and news media
- Assess the potential of the microbiota (probiotics) and diet (prebiotics) to achieve and maintain health
Assignments/Responsibilities, Grading, and Assessment
| Assignment | Points | Total Points |
|---|---|---|
| Examinations | 2 x 20 points | = 40 pts |
| Essays | 2 x 30 points | = 60 pts |
| Total | = 100 pts |
Two tests and two essays. One test and one essay will cover the lectures by Dr. Liping Zhao, the second test and one essay will cover the lectures by Dr. Dominguez-Bello. Each test will be 20% and each essay (1000 words at least) will be 30% of the total score of 100.
Accomodations for Students With Disabilities
Please follow the procedures outlined at ods.rutgers.edu/students/getting-registered. Full policies and procedures are at ods.rutgers.edu.
Absence Policy
Students are expected to attend all classes; if you expect to miss one or two classes, please use the University absence reporting website to indicate the date and reason for your absence. An email is automatically sent to me.
Course Schedule
| Topic | Lecturer |
|---|---|
| Lecture 1, Introduction: human superorganism and ecology of the microbiome | Liping Zhao M Gloria Dominguez-Bello |
| Lecture 2, Systems biology for human microbiome research | Liping Zhao |
| Lecture 3, Causality in human microbiome research: Koch's postulates still apply | Liping Zhao |
| Lecture 4, Multi-omics approach and datamining strategy | Liping Zhao |
| Lecture 5, Nutritional modulation of the gut microbiome for metabolic health: animal models | Liping Zhao |
| Lecture 6, Nutritional modulation of the gut microbiome for metabolic health: human obesity | Liping Zhao |
| Lecture 7, Nutritional modulation of the gut microbiome for metabolic health: human type 2 diabetes | Liping Zhao |
| Lecture 8, Nutritional modulation of the gut microbiome for healthy longevity: animal models | Liping Zhao |
| Lecture 9, Pharmaceutical modulation of the gut microbiome for metabolic health | Liping Zhao |
| Lecture 10, The gut microbiome and host immunity: animal models | Liping Zhao |
| Lecture 11, Are probiotic bacteria probiotic? Liping Zhao | |
| Lecture 12, Can dietary fiber cause liver cancer? | Liping Zhao |
| Lecture 13, Human microbiome research in nutrition: what's next? 1st test (one hour) | Liping Zhao |
| Lecture 14, Evolution of microbiomes | M. Gloria Dominguez-Bello |
| Lecture 15, Microbiomes other than digestive | M. Gloria Dominguez-Bello |
| Lecture 16, Microbiome functions | M. Gloria Dominguez-Bello |
| Lecture 17, Microbiota transmission: pregnancy and birth | M. Gloria Dominguez-Bello |
| Lecture 18, Microbiota transmission: postnatal | M. Gloria Dominguez-Bello |
| Lecture 19, Microbiota development | M. Gloria Dominguez-Bello |
| Lecture 20, Microbiota functions in early life | M. Gloria Dominguez-Bello |
| Lecture 21, Urbanization, microbiome and disease risks: microbial role | M. Gloria Dominguez-Bello |
| Lecture 22, Microbiota perturbations: medical practices | M. Gloria Dominguez-Bello |
| Lecture 23, Microbiota perturbations: hygiene and antibacterials | M. Gloria Dominguez-Bello |
| Lecture 24, Human microbiota degradation: evidence consequences | M. Gloria Dominguez-Bello |
| Lecture 25, Human microbiota degradation: solutions- One health | M. Gloria Dominguez-Bello |
| Lecture 26, Future of the microbial planet: one health. 2nd test (one hour) | M. Gloria Dominguez-Bello |
Final Exam/Paper Date and Time
Two tests and two essays. One test and one essay will cover the lectures by Dr. Liping Zhao, the second test and one essay will cover the lectures by Dr. Dominguez-Bello. Each test will be 20% and each essay (1000 words at least) will be 30% of the total score of 100.
Academic Integrity
Read the university's policy on Academic Integrity . The principles of academic integrity require that a student:
- properly acknowledge and cite all use of the ideas, results, or words of others.
- properly acknowledge all contributors to a given piece of work.
- make sure that all work submitted as his or her own in a course or other academic activity is produced without the aid of impermissible materials or impermissible collaboration.
- obtain all data or results by ethical means and report them accurately without suppressing any results inconsistent with his or her interpretation or conclusions.
- treat all other students in an ethical manner, respecting their integrity and right to pursue their educational goals without interference. This requires that a student neither facilitate academic dishonesty by others nor obstruct their academic progress.
- uphold the canons of the ethical or professional code of the profession for which he or she is preparing.
Adherence to these principles is necessary in order to ensure that:
- everyone is given proper credit for his or her ideas, words, results, and other scholarly accomplishments.
- all student work is fairly evaluated and no student has an inappropriate advantage over others.
- the academic and ethical development of all students is fostered.
- the reputation of the University for integrity in its teaching, research, and scholarship is maintained and enhanced.
Failure to uphold these principles of academic integrity threatens both the reputation of the University and the value of the degrees awarded to its students. Every member of the University community therefore bears a responsibility for ensuring that the highest standards of academic integrity are upheld.
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