Course Overview
Introduction to Microbiomes
11:680:104
Spring Semester
Cross-Listed with: Current Issues in Evolutionary Anthropology: Introduction to Microbiomes (01:070:297:01)
Contact Information
Instructor: Dr. Maria G Dominguez-Bello
Dept. Biochemistry and Microbiology
917-565-1142
mg.dominguez-bello@rutgers.edu
Office Hours: By appointment
Course Website, Resources, and Materials
Textbook: There is no textbook for this course, but lay public books on the microbiome will be recommended.
Articles on Microbiome, to discuss in class.
Examples of press articles:
Examples of review and original articles:
- Ley, R. E., et al. (2008). "Worlds within worlds: evolution of the vertebrate gut microbiota." Nat Rev Microbiol 6(10): 776-788.
- Mueller NT, et al. The infant microbiome development: mom matters. Trends in molecular medicine. 2015:21(2):109-117.
- Dominguez-Bello MG and Blaser MJ. Microbes as markers for migrations of individuals and human populations. Annual review of anthropology. 2011:40:451-474.
- Ruiz-Calderon et al. Walls talk: Microbial Biogeography of Homes Spanning Urbanization. Science Advances. 2016: 2(2):e1501061-e1501061.
- Lozupone, C. A., et al. (2012). "Diversity, stability and resilience of the human gut microbiota." Nature 489(7415): 220-230.
Course Description
This is a lecture course for students with minimal science background, including undergrads or graduate students from non-biological/health disciplines. There are no prerequisites for the course, which expects to attract students from natural sciences, health sciences, anthropology, sociology, engineering, urban studies, etc.
The course describes principles of host-associated microbes, how do humans acquire them, their functions, the terminology of ecological principles relevant to microbiomes (such as resilience, resistance, diversity and stability). The general content includes principles of evolution of microbial life and hosts, symbioses, ecology, pathogens, degradation of the human microbiota and restoration potential.
There is basic level discussion of press releases and of review papers. The main focus of the course will be on the importance of host-associated microbes to health (mostly to humans) and the consequences of the impact of human activities and lifestyles on the microbiome diversity.
The course will consist on classes with discussion, including in depth discussion of a lay public article and of scientific reviews or original scientific work towards the end of the course.
The course provides a top-down approach to learning about the microbial world and host associated microbes, providing students with a level of understanding on the general trends associated with urbanization, including understanding the many antimicrobial practices of urban societies that are impacting the early transmission, colonization and engraftment of microbes in the body, and their consequences for normal immune development and later disease risks. The subject is of interests to the fields of anthropology, sociology, biology, mathematics, ecology, computational biology, engineering, urban planning, architecture, medicine, nutrition, agriculture, biotechnology and fields of science related to modernization and industrialization.
Reading assignments will include articles and review papers, or book chapters that will be discussed in class, and on which students will write a summary. The class discussion of the papers and the written summary will be part of the student evaluation.
There will be three midterm evaluations, of general knowledge at adequate level of the course.
Assessment plan. As I recall, this is needed for every new course proposal.
Course number and level. Course level is 100.
There will likely be some students who have taken Living in the Microbial World (100-level) who will be interested in this course.
To familiarize students with microbial ecosystems living on hosts
To read scientific research papers and critically present their content
Learning Goals
The course aims to inform students on why and how the microbiome is a new field of study, why is it important and how it is being degraded by an urban lifestyle. The course will familiarize students with the field, and enable them to understand science news about advances that reach mass media, as well as the abstract of scientific papers.
Students in this course will:
- Understand the basic concepts and functions of host-associated microbiomes.
- Develop scientific literacy to understand current news on microbiome advances, value of probiotics, of natural birth and natural exposures, and impacts of modern lifestyle.
Assignments/Responsibilities, Grading, and Assessment
Course Grading (subject to change)
| Point Allocation | |
|---|---|
| First midterm evaluation | 10% |
| Second midterm evaluation | 20% |
| Third midterm evaluation | 20% |
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
| Lecture | Date | Topic | Lecturer |
|---|---|---|---|
| 1 | Tue Jan 22 | Introduction to the course | Dominguez-Bello |
| 2 | Thu Jan 24 | Evolution of microbial life on Earth | Guest lecturer |
| 3 | Tue Jan 29 | Symbiosis host-bacteria | Liping Zhao |
| 4 | Th Jan 31 | Microbiome functions- | Dominguez-Bello |
| 5 | Tue Feb 5 | Paper discussion microbiome 1 | Dominguez-Bello |
| 6 | Th Feb 7 | Paper discussion microbiome 2 | Dominguez-Bello |
| 7 | Tue Feb 12 | Paper discussion microbiome 3 | Dominguez-Bello |
| 8 | Th Feb 14 | Evaluation I (covers Lectures 1-7) | Dominguez-Bello |
| 10 | Tue Feb 19 | Microbiome in early life Dominguez-Bello | |
| 11 | Thu Feb 21 | Ecology: Niches, populations and communities | Guest lecturer |
| 12 | Tue Feb 26 | Basic ecology principles in ecosystems (Richness, assembly of communities) | Dominguez-Bello |
| 13 | Thu Feb 28 | Microbiome functions | Dominguez-Bello |
| 14 | Tue Mar 5 | Microbiome functions- nutrition | Liping Zhao |
| 15 | Thu Mar 7 | Microbiome and health | Dominguez-Bello |
| 17 | Tue Mar 12 | Microbiome and health | Liping Zhao |
| 16 | Th Mar 14-22 | SPRING BREAK | |
| 17 | Tue Mar 26 | Microbiome and health | Dominguez-Bello |
| 18 | Th Mar 28 | Evaluation II (covers lectures 10-16) | Dominguez-Bello |
| 19 | Tue Apr 2 | Paper discussion microbiome 4 | Liping Zhao |
| 20 | Th Apr 4 | Paper discussion microbiome 5 | Liping Zhao |
| 21 | Tue Apr 9 | Paper discussion microbiome 6 | Liping Zhao |
| 22 | Th Apr 11 | Microbiome and diseases | Dominguez-Bello/Liping Zhao |
| 23 | Tue Apr 16 | Probiotics | Liping Zhao |
| 24 | Th Apr 18 | Microbial anthropology - microbiome degradation | Dominguez-Bello |
| 25 | Tue Apr 23 | Microbial anthropology - microbiome degradation | Dominguez-Bello |
| 26 | Th Apr 25 | Pathogens - colonization resistance | Liping Zhao |
| 27 | Tue Apr 30 | How to restore Health | Dominguez-Bello |
| 27 | Th May 3 | Evaluation III (covers Lectures 1-27) | LZ 10 |
Final Exam/Paper Date and Time
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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