Fall of 2018

Human Microbiome Course

two students in a lab.

Composition and Function of the Human Microbiome is an elective course challenging students to explore and better understand those microorganisms living in and on our bodies and how they affect our health.

  • An elective for the PhD program in Biomedical Sciences, also for upper level undergraduate students.
  • Two credit hours
  • Two hours per week 

Course Outline

1: Introduction to the Human Microbiome

Instructors: Drs. Robert Genco, Yijun Sun, Michael Buck, Michael LaMonte

a) A overview of course; format, readings, syllabus, grading

b) Description of the bacteria, archaea, viruses, fungi and Protists that comprise the microbiome.

c) The human microbiome, composition at various sites in health.

d) Source of the organisms in the human microbiome.

e) Ecological concepts of disease eg. dysbiosis.

2: How the Microbiome is Studied

Instructor: Dr. Michael Buck

a)   DNA-based analysis of microbial communities, 16S rRNA gene amplicon sequencing and shotgun metagenomics sequencing methods.

b)   Functional analysis of the microbiome from DNA sequence functional analysis, metatranscriptome, metabolome, proteome, and glycome.

3: Techniques Used to Analyze Microbiome Data

Instructor: Dr. Yijun Sun

a)   Assignment of taxonomy; generating OTU tables, quality control.

b)   Describing the complexity of the microbiome eg. alpha and beta-diversity.

c)    Comparing microbial communities, phylogenetic trees, UniFrac, principal coordinate analyses, Venn diagrams, heat maps.

d)   Development of new bioinformatics methods for microbiome studies.

4: The Human Gut Microbes

Instructor: Dr. Susan Baker

a)   Composition and function along the GI tract eg., stomach, ileum and stool.

b)   Gut microbiome changes in various diseases including liver diseases, obesity, diabetes, and other disorders.

c)    Effects of diet and medications on the gut microbiome.

5: The Microbiota of the Oral Cavity and Nasopharyngeal and Respiratory Tracts

Instructors: Drs. Robert Genco and Sanjay Sethi

a) Site specific microbiota in the oral cavity; role in health and disease (Dr. Robert Genco).

b) Site specific microbiota – the lower respiratory tract and lung parenchyma in health and disease (Dr. Sanjay Sethi).

6: Use of the Microbiome in Epidemiologic Research

Instructor: Dr. Michael LaMonte

a) Methodologic consideration, eg., data reduction.

b) Statistical analytic methodologies, bioinformatics and regression analysis.

c) Design and interpretation of results combining microbiome, host genetics, and environmental data.

7: The Human Gut Microbiota

Instructor: Dr. Gary Iacobucci 

a) The gut microbiome in inflammatory bowel diseases, irritable bowel syndrome and colitis.

b) The gut-brain axis-effects of the gut microbiome on behavior, mood, cognition, and role in nervous system diseases.

8: Use of Animals

Instructor: Jiho Sohn 

a) Rationale for use of animal models in microbiome research.

b) Rodent models.

c) Other animal models.

9: The Role of the Microbiome in Skin Diseases

Instructor: Drs. Animesh Sinha/Kristina Seiffert

a)   The normal skin microbiome.

b)   The skin microbiome in various diseases of the skin.

10: The Microbiome of the Genourinary System

Instructor: Dr. Vanessa Barnabei 

a) The vaginal microflora and changes with disease and pregnancy.

b) The microbiome of the placenta and fetal tissues.

c) The microbiome of the breast and of milk.

d) The acquisition of the microbiome by the newborn and development in children. 

11: Modification of the Microbiome

Instructor: Dr. Robert Genco 

a) Effects of antibiotics.

b) Probiotics and prebiotics.

c) Fecal transplant.

d) Future strategies to modify the microbiome at various sites.

12: The Role of the Mycome, Virome in Health and Disease

Instructor: Dr. Mira Edgerton

a)   The mycome and virome in health and disease.

b)   The interaction of the components of the microbiome including bacterial-phage interactions and bacterial-fungal interactions.

13: Functional Studies of the Microbiome

Instructors: Drs. Richard Browne and Robert Genco

a)   Measurement of microbial products (the metabolome, proteome and glycome) (Dr. Richard Browne).

b)   Role of microbiome and its products, nutrition, metabolism, the gut brain axis, and in immune- inflammatory processing (Dr. Robert Genco). 

14 and 15: Realizing the Potential of the Microbiome to Prevent and Treat Diseases

Instructors: Dr. Robert Genco and other faculty. Students present papers on specific topics based on their written papers.

Suggested topics include:

a)   The dysbiosis concept of disease and strategies to shift a dysbiotic flora to one compatible with health.

b)   Designing an effective probiotic, eg., spores, encapsulation.

c)    Selecting and testing prebiotics that foster a healthy microbiome.

d)   Use of the microbiome in screening, diagnosis and monitoring diseases.

All topics selected by students and approved by faculty November 6, 2018 written papers due before session 14, and oral presentations during session 14.

16: Examination

Instructors: Dr. Robert Genco and all faculty.

Multiple choice and short answer exam