Human Microbiome Course

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.

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.

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.

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.

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).

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.

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.

Instructor: Jiho Sohn 

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

b) Rodent models.

c) Other animal models.

Instructor: Drs. Animesh Sinha/Kristina Seiffert

a)   The normal skin microbiome.

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

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. 

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.

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.

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). 

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.

Instructors: Dr. Robert Genco and all faculty.

Multiple choice and short answer exam