Faculty of the Microbiome Initiative are involved in several graduate programs, and teach courses relevant to the Microbiome Initiative mission. See below a sample of recent courses.

GRS BI 594: Topics in Biology: Quantitative Microbiology

Instructor: Prof. Joe Larkin

This course covers mathematical models used to describe bacterial behaviors and phenomena including growth, multispecies interactions, motility, and cell differentiation. Includes an introduction to python (no programming experience needed). Techniques/approaches learned are applicable to any area of the life sciences.

CAS BI 411/GRS 611: Microbiome: Our Intimate Relationship with Microorganisms

Instructor: Prof. Horatio Frydman

The microbial community - referred to as "microbiome" - that colonizes our body plays an important role in our health. Topics include (1) the human microbiome; and (2) fundamental aspects of the interactions between animals and the microorganisms that reside on them. Three hours lecture; one hour discussion.

Seeing is Believing: Exploring Marine Microbes through Fluorescence In Situ Hybridization Microscopy

Instructor: Prof Jeffrey Marlow

Microorganisms are the most abundant form of life in the ocean. From the sun-drenched surface waters to the dark abyssal plains, microbes play essential roles in recycling nutrients, supporting higher trophic levels, and absorbing climate and environmental changes. In recent years, scientists have discovered a stunning array of new microbial life thanks to rapidly advancing DNA sequencing technology. However, high-throughput sequencing often lacks quantitative replicability, and by sacrificing spatial arrangements, key symbioses or other microbial interactions are easily missed. Fluorescence in situ hybridization (FISH) is a critical tool in any microbiologist’s repertoire that uses sequencing as a springboard to develop a deeper sense of specific species’ roles in an ecosystem. The technique introduces fluorescent oligonucleotide probes that bind with target organisms and can be seen under the microscope. By visualizing distinct lineages with strategically designed fluorescent probes, a more quantitative understanding of abundance and potential inter-species relationships is possible. This project-based course will introduce upper-level undergraduate and graduate students to a range of FISH techniques and the research questions they can address, unfolding key topics of molecular biology, microbial ecology, and microscopy in the process. By focusing on microorganisms found in local salt marsh sediments, students will contribute new primary data to a marine ecosystem on the front lines of climate change.

ENG BF 571-A1: Dynamics and Evolution of Biological Networks

Instructor: Prof. Daniel Segrè

The course focuses on mathematical models for exploring the organization, dynamics, and evolution of biochemical and genetic networks. Topics include: introductions to metabolic and genetic networks, deterministic and stochastic kinetics of biochemical pathways; genome-scale models of metabolic reaction fluxes; models of regulatory networks; modular architecture of biological networks.

CAS BI 413 Microbial Ecology

Microbes (bacteria, archaea, and fungi) are the most diverse, abundant living organisms and microbial communities are key contributors to ecosystems. Topics include microbial cell structure and physiology, microbe-microbe interactions including biofilm formation and quorum sensing, and microbe-environment interactions.