AVS 254 Intro to Animal Microbiomes


This course introduces students to host-associated microbiomes; the genomic collection of bacteria, archaea, fungi, protozoa, and viruses present in a host ecosystem. In each lecture, we will focus on an anatomical location, and discuss the host and environmental pressures which select for the resident microbial community.  The material is primarily in animals (mammals, birds, fish, amphibians) but includes some human-specific comparisons. This course will introduce ecological theories (e.g. environmental selection, neutral theory) in the context of microbial communities, the history of host-associated microbiology, and how technology has contributed to or limited our understanding of organisms and their critical role in our health and development. The skill-set objectives include group discussions, reading scientific literature, and scientific writing in a variety of styles and both technical and non-technical formats. 

Course Goals

  • Introduce concepts, techniques, historical background, terminology, and technology of microbial ecology.
  • Familiarize students with online resources, including sequence and other databases, as well as analysis tools.
  • Discuss factors which shape host-associated microbiomes and how the microbiome can affect the host.
  • Review current literature on host-associated microbial ecology.
  • Communicate science in a variety of formats.
  • Discuss topics related to science, such as recognition for achievements and the role of scientists in communicating results to the general public.

In meeting the Population and Environment requirements specifically, students will be able to:

  • Describe how host-associated microbial ecosystems are affected by environmental (external to the body) conditions.
  • Describe how climate change affects range and diet selection, and how this can impact gut microbial communities and animal survival.
  • Describe vertical and horizontal transmission, as well as environmental exposure of microorganisms.
  • Describe the effect of pollution and air quality on health and the microbiome.

Taught every fall. Selected course materials are available through GitHub.


** The syllabus is subject to change.


To describe some common host-microbe interactions, the AVS254 students collaborated on some playlists! Check them out on Spotify:


Attendance: Students are expected to attend lectures, but it is understood that life often precludes this.  Students may attend class virtually, through Zoom, but at least 1 hour of advanced notice is requested.  Students who will miss a significant number of classes, or who require additional accommodations, may contact me to make alternate arrangements.

Class participation: Students are expected to participate in discussions in class.  I strive to create inclusive discussions, but if students still find it challenging to participate please notify me and I will alter the discussion format as needed.

Late Assignments: Assignments will be accepted after the deadline, with a 10% reduction in grade per day.  Assignments will not be accepted after the \ the final exam slot for this class.

Classroom: Supporting inclusion and community in science is an active process that involves both invitation, and support to ensure that the scientific community is and remains an equitable and inclusive place. Students are expected to conduct themselves in a professional and courteous manner, and to abide by University policies.

Campus: “The University of Maine is an EEO/AA employer, and does not discriminate on the grounds of race, color, religion, sex, sexual orientation, transgender status, gender expression, national origin, citizenship status, age, disability, genetic information or veteran’s status in employment, education, and all other programs and activities.” Follow the links for more information.

** I am a “mandatory reporter”.  If you disclose something to me, I am obligated to disclose to the relevant campus Title IX office.  This includes information revealed in class assignments.