“Now what? Science journeys into host associated microbiomes”

With the closing of the fall semester, I said goodbye to the students in my AVS 254: Introduction to Animal Microbiomes class. Despite the challenges and turmoil of fall 2020, these students have been engaged, enthusiastic, and creative. After presenting lectures on the microbial communities in and on animal hosts and how they can impact health and fitness, for the final class of the semester, I wanted to close with perspectives from the broader world of science.

To that end, I compiled several videos of “science journeys”, as told by active researchers in host microbiology, with an introduction to the class/video and my own science journey. I hope to compile a new volume each year I teach the class, to gather diverse paths.

I am extremely grateful for the time, effort, and thoughtfulness of the researchers who were able to contribute during a hectic semester to volume one:

  • Edna Chiang, University of Wisconsin Madison, @EdnaChiang  
  • Dr. Kaitlin Flynn, Benaroya Research Institute in Seattle, @microkaitlin  
  • Kiran Gurung, University of Groningen, @kirangurung29  
  • Jocelyn R. Holt, Texas A&M University, @JocelynRHolt  
  • Chissa Rivaldi, University of Notre Dame, @Powerofcheez  
  • Dr. Laura Tipton, Chaminade University of Honolulu, @lauraomics  
  • Dr. Benjamin Wenner, The Ohio State University, @Bynjammin

Reblog: “Animal and veterinary sciences seniors: Capstone stories”

Starting this fall, I have been teaching the UMaine Capstone Experience courses for Animal and Veterinary Sciences students (AVS 401 and 402). To complete the University of Maine requirements for graduation, students must participate in a Capstone Experience to knit together the work of their undergraduate degree into a cohesive project. AVS students are required to part pate in research under researcher mentorship. Some of those students felt comfortable sharing short descriptions of their project. The slightly edited summaries and my intro were posted to the University of Maine news page for teaching experience updates.

All 3 UMaine undergrads in the Ishaq Lab made Dean’s List Spring 2020 !

Congratulations to all three University of Maine undergrads in the Ishaq Lab for making the Dean’s List in Spring 2020: Jade Chin (AVS), Nicholas Hershbine (EES), and Emily Pierce (AVS)!!

Note, the Bowdoin Dean’s List is announced annually in the fall.

New course approved: AVS 454-554 DNA Sequencing Analysis Lab

A second course that I developed was accepted at the University of Maine! AVS 454-554 DNA Sequencing Data Analysis will be offered to undergraduate and graduate students starting Spring 2021.

AVS 454-554 teaches bioinformatics using DNA data. Starting with raw DNA sequencing data, students go through the process of quality assurance, statistical analysis, graphics design, as well as drafting a scientific manuscript. The course integrates research into teaching by using unpublished data, ideally data the students bring from their own research projects. Not only do students learn highly sought-after analytical and scientific writing skills, but it makes them active participants in research and their own learning. Most of the course time and skillset are focused on amplicon sequencing data, but we’ll also dabble with whole-genome, metagenomics, and metatranscriptomics.

Along with my Introduction to Animal Microbiomes course, I hope to get students interested in microbial ecology earlier in their studies, such that they have time to get involved with microbial ecology research in Maine in time for them to develop a Capstone research experience around it in their senior year. And what a coincidence, I’ll be teaching the Capstone courses for AVS (401 and 402) starting in fall 2020, as well.

This course is based on the precursor version, AVS 590, which I taught as a small, special topics version in the 2020 spring semester. And, even that is conceptually based on a lab section I taught at Montana State University in 2015 and 2016. DNA data analysis and I go way back.

Photo credit: Tom Rayner, Tenure Chasers

It can take several months to get course proposals approved, especially if you are proposing they meet general education requirements, are listed as required for a major degree, or have other levels to them. I started Sept 1, and the AVS faculty curriculum committee, the first step in the approval process, was meeting in early October. I didn’t have time to develop two course proposals in time, so I first proposed my data analysis course as a “special topics” version. These versions are offered selectively and are not counted the same way as an approved course. But, it gave me time to shore up my teaching materials, and teach several students who were graduating and couldn’t wait another year to learn these skills.

DNA sequencing data analysis is challenging to teach as well as to learn, but once over the learning curve, it can be extremely fun and rewarding. I’ve previously taught bioinformatics to undergraduates, and have or continue to publish with a number of them. In AVS 590 in the 2020 semester, there were 4 datasets being analyzed, and 3 of those led to manuscripts which are anticipated to be submitted to for review in scientific journals sometime this year!

R coding group at the University of Oregon, 2018

Podcast interview on the Maine Beacon

This week, I chatted with Mike Tipping, Communications Director of Maine People’s Alliance, and Ben Chin, Deputy Director of Maine People’s Alliance, on my recent publication on ‘microbes and social equity’ in PLoS Biology and the blog version found in the Conversation. We chat about social policies currently under discussion and how they can impact your microbes, why you should care about your neighbor’s microbes, and steps you can take to be a mire microbially-minded and socially-minded community member.

Check out the podcast here:

You can catch up on previous interviews at these fine outlets:

AVS 254: Introduction to Animal Microbiomes

My first official course at the University of Maine has been approved! Starting Fall 2020, I will teach AVS 254: Introduction to Animal Microbiomes!

This 3-credit course is geared towards undergraduates with a science background, with sophomore status or higher. Some familiarity with microbiology, genetics, mammalian anatomy, or microbial ecology would be helpful, but is not specifically required.

The working syllabus can be found here, with more information on lectures, assignments, workload, classroom policies, and more:

Description:  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. 

Application open for the Microbial Friends & Foes Research Experience for Undergraduates (REU) Summer Program at Cornell.

Poster describing The Cornell Institute of Host-Microbe Interactions and Disease (CIHMID) program for Microbial Friends and Foes Summer Program.

“The Cornell Institute of Host-Microbe Interactions and Disease (CIHMID) is accepting applications for the NSF-funded Microbial Friends & Foes Research Experience for Undergraduates (REU) Summer Program (bit.ly/REU-CIHMID).  Applications are due February 1, 2020.

The Microbial Friends & Foes Program will take place from June 8 to August 14, 2020.  The program will provide training in the concepts and experimental approaches central to understanding microbial interactions with eukaryotic hosts.  Students will learn about broad diversity of microbe-eukaryote interactions through conducting independent research projects, participation in weekly research group meetings, seminars presented by CIHMID faculty, Microbial Friends & Foes Synthesis Panels, CIHMID Summer Symposium, and Microbial Friends & Foes Poster Session. Emphasis will be placed on appreciation of the scientific method and developing effective strategies for conducting research as well as on the synthesis of concepts important to interspecific interactions across diverse systems.  In addition, workshops in electronic database literacy, science citation software, research ethics, science communication, and planning for graduate study will be offered to the Microbial Friends & Foes program participants. Students will receive a stipend of $6000, travel subsidy, meal allowance and on-campus housing.  Applicants will be asked to identify 3 laboratories of interest, and will be selected in a two-step review process by the program organizers and potential mentors. A flyer describing the program is attached and more information can be found at bit.ly/REU-CIHMID.


*All undergraduate students interested in understanding microbial interactions with eukaryotic hosts.

*Members of minorities underrepresented in science, undergraduates from small colleges, and first-generation college students.

*Applicants must be United Stated citizens or permanent residents and at least 18 years old.”