Summer 2023 wrap up

It feels like the summer semester just began, and here we are, already preparing for fall classes! There has been so much going on in the lab that I wasn’t able to keep up with regular posts, so here are some of the highlights.


I attended four symposia/conferences this summer, starting with the virtual MSE 2023 summer symposium in early June, featuring 4 days of invited talks organized around themes, and a 5th day featuring contributed short talks (something new we tried this year). The whole week was fantastic and sparked thoughtful conversation on the using of microbial communities to reduce disparities in positive and negative health outcomes, living conditions, and more. You can find the recorded content on the symposium event page.

Next, I went to the Microbiome Day at Boston University in early July in Boston, MA, where I gave the keynote talk.

I went to the annual meeting for the American Society for Nutrition in Boston, MA in mid-July, where PhD students Johanna Holman, Lola Holcomb, and master’s student Marissa Kinney all presented posters, and most of the lab was able to make it to a puzzle quest at Boda Borg.

And, I went to the Ecological Society of America annual meeting in Portland, OR in August to present some recent work on scallop larval rearing tanks and the bacterial communities we found there. That included an unexpected effect of coastal water dynamics and the phase of the moon. That work has recently been published.


The lab has been bustling all summer as we work on several projects. Master’s student Ayodeji Olaniyi has been working on a project to identify Vibrio bacteria isolated from the sides of scallop larvae hatchery tanks, as part of a larger project investigating microbial communities in hatcheries.

Marissa and visiting postdoc Gloria Adjapong have been preparing a 16S rRNA sequencing library for hundreds of scallop tank biofilm samples we collected last year, although I don’t have any photos of that.

Johanna has been leading a team of students (Alexis Kirkendall, Lilian Nowak, Aakriti Sharma, and Jaymie Sideaway) on a culturing project to screen hundreds of bacterial isolates that were collected from the gastrointestinal tracts of mice eating borccoli sprouts. We are testing them for their capacity to metabolize different glucosinolates into anti-inflammatory compounds, as well as grow on different media types. In the process, we found that the bacteria we are using as a positive control likes to move from one test well to another when its favorite media is available — but not when glucose is present.

Looking ahead to fall

This fall, the lab will be supporting Ayodeji to write and defend his thesis, as he is currently looking for research/technician jobs. His thesis focuses on Vibrio bacteria in scallop larvae hatcheries.

We’ll also be preparing to welcome Alexis back as a graduate student in January 2024, to continue her work on bacteria isolated from mice eating broccoli sprouts.

I’ll be teaching two classes this fall, AVS 254 Intro to Animal Microbiomes, and AVS 454/554 DNA Sequencing Data Analysis lab, and with 90 students enrolled between them I will luckily be assisted by Ayodeji and Lola, who will be co-grading assignments with me.

Finally, I’ve got more travel coming up soon, as I’ll be giving a talk at the 9th SoCal Microbiome Symposium in September!

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