Jonathan Rondeau-Leclaire

MSc student (January 2024 - [...])

BSc Biology, BSc Economics, Craft beer specialist

Main project: Assessing the impact of methodological choices in metagenomic studies, with a focus on taxonomic profiling and differential abundance analysis.

Carrer in a nutshell: Since 2011, I've been working in the craft beer sector as a speaker, tap bar manager, events organiser, staff trainer, private events entertainer, radio contributor, occasional writer, homebrewer, collaborator with various regional breweries, and independent craft beer advocate. Most of all, the science of beer always fascinated me; people say I'm really good at explaining complex concepts. Beer is certainly what drove me back to campus to get a degree in Biology, however not with beer-related intents, to the great surprise of my entourage. I am now completing a MSc in Biology and hope to keep doing research and teach bioinformatics and statistics.

Fun facts about me: I am a self-taught German speaker, I shave with a straight razor, my favourite malt is rye, I am partial to British English spelling, I never owned a car, I am a metalhead, I can whistle with my mouth open, I love cilantro, I never use cream for carbonara, and I collect hardcover Stephen King novels.

Academic goals: After joining Isabelle's lab (first as an undergrad intern), I quickly fell down the rabbit hole of bioinformatics, reignited a love for coding lost in the distant past of my Economics studies and got interested in the methods of metagenomics. I want to find out the extent to which methodological choices can influence the biological interpretation of metagenomic data. Why? Because in microbiome research, the path from raw data to actual hypothesis testing is multifaceted and nobody really knows which approach works best. Metagenomes – the digital representation of all DNA found in a sample – are complex sets of data that require multiple steps of processing before being interpretable. As this field is quite young, newly developed methods abound, each tackling various aspects of the typical workflow aimed at generating biologically sound results from extremely noisy data. However, few gold standards exist. My mission is to better understand how to decide on methodology for any given project in order to help microbiome scientists do better science.

After my first internship in this lab, I was privileged to be sent by Isabelle to attend STAMPS 2022, an intensive course on microbiome analysis for advanced graduate students. In 2023, I did an internship at EMBL-EBI in the Microbiome Informatics group, getting hands-on experience with metagenome assembly and novel species discovery. Additionally, I attended a lichen metagenomics hackathon at the Sanger Institute in 2024, exploring these complex organisms through long-reads assemblies. For more about me, you'll find my resume below and more information about my goals on my github page.