Dr. Erik Bakkeren

PhD

Pronouns: He/Him

Positions

Assistant Professor

Faculty of Science, Department of Biological Sciences

Contact information

erik.bakkeren@ucalgary.ca

Web presence

Lab website

Phone number

Office: 403.220.8473

Location

Office: BI429C

Preferred method of communication

Background

Educational Background

BSc Honours in Microbiology and Immunology, University of British Columbia, Canada, 2015,

MSc Microbiology and Immunology, ETH Zurich, Switzerland, 2017,

PhD Sciences, ETH Zurich, Switzerland, 2020,

Biography

Dr. Bakkeren obtained his PhD from ETH Zurich in the lab of Dr. Wolf-Dietrich Hardt, working on the evolution of bacterial pathogens in the gut, using Salmonella Typhimurium as a model system. Then, Dr. Bakkeren went to the University of Oxford for his postdoctoral research in the lab of Dr. Kevin Foster to study the ecology and evolution of microbial communities, such as the gut microbiome. Dr. Bakkeren then started his lab in 2025 at the University of Calgary as an Assistant Professor.

Research

Areas of Research

Understanding the gut microbiome

I am interested in how the microbes that colonize our gastrointestinal tract affect us. These microbes, collectively called the gut microbiome, have important properties like helping us extract nutrients from our diet, developing our immune system, and protecting us against disease caused by pathogenic microbes. The gut microbiome is also both very diverse and highly individualized, meaning that compositional context is incredibly important for understanding microbiome effects. Therefore, my approach is to test properties of the gut microbiome across a wide-range of microbiome community compositions to find general mechanisms and understand their context-dependence. The overall goal is to understand how and why some microbiomes predispose us to colonization by harmful strains, and why some microbiomes modulate disease outcomes.

Microbial interactions

Microbes commonly live in communities where they interact with both each other and their environment, such as in the gut microbiome. Microbial interactions are wildly diverse: Strains can compete for resources like nutrients and space, encode deadly microbial weapons that actively kill competitors, or feed end-products of metabolism to promote another species' growth. How do microbial interactions within the gut microbiome influence community composition and function? Which types of interactions are most influential in determining success of a given species? My goal is to answer these questions in order to design new strategies to edit the composition of the microbiome for our own benefit.

Antibiotic resistance

Antibiotics are still one of the best strategies to control pathogenic bacteria, despite widespread resistance that can lead to treatment failure. The gut microbiome can be a reservoir of antibiotic resistant strains that can cause problems if resistance spreads to harmful species. I am interested in both how antibiotic resistance can spread with microbial communities like the gut microbiome, as well as how one can come up with alternative strategies to control harmful bacteria to synergize with antibiotics, or even replace them.