On the Map: Experimental Research Uses Cultured Mini-Organs to Study Infections

In what ways do bacteria behave and evolve? How do they make us sick — and what happens when they’re resistant to treatment? 

Lars Barquist, an assistant professor in the Department of Biology, studies bacterial pathogens using functional genomics technologies, collaborating on diverse projects with researchers all over the world.

Prof. Barquist is quite new to the University of Mississauga; he joined the biology department in 2024 after spending the past 15 years working at research institutes across Europe. Barquist was most recently at the Helmholtz Institute for RNA-based Infection Research (HIRI) in northern Bavaria — which, he laughs, is a long way from the bustle of Toronto. 

Now, he’s settled in at UTM and is busy recruiting students for his research team, which currently includes graduate and undergraduate students from across disciplines, along with three postdocs who are based in Germany. Barquist’s is a computational lab; his collaborators typically conduct their work in their respective wet labs and then funnel the data to the Barquist Lab to parse.

The field changed shape quickly across the four short years he was doing his PhD at the Wellcome Sanger Institute, a world-leading genomics and genetics research institute based in the UK. 

“When I started, it was still difficult to do more than a couple of bacterial genomes at a time,” Barquist says. “But by the time I ended my PhD, students were working with sets of thousands of bacterial genomes, and we were starting to think about population genetics and epidemiology. Students were doing ambitious studies where they were tracking the carriage of bacteria across hospitals or refugee camps.”

But Barquist points out that the trouble with genome sequencing is that it tells you what the genome is, but not what it does. 

Bacteria, he explains, are very diverse. Each one has up to 5000 genes. But if you look at a particular species, hundreds of thousands of genes might go into any one genome.

A core genome encodes the basics the bacteria need to survive, but there are a lot of accessory genes present as well. These might enable the bacteria to survive in a particular niche or to cause infection or disease in a host organism.

In the past, researchers would look at a single gene at a time, but these days sequencers allow researchers to measure thousands of genes simultaneously. The sheer volume of data requires machine learning and statistical models to make sense of the data sets.

“That’s where these functional genomics technologies become very powerful,” says Barquist, “because they give you a way to measure functional aspects of all these different genes.” 

“And the technologies are generic,” he adds. “You can use them to approach all kinds of questions, such as which genes are important for antibiotic resistance, or which genes are involved in degrading plastics.”

Over the past several years, Barquist has been working with collaborators from HIRI and Sweden’s Uppsala University on a new system which uses lab-grown miniature intestines derived from stem cells to ‘map’ how the Shigella bacterium infects the human gut. 

Their research was just published in Nature Genetics* — and it offers a new way for researchers to investigate other serious infections that affect humans.

Shigella is an invasive pathogen which causes millions of intestinal infections each year globally, with nearly 900 cases reported annually in Canada — and, for susceptible populations, such as young children and the elderly, and people with co-morbidities, it can lead to death. 

For this project, the team established an organoid model for Shigella flexneri, a classic model for Shigella infection. Barquist explains that Shigella has historically been studied using cancer cell lines, but it wasn’t clear how relevant the previous findings were to human infections. These organoids were derived from primary tissue of actual patients and recapitulated key aspects of how the human intestine is organized. 

Focusing on the genes responsible for Shigella’s invasion of the intestines, the team developed the experimental pipeline, optimizing every step as they moved between wet and computational labs: growing bacteria in cells, infecting the organoids, extracting the DNA, and then sequencing it.  

They ultimately developed a statistical model to generate a comprehensive map of the genes Shigella uses to invade human tissue and establish infections. 

It’s groundbreaking work.

“Once you have that map, it gives you a bunch of leads to follow up on — we found that of 5,000 genes, about 100 of them are really important for infection,” Barquist says. “So, in terms of treatment and drug development, there could be some underlying molecular mechanism that might be a target to interfere with, or these leads could give us new insight into how the infection is established and how it progresses.”

“Essentially, we can start thinking about ways to intervene, targeting the virulence factors of a particular bacterium.”

The team has been following up on those various Shigella leads, and they have a new paper, which focuses on one of them, now in review. Barquist says they plan to explore the strains which are more relevant to the disease that's currently circulating.