Thesis defense Cayetano Pleguezuelos Manzano: Modeling host-microbiota interactions in disease using organoid co-cultures

Trillions of bacteria inhabit our body. While most of these bacteria are harmless or even beneficial for us, their presence can cause diseases as well. The mechanisms by which these bacteria cause diseases nevertheless remain largely unknown. In his thesis, Pleguezuelos Manzano took a novel approach to fill this knowledge gap.

Infection in a dish

To find out how bacteria trigger diseases, he developed new model systems that allowed him to study the interaction of bacteria with human cells. He explains: “Current in vivo models and bacterial cultures to study these interactions have several disadvantages. We now made use of the fact that it has become possible to grow mini-organs in the lab, called organoids and added bacteria to them. The fact that the organoids are simplistic versions of our organs makes it possible to look into the interaction of our cells with the bacteria in a clean manner and shed light on how they cause diseases.”

Bacterial footprints

In a collaboration with Jens Puschhof (Organoid group) and Axel Rosendahl (PMC), Pleguezuelos Manzano used these so-called co-cultures to study the effect of pks+ E.coli bacteria in our gut on the development of colorectal cancer. Although the presence of these bacteria had long been associated with the disease, their role in its onset remained undetermined. Pleguezuelos Manzano: “We discovered that the bacteria left a very specific mutational signature in gut cells of the organoids. This mutational signature is like a footprint left on our DNA by the bacteria.” The researchers then examined the DNA of colorectal tumors and found that these samples from colorectal cancer patients frequently show this same footprint. “I think that this discovery was the main highlight of my PhD, as we were the first to show that bacteria induce mutations that are found in cancer samples. The results could therefore have broad implications. For example, in the identification of individuals at high risk of developing cancer.”

A conversation with bacteria

Another bacterial problem that is increasingly prominent nowadays, is the rise of antibiotic resistant infections. In that light, Pleguezuelos Manzano set-up a second co-culture of airway organoids and P. aeruginosa bacteria to model chronic infections of the airways in collaboration with Wouter Beenker (Den Hertog lab). These infections are a common issue in patients that suffer from cystic fibrosis and lead to severe complications. “We discovered that the presence of the airway cells in our culture changed the behavior of the bacteria. This emphasized that communication between cells of the host and bacteria has a large impact on the behavior of bacteria and thereby possibly on drug responses as well. Our co-cultures are a unique tool to study this communication in more detail and get a better understanding of how bacterial infections arise.”