Modeling Host-Microbe Interactions with Intestinal Organoids

Martina Polleti, Ph.D. Student, Korcsmaros Lab, Earlham Institute
Martina Poletti

Martina is a PhD student at the Earlham Institute and the winner of our Organoid Training Video Contest! Martina's current work focuses on the interactions between Bifidobacterium and the intestinal epithelium in inflammatory diseases such as Crohn's and Inflammatory Bowel Disease (IBD). Read more about Martina's work and watch her video submission below.



 

The Scientist

What inspired you to pursue scientific research?

Since I was young, I was fascinated by the fundamental question of why certain people live healthy and others become sick, and the role played by the environment in determining health and disease. I have always been interested in finding the mechanism responsible for the phenomena surrounding me; choosing to pursue scientific research was a natural step to take.

Do you have a scientific idol that influenced the scientific path you’ve chosen?

Not one in particular, but I will always be grateful to my biology teacher in high school, who inspired me to be curious and to value the scientific method consisting of formulating a strong hypothesis or research question, finding the appropriate methods to test your hypothesis, and validating your results.

What led you to studies in your current field?

During my Masters degree, I discovered how nutrition shapes the gut microbiota, and how commensal bacterial play a key role in gastrointestinal diseases such as Inflammatory Bowel Disease. I also learned how bioinformatics and computational approaches for analyzing big datasets can help generate valuable hypotheses and models to be tested in relevant models. My PhD project, which combines computational and experimental approaches to study the effect of the probiotic Bifidobacteria on intestinal cell function, was the perfect match for me, allowing me to combine these different interests.

What hobbies do you have outside of the lab?

Outside the lab, I pursue my interest for music by playing guitar and singing with my sister and friends, as well as participating in festival and music events. I also love travelling, cooking and trying food from different places in the world.


 

The Science

Please describe the focus of your current research.

My current research is focused on investigating how Bifidobacteria regulate the function of intestinal epithelial cells, their contribution to gut homeostasis, and their potentially beneficial effect against gastrointestinal diseases such as Inflammatory Bowel Disease (IBD), in which intestinal epithelial cell function is altered.

Bifidobacteria are one of the first colonisers of the human gut, and previous studies have shown that they confer positive health benefits to the human host. However, there is a lack of knowledge concerning the specific mechanisms and modulating factors involved, which is mainly due to the absence of good in vitro models to study host-microbial interactions. Intestinal organoids are currently one of the best systems to investigate the interaction between microbes and the specific intestinal epithelial cells.

As part of my PhD project, I generate 2D intestinal organoids (currently from mice models but soon from patient-derived biopsies), which I use to look at the effect of Bifidobacteria on intestinal epithelial cells function. Because this system contains all types of epithelial cells normally found in the intestine, when challenged with bacterial cocktail or products from the apical side, they allow me to look at the effect of microbes on the regulation of epithelial cell functions in a cell-type specific manner. By generating multi-omics data, in combination with computational approaches, I can identify mechanisms by which these Bifidobacteria affect intestinal epithelial cell functions, thereby having an effect on intestinal homeostasis.

I feel extremely lucky to be working with Dr. Tamas Korcsmaros and Dr. Lindsay Hall from the Earlham Institute and Quadram Institute in Norwich, who bring their expertise in network biology and Bifidobacteria research, supporting me with their knowledge and experience to make the realisation of this project possible.

What do you consider to be the most important advance(s) in intestinal organoid research in the last five years?

I think that the biggest advance was the development of intestinal organoid monolayers that are able to self-sustain and can be kept in culture for up to 3 weeks. This is extremely useful for researchers studying host-microbe interaction, as it allows study of cell-specific effects (overcoming the limitations of immortal cancer-derived cell lines such as Caco-2 cells) as well as more high-throughput experiments, by circumventing the need to microinject 3D intestinal organoids with microbes and avoiding the drawbacks associated with that method.

What breakthroughs would you anticipate in the next five years?

I believe that we will see the advent of more co-culture systems to allow study of the complex interplay between micro-organisms, intestinal epithelial cells, and immune cells or other cell types. Furthermore, the incorporation of organoids within microfluidic devices simulating the gut ecosystem will allow high-throughput studies of host-microbial interactions in a highly controlled environment, as well as the possibility to study the effect of the microbiota on intestinal health.

What are the primary research techniques you use in your research?

During my daily work in the lab, I use microbiology techniques to grow my bacterial cultures of Bifidobacteria, which I can subsequently use to challenge organoids. I use cell culture techniques to grow intestinal organoids from mice intestinal tissue, and I will soon also grow human-derived colonic organoids thanks to the state-of-the-art in-built NNUH Endoscopy Centre at the Quadram Institute. I then use single cell and low input sequencing technologies established at the Earlham Institute to generate transcriptomics and methylomics data from organoids. These data can be used to computationally predict the potential beneficial effect and the effect of imprinting of Bifidobacteria on specific epithelial cell functions and on the overall epithelial homeostasis. Besides next generation sequencing, I also apply microscopy- and flow cytometry-based approaches to further characterise organoids upon microbial challenge, as well as to validate the computational predictions.

What has the adoption of organoid cultures added to your research? What types of biological questions has this technique enabled you to probe?

The use of organoid cultures allows me to study the effect of probiotic bacteria on an in vitro controlled system closely reflecting the in vivo structure and function of the intestine. Because organoids contain different intestinal epithelial cell types, I can look at the cell type-specific effect of Bifidobacteria, by separating individual host epithelial cell types through Fluorescence Activated Cell Sorting (FACS). In our group, we use intestinal organoids to generate cell type-specific transcriptomics and proteomics data readouts, which can be integrated into multi-layered networks using bioinformatics and allow the prediction of cellular processes affected by the gut-microbe interaction at the transcriptional, post-transcriptional and post-translational levels. We can subsequently validate some of these predictions experimentally in the lab using organoids, which is very useful to refine the initial hypothesis.

What impact do you see organoids having on your field? What technical hurdles remain before this can be realised?

I strongly believe that by using this system, we can open new horizons in our understanding of 1) how Bifidobacteria interact with host cells 2) which changes contribute to the pathogenesis of Inflammatory Bowel Diseases and 3) how we can restore normal cell functions using probiotics. These approaches are not restricted to study only Bifidobacteria and could be applied to other commensals or pathogens, as well as to study intercellular interactions between epithelial cells and other host cells in co-culture systems (e.g. immune cells).

However, a few technical challenges still need to be tackled. In projects like mine, the main technical difficulty consists in co-culturing the organoid monolayer together with commensal bacteria such as Bifidobacteria, as the former requires the presence of oxygen while the latter mainly requires anaerobiosis. Another hurdle is to maintain the organoid culture conditions standardised, so that experiments can be reliably repeated, and results comparable between different research groups.


Martina is supported by the UKRI Biotechnology and Biological Sciences Research Council Norwich Research Park Biosciences Doctoral Training Partnership [grant number BB/M011216/1]