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Women in Science: Elena Rodriguez - the mind of the gut microbiome

Elena, a student on EI's Year in Industry programme, has been investigating the interaction between microbes and the gut, focusing on how probiotics can improve intestinal health, and what this means for the future of IBD research.

July 31, 2019

Elena Rodriguez from our Year in Industry programme is studying the interaction between microbes and the gut, particularly focusing on how probiotics can improve intestinal health, reducing the risk of disease. Elena talks to us about the new cell analysis pipeline she has developed to capture the interaction between bifidobacteria and gut cells, and how this will help future IBD research.

I’m an undergraduate student at The University of Manchester, doing a BSc Biotechnology with Industrial/Professional experience, and spending my third year doing a year-long placement at EI.

In my second year of university, my dissertation supervisor was Professor Simon Hubbard, who was the first person to mention doing my placement at EI. My dissertation was on how fibre affects human health through the study of the microbiota, and when he mentioned that the Korcsmaros Group at EI has an expertise in the microbiota, I was immediately interested.

From the EI website, I was impressed by the state-of-the-art projects and the bioinformatics expertise within the Institute and became very enthusiastic about becoming part of the EI community.

From Elena's first glance at the EI website, she was impressed with the projects and then became very enthusiastic about joining EI

From Elena's first glance at the EI website, she was impressed with the projects and became very enthusiastic about joining EI

Probiotics and Paneth cells

I was already very interested in the study of the microbiota while at The University of Manchester, therefore, it was a big step coming to EI and being able to apply the knowledge that I acquired at university. I went from the theoretical aspect of research to be full-hands-on the laboratory, seeing all the biological mechanisms in action that I learnt during class was amazing!

When I started at EI, I spent my first months understanding the biological background of our research, specifically about bifidobacteria which is a gut commensal commonly used as a probiotic, and about some function-specific cells within the gut’s small intestine, called Paneth cells - essential for regulating the gut microbiome and the renewal of the gut lining.

Paneth cells are one of the key cells important in gut homeostasis – if they work well, we are healthy. We were interested in whether the beneficial effect of bifidobacteria is related to helping Paneth cells working properly.

During her Year in Industry placement at EI, Elena had the opportunity to present a poster at a symposium in London, along with EI colleague Amanda Demeter

During her Year in Industry placement, Elena had the opportunity to present a poster at a symposium in London

Gut bacteria

From this research, we organised and developed the experimental workflow to answer our hypothesis “how does Bifidobacterium breve affect Paneth cells?”. In February, the whole project started to take shape, carrying the laboratory experiments in March. I was very excited to see how my research had gone from literature to experimental actions!

Due to the nature of my project, I was mainly laboratory-based. Nonetheless, systems biology and multi-omics approaches will be essential to accomplish my project objectives. We wanted to develop a robust workflow to expand the research of how other bacteria affect other cell types within the intestine.

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From this research, we organised and developed the experimental workflow to answer our hypothesis “how does Bifidobacterium breve affect Paneth cells?”

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Biomedical treatment

Paneth cells don’t function properly in Crohn’s disease, which is a type of inflammatory bowel disease. We also know that patients with Crohn’s disease have less bifidobacteria in their gut microbiome. Therefore, our main scientific question is very relevant from a biomedical point of view, as well as understanding whether bifidobacteria supplementation can increase the therapeutic efficiency of patients with Crohn’s disease.

The new gut microbiota interaction pipeline we have established will also be used to directly analyse patient samples in the recently opened Quadram Institute (QIB) that will be useful to understand patient-specific effects of Bifidobacteria and possibly design patient-specific therapies.

As our Group is jointly affiliated to both EI and QIB, I was happy to see that a pipeline we established in one Institute can be easily applied in the other Institutes, leveraging cross-collaboration with the research centres’ resources.

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...our main scientific question is very relevant from a biomedical point of view, as well as understanding whether bifidobacteria supplementation can increase the therapeutic efficiency of patients with Crohn’s disease.

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Complex microbiota

The study of gut microbiota has become a hot topic for research in the last decade, and there is still a lot to discover. We believe that through the development of this new workflow, we will be able to better characterise the mechanisms of how the microbiota is affecting us.

By using the cutting-edge bioinformatics analysis at EI; such as multi-omics analysis, combining transcriptomics and DNA methylation data, and systems biology, we will integrate data to better understand this complex interplay, in a more accessible and reusable way for the scientific community.

I also believe that we will help to expand the knowledge on the effects of bifidobacteria on Paneth cells, therefore refining its use as a probiotic treatment for patients.

Elena has gained lots of lab skills during her Year in Industry at EI, from using the FACS to antibody staining in order to achieve some solid results

Elena Rodriguez using computer in the lab

Cross-discipline research

Due to the Korcsmaros Group collaboration with the Quadram Institute, in particular with Lindsay Hall’s Group, who provided us with the expertise and resources to work with bifidobacteria, I have been able to develop many professional and personal skills during my placement.

For instance, I have obtained expertise in the laboratory, especially using the Fluorescence Activated Sorting Machine (FACS), with the help of EI’s Iain Macaulay. The FACS enables us to sort specific cell types based on markers which allow us to analyse the effects of bifidobacteria on Paneth cells only - essential in studying bifidobacteria effects on health.

I also discovered the use of antibody staining with the help of Isabelle Hautefort and Amanda Demeter (Korcsmaros Group), these are important for the technical research aspect: either to sort the specific cells we require (the FACS machine recognises the fluorochromes on the antibodies that stain the cells in order to sort them) or to ensure that we separated the Paneth cells correctly (with the anti-lysozyme staining).

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I have improved my organisational, team-work and communication skills by joining the EI stand at several public engagement events such as the Norwich Science Festival, the Women in STEMM event in Norwich City College, as well as presenting a poster in the JSPS-Crick Symposium on Gut Circuits in London.

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Personal skills

By being part of two different Institutes, EI and QIB, with very different expertise domains, I have been able to attend a wide variety of weekly seminars, widening my knowledge on the gut microbiome-host interaction and bioinformatic analyses in both animals and plants. I have also had the chance to attend multiple courses and workshops, such as Network Biology, Flow Cytometry, and RNA-sequencing, which will be definitely very useful for my future career.

I have improved my organisational, team-work and communication skills by joining the EI stand at several public engagement events such as the Norwich Science Festival, the Women in STEMM event in Norwich City College, as well as presenting a poster in the JSPS-Crick Symposium on Gut Circuits in London (May 2019).

The people at EI are very welcoming and the shared-kitchen in the Institute makes it very easy to meet and socialise with the staff.

Elena enjoying a morning coffee break with Harbans Marway, in the Earlham Institute kitchen

Elena Rodriguez with Harbans Marway enjoying a morning coffee break in the Earlham Institute kitchen

Professional development

Next year, I will go back to The University of Manchester to finish my BSc in Biotechnology. Once I graduate, I am considering doing a Master’s or a PhD in the UK or abroad. Even if I am not sure about what I will do, doing a PhD is something I would have never thought of doing before coming to EI.

So far, with my experience from my University and EI, both have a very wide policy, making sure that men and women alike have the same opportunities in science. In fact, I may have been lucky, but I think that the main selection factor for placements, internships and other professional development opportunities to which I have applied are mainly driven by grades, extra-curricular activities (e.g. volunteering), and skill development events (e.g. mentorship).

I’d like to thank everyone in the Institute, mainly the Korcsmaros Group and Emily Angiolini who gave me advice and support during the whole year.

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Even if I am not sure about what I will do, doing a PhD is something I would have never thought of doing before coming to EI.

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