As a postdoc Alex Almeida used bioinformatics to push the boundaries of what we know about the gut microbiome. Here, Almeida explains how his time at EMBL-EBI generated new research avenues, and how the skills and connections from his postdoc prepared him for leading his own research group at the University of Cambridge.
My postdoc fellowship was split between Rob Finn’s group at EMBL-EBI and Nick Thomson’s group at the Wellcome Sanger Institute. My role involved a strong research element, and in addition I helped to develop EMBL-EBI’s MGnify data resource for microbiome data.
The work I did at EMBL-EBI really set the foundation for what I do now, and opened up opportunities to set up my own research group.
“I was a self-taught bioinformatician, but at EMBL-EBI I learned how to manage huge datasets, much bigger than anything I had worked with before, which is absolutely crucial for microbiome research.”
During my postdoc I used computational methods to get a global picture of the composition and diversity of the microbe communities living in the human gut. The gut microbiome has been a hot topic for over a decade, and we weren’t expecting to find many novel bacteria and viruses living there. So you can imagine how shocked we were when 70% of the bacterial species we identified using computational methods turned out to be basically unknown to science. This is because many of the bacteria that happily live in the human gut haven’t yet been cultured in a lab, so they are essentially invisible to experimentalists.
We were then able to show that certain groups of bacteria were linked with aspects of human health. This opened up an exciting new area of study, which I was keen to pursue.
I’m a Principal Investigator for the Microbiome Function and Diversity lab at the University of Cambridge. This is continuing my postdoc work on the study of human gut microbes that can’t yet be grown in a lab, and what role they play in human health.
Many groups tend to focus on studying the links between the microbiome and a specific disease, such as inflammatory bowel disease or colorectal cancer. We’re taking a different approach and looking at the overlap between diseases to see if there is a common trend of the microbiome in unrelated diseases. This becomes particularly interesting when you start incorporating diseases that are not directly associated with the gut, such as Parkinson’s or Alzheimer’s disease for example.
EMBL had a tremendous impact on my career. It gave me the training and skills I needed on the technical and leadership side, to become a principal investigator.
On a personal level, my time at EMBL was marked by major life events. I got married, my son was born, I bought my first home, and lived through a pandemic. I was incredibly lucky to have a supportive team and supervisor, and I’m thankful for the opportunity to grow alongside the organisation.
My work at EMBL was purely computational, so I was able to really hone my bioinformatics skills. This was incredibly useful because until then I was a self-taught bioinformatician, but at EMBL-EBI I learned how to manage huge datasets, much bigger than anything I had worked with before, which is absolutely crucial for microbiome research.
I also had a chance to learn and apply leadership skills. I was appointed to supervise several colleagues, which was useful for learning how to delegate tasks, manage and support others. These skills are essential in my current role as a Principal Investigator.
I also took advantage of the in-house training EMBL offers to postdocs and staff. The courses on grant writing, scientific writing and leadership skills were particularly useful and I still apply the learnings on a daily basis.
The scientific courses and seminars I had access to at EMBL and on the Wellcome Genome Campus were invaluable, not just for hearing what other researchers were doing, but for sharing my work, which resulted in new questions and collaborations. I was also involved in teaching a few courses, and this was a worthwhile experience.
One thing is just how important open data is. All my research since 2017 has used primarily publicly-available data, such as those managed by EMBL-EBI data resources. The discovery of novel viruses and bacteria in the gut microbiome wouldn’t have been possible if other researchers had not shared their data in public archives.
I’m incredibly grateful to the researchers taking the time to make their research data open because they are driving discovery. Having done lab work myself, I understand the effort that goes into field work, collection, processing samples, and I realise the extra steps involved in sharing data. But it’s so valuable to the community and for moving science forward. Comparing and contrasting datasets is essential, as having access to data from different origins allows us to compare the results, see how robust they are and observe wider trends.
“I’m incredibly grateful to the researchers taking the time to make their research data open because they are driving discovery.”
I hope to make significant contributions to the field, showcasing the power of genomics and metagenomics to investigate the things that are hidden within the gut microbiome. Importantly, I also want to help the members of my group have a positive experience, and support them in their research, training and career progression.
There are a lot of discussions about the challenges of academia, and I hope I can contribute to a positive and inclusive culture.
I know from experience that in research it’s important to be flexible so you can find a niche that interests and motivates you. So giving freedom to people on my team is important. I also want to understand what their career goals are and how I can help them progress towards that.
And of course, creating a positive atmosphere in the team is important, and being understanding about individual challenges and circumstances.
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