Building a genomics career exploring the nasal microbiome

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For Katie Bellis, her curiosity about how bacteria can influence human health and disease inspired her career exploring the nasal microbiome. At the Wellcome Sanger Institute, Katie is investigating bacteria such as Staphylococcus aureus, which can switch from living harmlessly in humans without symptoms to causing infections. Many people have S. aureus bacteria living on them without symptoms, which is known as bacterial carriage. However, some people go on to develop infections. Moreover, if S. aureus acquires resistance to the penicillin group of antibiotics, it becomes the infamous superbug MRSA (methicillin-resistant Staphylococcus aureus).

As part of Dr Ewan Harrison’s group, Katie is exploring questions around S. aureus and bacterial carriage, and what this could mean for the global health challenge of antimicrobial resistance. We recently caught up with Katie to discuss her career in disease genomics and explore the life of a staff scientist at the Sanger Institute.

Right now, most of my time is spent managing studies to increase our understanding of the nasal microbiome in health and disease, but each day looks quite different. Some days I am full-time in the lab, while on others my calendar is filled with meetings or writing. Today really shows how varied my work can be. I started my day in the lab, preparing and processing samples, then I joined a technical meeting about handling microbiome data. Later, I worked on lab logistics, planned out our lab resources, reviewed our latest manuscript, spoke to you, and after this, I will return to the lab. I enjoy this variety and working across different projects.

I’m fascinated by human health and disease dynamics, especially understanding how common microbes can make some people ill and leave others completely fine. How can the same pathogens affect people so differently? The group I am a part of investigates many microbes like this, and especially S. aureus, given its connection to MRSA and the global challenge of antimicrobial resistance. We are focused on the nasal microbiome right now because it is turning out to be a key player in human health and disease, and I hope our work contributes to interventions and maybe even shapes public health policy.

The job title ‘Staff Scientist’ confuses many people looking for a career in genomics – I know it confused me when I considered applying! The staff scientist job description covers a range of things, and there are many options for progression into leadership roles, such as a senior staff scientist, technical lead, or project manager. People in this role can also move around – some go back to teaching or research-based academic roles, while others shift into industry.

My first lab experience was a year’s placement with Public Health England researching Group B strep, or Streptococcus agalactiae, a common bacterium that is usually harmless in adults but can cause serious illness in newborns and can be passed on by the pregnant mother. Specifically, I investigated interactions between Group B strep and the antibody immunoglobulin A in breast milk samples from the Gambia. Thankfully, I discovered I really liked lab work, which was a relief since I’d signed up for an entire year! This was also my first introduction to the science of carriage and disease.

Between working in the lab and spending a summer out in the field counting bats, I figured I needed a career with plenty of hands-on science. I then took a role at the University of Cambridge focused on extracting DNA from bacteria and library preparation, which involves tagging and copying genetic fragments so they are ready for the sequencing machine. We then submitted them to the Sanger Institute for 16S RNA sequencing, which focuses on a highly conserved gene unique to bacteria, which has species-level variations.

During this time, I started working on the CARRIAGE study, which aims to identify why some people carry the bacterium S. aureus, while others never do. Later, I transferred into a microbiology research assistant role, which involved rapidly learning about lab management and setting up the CARRIAGE lab at the Sanger Institute. At its busiest, the CARRIAGE study handled just over 650 samples a week, each taking five days to process, so there were many moving parts. I also managed sourcing lab supplies, including media and reagents. At the start of the COVID-19 pandemic, we paused recruitment to the CARRIAGE study and reapplied our groups’ efforts and experience in diagnostics, genomics, and lab set-up to support the COVID-19 Genomics UK (COG-UK) Consortium and the initial phases of the SARS-CoV-2 sequencing project at the Sanger Institute. We were able to resume CARRIAGE recruitment in 2021 and continued recruitment until 2024.

I was excited for the next analytics phase of the CARRIAGE study, and had learnt so much about working with viral samples, so I was keen to apply for the staff scientist role at the Sanger Institute, which was linked to the CARRIAGE study. The role offers even more variety, working across several projects related to respiratory infections. It allowed me to become more involved in the setup of projects, including the logistics and data management, alongside setting up lab processes for preparing various samples for sequencing.

The CARRIAGE study sample collection is complete, and we have 60,000 nasal microbiome samples from 20,000 participants, alongside their genetic and lifestyle data. We are now at the stage of analysing the data. By understanding who carries S. aureus, and why they do, we hope to be able to predict and potentially reduce the spread of antibiotic-resistant strains, including MRSA. This is crucial for future infection control and potentially reducing the spread of more infectious or resistant S. aureus in the community.

The Sanger Institute is perfect for working on the nasal microbiome because it is set up to handle huge genomics projects efficiently. Another benefit for me is the bioinformatics expertise here, which complements the bioinformatics skills I have been building across my career.

Unlike universities, which can be vast, individualised and spread out, the Sanger Institute’s compact setting means it is easier to find someone with the expertise you need. This closeness is essential for infectious disease research – you can’t exactly hop on a bus with a box of pathogenic bacteria! We have continuity in equipment support, training and maintenance, all of which can be challenging for University systems. Our close-knit environment creates a strong, collaborative culture, which is supported by our outstanding scientific operations teams, who keep the research groups working well together, as well as the logistics and lab media teams. This teamwork really paid off during the COVID-19 pandemic, allowing the Sanger Institute to set up the Genomic Surveillance Unit (GSU) and rapidly sequence and track the virus. Building on the success of this, the Respiratory Virus and Microbiome Initiative (RVI) was set up to track the transmission and evolution of respiratory viruses and understand their interactions with other respiratory microbes.

We have reached an exciting time in the CARRIAGE study because the data are finally ready, so we can start the analysis and address our research questions. Many brilliant nasal microbiome studies have been unable to provide definitive answers because they have been too small in scale. But that is set to change with the CARRIAGE study refining methods and hypotheses, alongside a sector-wide reduction in sequencing costs. This should help us get even larger, more definitive studies. I am also passionate about improving quality control and best practices in microbiome studies. I realise that ‘establishing best practices’ doesn’t sound very exciting, but it is crucial for producing reliable and impactful scientific data. This has also been essential in setting up the RVI sample preparation pipelines. Whilst it has taken time to establish best practices, we can now analyse huge datasets with confidence.

We have seen significant progress with gut microbiome research and public awareness of its importance. I would love to see people start to appreciate the nasal microbiome in the same way, understanding how our nasal bacteria interact with our bodies and influence our health. I hope people also remember that not all bacteria are harmful; even the ones that sometimes are, are not always! So many of our pathogens can also interact with us without causing disease. I am sure that as we build on our knowledge and techniques, we will also be able to include viral and fungal information from the nasal microbiome. I also hope our research will help inform public health policies, reducing the need for antibiotics and preventing infections in other ways. But we can only achieve this through collaboration across the scientific community. Science is a team effort, even if we are working on separate projects.

I keep busy outside of the lab. I am a keen reader – both fiction and non-fiction. I love cooking and enjoy dancing, especially ballet and jazz. I am also a big fan of walking, especially along coastal paths. I do all sorts of handicrafts, though admittedly, depending on the handicraft in question, results may vary!

If I could talk to my younger self about my career, there are probably two things I would say. On a practical note, I would advise myself to take A-level maths because it would have made my time at university easier! More broadly, I would encourage myself to embrace every opportunity, even when I feel it is beyond my expertise or experience. Enthusiasm, interest and curiosity can take you a long way.