Could you tell us a bit about what you’re working on?
I am currently studying the human gut microbiome and its transmission and evolutionary processes in disease conditions (e.g. inflammatory bowel disease: IBD) and within families in the Hildebrand group. Most of my research relies on metagenomic sequencing and using this data to explore the relevance of intra-specific variation in the microbiome. For example, preliminary data from our ongoing meta-analysis suggest microbiome shifts at the intra-specific strain level that seem to differ from those observed considering only species-level data, both of which appear to be associated to disease status.
Currently, I am developing approaches to identify strains and their associated gene content to leverage the information available at the intra-specific level to better understand human microbiome dynamics.
I was hooked on the relevance on intra-specific variation in host-associated microbiomes and I decided to explore these kinds of questions in a much more complex system – the human microbiome.
And how did you come to be working in this particular research area?
I have always been fascinated by symbioses, more specifically the interaction between microorganisms and eukaryotic hosts and their evolution. During my PhD in the Symbiosis Department of Prof Dubilier at the Max Planck Institute for Marine Microbiology, I studied a highly specific intracellular symbiosis between sulfur-oxidizing bacteria and mussels that occur at hydrothermal vents in the deep sea. These mussels rely on their bacterial symbionts to produce biomass from an inorganic, chemical energy sources. Even though initially this system seems very simple, we soon realised the devil is in the detail. We discovered that despite representing a single bacterial species, we find various strains of this species inside the mussels. We hypothesised that this strain diversity, instead of being detrimental, represents an adaptive advantage for the host making it more adaptable to sudden environmental changes.
we are trying to push the limit of taxonomic resolution and associated gene content
After my PhD, I was hooked on the relevance on intra-specific variation in host-associated microbiomes and I decided to explore these kinds of questions in a much more complex system – the human microbiome. Like the deep-sea mussels also we humans rely on our microbiome to thrive and survive. Even though this system is very different from marine symbioses, most of the questions are essentially the same in both, and many other, environments: what is the relevance of intra-specific variation for the host-microbe interaction? Does it matter which strain is present? Does host-microbiome interaction manifest at the intra-specific level and what can we learn by studying this?
What would you say is the highlight of the research you are doing?
I think it is difficult to pinpoint a single highlight of my research. One of my favourite aspects is that we are trying to push the limit of taxonomic resolution and associated gene content to improve our understanding of microbe-host interaction in health and disease.
The realisation that these bacteria can essentially make entire pieces of iron disappear with potentially huge consequences in the environment, such as oil pipeline corrosion, really blew me away.
Was there someone/ something or an event that inspired you to work in environmental microbiology?
I think my passion for microbiology started when I was still in my Bachelors and worked a part-time job at the Max Planck Institute for Marine Microbiology with Dr Dennis Enning in the Department of Prof Friedrich Widdel. In this position I worked on a project studying iron-corroding bacteria that occur in marine sediments. The realisation that these bacteria can essentially make entire pieces of iron disappear with potentially huge consequences in the environment, such as oil pipeline corrosion, really blew me away. The second factor that played a big role for me was the International Max Planck Research School for Marine Microbiology (MarMic) where I did my Masters and PhD. It included a lot of training in research labs as well as field work in marine sediments. I think getting hands-on experience with samples, protocols, microscopy and molecular biology as well as the theory behind all has been a big part of my excitement for environmental microbiology.
But I think the realisation that no environment, animal or plant can exist without microbes has driven me to study symbioses, interaction and community dynamics in environmental samples rather than focusing on laboratory conditions.
How have you found working through a pandemic? Has this affected your research?
I consider myself one of the lucky scientists where the pandemic had relatively little impact directly on my research. Most of my work is computer-based and we already had the data for one of the projects that I am working on. Also, I did not have any personal caring responsibilities which I think would have made things much harder. That being said, I have worked most of the time during the pandemic from home which is becoming increasingly difficult. The lack of personal contact and scientific (and non-scientific) exchange with friends and colleagues has a detrimental effect on focus and motivation in my opinion. I think a lot of scientific discussion happens by just asking that quick question to your office-neighbour, and this casual exchange has been completely erased by working from home.
What are your plans after you complete your current research project?
I am really enjoying the work I am currently doing, and finishing my ongoing projects will take some time as I am less than 1 year into the position. In the long term, I would like to apply for funding to focus and deepen my own research questions about the human gut microbiome and its interactions with the host.
I think we are already knee-deep in a trend of producing a lot more data than we currently have the knowledge and tools to analyse at this scale.
What do you imagine environmental microbiology would be like as a research area in 10 or 20 years’ time?
I think we are already knee-deep in a trend of producing a lot more data than we currently have the knowledge and tools to analyse at this scale. I think the next 10 to 20 years will need the computational methods to catch up to sensibly analyse and connect the vast amount of metagenomics, transcriptomics, metabolomics, environmental data and more. So, I think this is going to be a great time and challenge for computational biologists. That being said, in my opinion what is needed to ultimately prove a process or interaction we often need experimental microbiology, and the current efforts of upscaling high-throughput bacterial culturing are important to keep up with and complement the culturing-independent methods.
Do it with an open and curious mind.
What advice would you give to anyone wanting to embark on a career in environmental research?
Do it with an open and curious mind. One key aspect that I have learned during the short time of my career is that sometimes we focus too much on just our system or that one method. But by looking to other fields and systems we find so many transferable theories and ideas. By zooming out and learning about these we make our own research so much richer and may be able to see broader patterns as well.