The new Editor-in-Chief of Microbial Genomics: Professor Kat Holt

Posted on February 11, 2019   by Professor Kat Holt

This year, Professor Kat Holt, computational biologist specialising in infectious disease genomics at Monash University and the London School of Hygiene and Tropical Medicine, took over as the Editor-in-Chief of Microbial Genomics. Here, she discusses her work and why the journal is special.


I am primarily a computational biologist, specialising in microbial genomics and its application to the study of infectious disease and antibiotic resistance. I combine microbial genomics with techniques in evolutionary biology, epidemiology and statistics to study how bacterial pathogens spread and cause disease, how they interact with broader microbial communities and how they evade the interventions we use to try to control them, such as antibiotics and vaccines. I also spend a fair bit of time working out new bioinformatics methods to get the most out of microbial genomics data. 

My main research interests are genomic epidemiology of healthcare-associated infections, especially Klebsiella and Acinetobacter, and pathogens of global health importance, such as those causing tuberculosis, typhoid, and dysentery. My research program is based at the Department of Infectious Disease, Monash University in Melbourne, and the London School of Hygiene and Tropical Medicine.

Microbial Genomics (MGen) is uniquely positioned at the intersection of microbiology and genome sciences. While genomics approaches are now widespread and frequently feature alongside other analysis tools in studies published in more traditional microbiology journals, MGen is the place for studies where genomics techniques are central to deriving novel insights. This includes genomic epidemiology and outbreak tracking; functional studies exploring expression of the genome and downstream molecular functioning such as proteomics or metabolomics; and studies of microbial communities or microbiomes.

All areas of application are welcome, from environmental microbiology to infectious disease. We also publish methods papers and are becoming a popular place to report new techniques for analysing and extracting insights from microbial genomic data. MGen has an open data policy, which means all data analysed in our papers are made publicly available so that readers can reproduce and build on the work published in the journal. This is really important in the pathogen genomics field, as pathogen genome sequences can have immense public health utility long after the initial publication. As a lot of papers in our field report phylogenomic analyses, we also encourage our authors to deposit their phylogenies and associated spatial and temporal information with MicroReact, so that our readers can interact easily with this kind of data.

Microbial genomics was still an emerging field when I first became acquainted with it, right around the time that high throughput DNA sequencing became a thing. It’s amazing to see how it has developed and matured since then, and the broad range of applications and insights that the field now supports. The launch of MGen provided a focal point around which to grow the international community of researchers and practitioners working in the field that I love, and so I leapt at the chance to serve that community. I think the community that has crystallised around MGen so far is excellent, with a culture of constructive and rapid reviews, open data etc., and there is a lot more potential to grow and innovate. The field itself is also growing rapidly, thanks to new sequencing tech (portable long-read sequencing chief among them!) and the integration of microbial genomics into public health and diagnostics. I think MGen will serve the community well and continue to be a go-to place to publish new methods and applications as we explore these new challenges and possibilities.