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News : Microbial Genomics Spotlight On: Systems Microbiology

28 March 2017

In July 2016 we celebrated the one year anniversary of the Microbiology Society’s newest journal Microbial Genomics. To mark the occasion we have been interviewing the journal’s Senior Editors to find out which topics they are on the look-out for in each of their subject categories. This month we talk to Dr Christos Ouzounis to discuss the hot topics in ‘Systems Microbiology’, to find out what papers he’d like to see more of in his category and discover who inspired him to go into scientific research.

1. What is currently a hot topic in your area of research?
One of the most significant challenges in the area of Systems Microbiology is the comprehensive recording of the omics elements at the genome, transcriptome, proteome and metabolome levels for the systems integration of both data and models. Of course, this is an activity with open-ended objectives that has been growing steadily in the past 10-15 years and there is no sign of it slowing down in the foreseeable future, as all of biology has been following this direction with an unprecedented intensity.

2. Describe your subject category in one sentence
The Systems Microbiology section focuses on the large-scale analysis of microbial genome collections or pangenomes, the comparative analysis of model organisms and metagenomics datasets, transcriptomics and proteomics, interaction networks – as well as predictions of functional significance, such as high-throughput annotations, pathway inferences, ancestral state reconstructions and detection of horizontal gene transfers that perturb phylogenies. Anything to do with big-data acquisition and systems modelling for microbiology.

3. Who has inspired you in your research?
Very many people have inspired me in my research: I have worked with highly intelligent scientists, some of the greats but also many fledgling early-career peers. I have been blessed with very creative and talented colleagues during this journey. One of the most influential people in my career was the late Carl Woese. My thesis advisor Chris Sander guided me during those days at EMBL in the early 1990s and Peter Karp at SRI during my post-doctoral research. Many dear colleagues at the EMBL-EBI, peers and friends from the ISCB/ISMB community, current co-workers at CERTH, associates and collaborators everywhere, and many, many others.

4. What would you like to see Microbial Genomics publishing more of?
In the near future we would like to encourage further submissions in the area of Systems Microbiology perhaps with a twist, preferably shying away from pure hypothesis-free science: a more hypothesis-driven, resource-aware approach for scientific research combined with a view on novel, ground breaking applications would probably be an optimal scenario. Personally, I am interested in the issue of harnessing the unknown planetary biodiversity we have just started exploring with some diligent reverence and those applications that will truly transform our existence from a resource-hungry existence to a more sustainable future.

5. What would you be if not a scientist?
This is a difficult one: somewhere between an adventurer and an archaeologist – combining the outdoors with key intellectual challenges. There are still many mysteries in the world today that remain unexplored, and fieldwork ranging from ecosystem preservation to human history is as important as ever, with evidence being crushed under the weight of our civilization. Despite my strong preference for the natural sciences, this domain still fascinates me, and who knows, one day I might consider a career change! It’s never too late.

Find out more about the journal and how to submit here .

Previous ‘Spotlight On’:

Spotlight On: Microbial Communities with Dr. Alan Walker
Spotlight On: Microbe-Niche Interactions with Prof. Carmen Buchrieser
Spotlight On: Genomic Methodologies with Prof. Jukka Corander
Spotlight On: Microbial Evolution and Epidemiology with Dr. Jennifer Gardy

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