In your opinion, what have been the most noteworthy advances in the field of microbiology research in the past 15 years? Looking forward, what do you expect to be the most exciting advances in the next few years?

In my view, the progress of microbiology in the last 15 years has been tremendous, the entire face of the field has changed. The principal force behind this incredible progress has been metagenomics and single cell genomics. These approaches have not “just” vastly expanded the genomic universe but qualitatively changed our understanding of the microbial world. One should never forget that only a tiny minority of microbes can be grown in the laboratory, and before the advent of metagenomics, this microbial dark matter remained virtually inaccessible. The discoveries of the bacterial “Candidate Phyla Radiation” and new archaeal phyla, in particular, the Asgard archaea, the direct ancestors of eukaryotes, show that until very recently, we have had only a highly skewed view of the earth microbiota.

From a more biological standpoint, the most spectacular development was the discovery of novel microbial defense systems. CRISPR-Cas is the most obvious and spectacular case in point, but biologically, prokaryotic Argonauts, BREX and other recently identified, diverse defense mechanisms are of no lesser interest, and so are also the antidefense systems evolved by viruses. 

In the years to come, the accelerating expansion of metagenomics and single cell genomic studies can be expected to allow us to chart the earth microbiome (almost) completely. I have a hard time imagining a more exciting development. However, I also very much look forward to a vastly improved understanding of host parasite coevolution, and in particular, the role and mechanism of “altruistic” programmed cell death in microbes. 

Do you have a favourite article that was published in Nature Reviews Microbiology, and if so, can you tell us why?

To begin with, I want to congratulate Nature Reviews Microbiology on its 15^th anniversary. It is coming of age, and I wish the journal even greater success in the next 15 years and beyond! Nature Reviews Microbiology has published numerous important, exciting and highly readable papers, so it is quite difficult to choose one, and doing so objectively is simply impossible (although citation statistics would be of interest). I will make a completely subjective and controversial choice: an Opinion paper with the main idea of which I do not quite agree but that I find uniquely thought provoking:

Ten reasons to exclude viruses from the tree of life
David Moreira & Purificación López-García
Nature Reviews Microbiology 7, 306–311 (2009)

This paper caused a barrage of objections, many of these published in letters to Nature Reviews Microbiology, including one written by my colleagues and myself, but to me, the outcome was what I consider to be a deeper understanding of the world of viruses and their relationships with cellular life. For this, I have to thank the authors – and Nature Reviews Microbiology that did not shy away from the controversy.

You have written for Nature Reviews Microbiology in the past, can you tell us about the experience?

I have been fortunate to publish many papers in Nature Reviews Microbiology including two Analysis articles on classification of CRISPR-Cas systems that became influential in the field.

So, on the whole, the experience has been highly positive. The publication process is unusual in that it involves a much closer interaction with the editor than in any other journal I am familiar with (with the exception of other Nature Review journals). Admittedly, working through multiple rounds of an editor’s comments and suggestions is not always easy and pleasurable, but I do believe this process makes the articles better, above all, more readable. 

I have had one important (to me at least) paper rejected by Nature Reviews Microbiology on the basis of what I consider to be a misguided and unfair review. No journal can avoid such problems but even in this case, the final outcome has been positive because an expanded version of the paper published elsewhere was, I think, considerably improved. I hope to publish more in Nature Reviews Microbiology in the years to come and look forward to work with the journal.

Read the Reviews by Eugene V. Koonin and colleagues here:

Diversity and evolution of class 2 CRISPR–Cas systems
Sergey Shmakov, Aaron Smargon, David Scott, David Cox, Neena Pyzocha, Winston Yan, Omar O. Abudayyeh, Jonathan S. Gootenberg, Kira S. Makarova, Yuri I. Wolf, Konstantin Severinov, Feng Zhang & Eugene V. Koonin
Nature Reviews Microbiology 15, 169–182 (2017)

An updated evolutionary classification of CRISPR–Cas systems
Kira S. Makarova, Yuri I. Wolf, Omer S. Alkhnbashi, Fabrizio Costa, Shiraz A. Shah, Sita J. Saunders, Rodolphe Barrangou, Stan J. J. Brouns, Emmanuelle Charpentier, Daniel H. Haft, Philippe Horvath, Sylvain Moineau, Francisco J. M. Mojica, Rebecca M. Terns, Michael P. Terns, Malcolm F. White, Alexander F. Yakunin, Roger A. Garrett, John van der Oost, Rolf Backofen & Eugene V. Koonin
Nature Reviews Microbiology 13,  722–736 (2015)