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Microbial systems biology

Microbiology goes big: microbial systems biology

Gail Teitzel
Editor, Trends in Microbiology

At the conferences I have recently attended, it is remarkable to me that more and more of the research presented is based upon large data sets with the ability to address very broad biological questions, including systems biology approaches with the goal of understanding the whole cell. This marrying of computational techniques to large-scale omics experiments has allowed scientists to address the role of microbes in complex systems, for example within the host or as part of complex assemblies of microbes. As we have long appreciated that a single microbe does not act in isolation, this is an exciting time to be able to harness the power and promise of systems biology to understand microbial life in complex situations. This themed review issue contains a selection of particular areas in microbiology where systems biology approaches have been applied. One aspect of microbiology where systems biology could have an impact is in understanding how microbes evolve and adapt. Zaneveld et al. discuss how high-throughput genomic and phylogenetic studies can be used to understand how microbes have adapted to diverse habitats. Challenges include how to standardize contextual data about sequence samples and how to best sample across microbial communities. Once this has been done, researchers can then begin to address the potential genomic basis for microbial associations and possible horizontal transfer of genes. Tal Dagan then discusses how networks can be applied to phylogenetic data (phlyogenomic networks) to better model evolutionary processes that are both tree-like and non-tree-like and how these can be used to understand the evolution of microbial genomes. Comas and Gagnuex introduce us to the concept of systems epidemiology where interactions between Mycobacterium tuberculosis and its human host are

combined with host-pathogen diversity, human demography, socioeconomic factors and environmental factors. Not only will this help to understand the diversity and adaptation of M. tuberculosis strains, it is hoped that this will also lead to better control of tuberculosis. Genome-wide screens such as yeast two-hybrid, RNA interference, and transcriptomic approaches have been widely used, and one research direction has been to use these to examine host-microbe interactions. One goal of these studies is to understand which host proteins interact with which microbial proteins. Friedel and Haas examine the results of genome-wide screens as applied to the immune response and factors that might aid in viral infection. They summarize what has been learned about host proteins that facilitate a broad range of viral infections and how this might be used for the creation of new antivirals. Rizzetto and Cavalieri discuss what has been learned in genome-wide approaches of fungal infections including the immune response to fungi, immune evasion by fungi and how fungi might have evolved to become opportunistic pathogens. Systems biology can also be used as a tool in more applied aspects of microbiology. Gowen and Fong review how systems biology can be used to identify microbes that have natural abilities to produce biofuels, as well as how systems biology can be used to predict and optimize the metabolic capacity and stress response of these organisms to further their ability to produce biofuels. I hope that you enjoy this selection of ways that systems biology can be used in microbiological research, and I look forward to hearing about further developments at the interface of systems biology and microbiology in the coming years.

Corresponding author: Teitzel, G. (

0966-842X/$ see front matter 2011 Elsevier Ltd. All rights reserved. doi:10.1016/j.tim.2011.08.001 Trends in Microbiology, October 2011, Vol. 19, No. 10