Vision: Microbial Individual-Based Ecology (µIBE)

I am pleased to announce the publication of our opinion article in PNAS. This paper represents a milestone in our continuing crusade to change modeling of microbial ecology. You know, we used to (and often still do) model microbes as if they are chemical molecules. This approach does not allow us to account for their heterogeneity and it limits how much complexity we can include. Also, and this is the main point of this specific paper, it prohibits us from using any of the individual-based observations (IBOs) generated using novel single-cell observational and experimental techniques. Microbial ecologists are drowning in a flood of IBOs and, just as with systems biology years ago, new analysis tools are needed. Individual-based models (IBMs) to the rescue! This paper lays out our vision for combining IBMs and IBOs, which leads to microbial individual-based ecology (µIBE). Here are links to the paper and a couple of news coverages:

http://www.pnas.org/content/110/45/18027.full
http://www.northeastern.edu/news/2013/11/hey-bacteria-are-individuals-too/
http://www.nimbios.org/wordpress/2013/11/06/modeling-of-microbial-world-comes-of-age/