Modeling Microbial Communities: A Call for Collaboration between Experimentalists and Theorists

Abstract

With our growing understanding of the impact of microbial communities, understanding how such communities function has become a priority. The influence of microbial communities is widespread. Human-associated microbiota impacts health, environmental microbes determine ecosystem sustainability, and microbe-driven industrial processes are expanding. This broad range of applications has led to a wide range of approaches to analyze and describe microbial communities. In particular, theoretical work based on mathematical modeling has been a steady source of inspiration for explaining and predicting microbial community processes. Here, we survey some of the modeling approaches used in different contexts. We promote classifying different approaches using a unified platform, and encourage cataloging the findings in a database. We believe that the synergy emerging from a coherent collection facilitates a better understanding of important processes that determine microbial community functions. We emphasize the importance of close collaboration between theoreticians and experimentalists in formulating, classifying, and improving models of microbial communities.

Understanding the evolution of interspecies interactions in microbial communities

“…To test our intuitions about general principles of community evolution, one powerful approach is to use mathematical and computational models. Such models allow us to abstract a system to its minimal components and assess how different features of the system interact, ideally generating testable hypotheses that can be addressed using carefully designed experiments [68,69]. In particular, they allow us to test a wider range of possibilities, such as environmental conditions or combinations of species, than would be experimentally feasible.…”

Machine metaphors and ethics in synthetic biology

“…In the seventeenth century, the mechanical clock was used to this end, in the eighteenth century the balance was an influential metaphor, in the nineteenth century the steam engine metaphor appeared, and in the twentieth century and up to day the computer, the information processing machine, replaced these older machine metaphors (Lunteren 2016, Zaccaria, Dedrick, and Momeni 2017). All of these machines are artefacts designed by humans, and their structural and material make-up serves as a means to attain a predefined state of affairs and thus fulfills a specific purpose for humans.…”

“…In microbial multispecies communities, bacteria influence each other via direct physical contact, metabolic interdependencies and coordinative signaling systems, thus maintaining ecosystem equilibrium (Guo, He, and Shi 2014). With regard to microbial communities, this modelling requires close ongoing collaboration between theorists and experimentalists (Zaccaria, Dedrick, and Momeni 2017). Modelling a multispecies ecosystem not restricted to microbes obviously would be an even greater challenge.…”

Model-free prediction of microbiome compositions

“…Current methods to predict the composition of microbial communities commonly rely on prior reconstruction of a mediating network model. Such approaches mainly describe an effective population dynamics model whose parameters are chosen by fitting to the available data, or from detailed knowledge of the biochemical reactions [6][7][8][9]. These models predict the personalized response of a particular microbial community to a given perturbation by tracking the resultant time-dependent dynamics.…”