U.S. Department of Energy

Pacific Northwest National Laboratory

A Unified Framework for Predicting and Controlling Microbiomes

Overview of a unified conceptual framework for understanding microbiome temporal dynamics to enable prediction and control towards beneficial outcomes.

Applying a systems approach to studying microbiome changes could pave the way toward predicting system function and directing microbial activities.

The Science

PNNL scientists developed a conceptual framework for process-based understanding of how microbiomes change over time. Coordinating the following types data from models and molecular-based characterization of microbiome dynamics: (i) biotic and abiotic historical conditions, (ii) internal microbiome interactions, and (iii) external environmental influences, provides researchers with a holistic view of microbiome dynamics that underlie system function.

The Impact

This unified framework places microbiome analyses within one globally applicable conceptual context that can be used across systems to draw out generalizable knowledge of the processes governing microbiome dynamics. This paves the way toward improved predictions of how ecosystem function (e.g., watershed biogeochemical fluxes) will respond to ongoing perturbations (e.g., altered hydrologic dynamics), as well as the development of strategies to optimize microbiomes for improved environmental and human health.


Microbiomes impact nearly all systems on Earth. While there is a need to understand and ultimately control microbiomes, there is significant uncertainty regarding the factors that govern their changing dynamics. To this end, PNNL researchers contend it is important to develop a coordinated and unified conceptual framework to study microbiome dynamics across all systems.

The conceptual framework presented in this study posits that factors influencing the dynamics of microbiomes can be grouped into three broad categories: biotic and abiotic historical conditions, microbial community internal dynamics, and external environmental forces. Historical conditions set the stage and impact how microbiomes respond to environmental change. Internal dynamics are associated with autogenic succession, whereby interactions among microbes combine with microbe-driven changes to the abiotic environment to influence microbiome dynamics. And, external environmental forces drive allogenic succession, whereby changes to the abiotic environment cause some microbial taxa to increase and others to decrease in abundance and/or level of metabolic function. These three factors—history, internal dynamics, and external forcing—are not always easily distinguished, which emphasizes that they continuously interact and feedback with each other to collectively influence microbiome dynamics. This integrated view of the factors driving microbiome dynamics provides scientists an opportunity to more systematically and holistically discover generalizable processes that govern microbiome dynamics. This more integrated understanding can, in turn, be leveraged to enhance mechanistic models aimed at predicting system function (e.g., watershed biogeochemical responses to perturbation) and may enable the design of microbiomes for sustainable energy and improved ecosystem and human health.

September 2018
| Pacific Northwest National Laboratory