EcoFAB: Model Ecosystems to Advance Microbiome Science

Fabricated Ecosystems (EcoFABs)

In recent years, our understanding of microbiomes has grown dramatically. We increasingly recognize their importance in soils for nutrient cycling and sustainable agriculture, in the human gut for maintaining health, and in aquatic systems for nutrient cycling. One of the major challenges for developing a generalized understanding of microbiomes in these complex environments is a lack of controlled, reproducible, and standardized study systems. Most approaches aimed at improving our understanding of microbiomes are focused on examination of extremely simple lab consortia or fully-complex natural communities. Consortia have the advantage that the constituent isolates can (in most cases) be characterized independently and even genetically manipulated to determine causal mechanisms. The validity of extrapolating consortia-based finding to authentic communities is unclear, yet natural communities (e.g. field or clinical studies) are so unconstrained that it is difficult to establish causation and vast studies would be required to adequately constrain the large number of experimental variables. While model systems exist for some microbiomes and their ecosystems (e.g. gut microbiomes), there is a lack of consensus and standardization of study systems for many other microbiomes.

Fabricated ecosystems, or EcoFABs, hold promise for replicating important ecosystem dynamics while at the same time streamlining studies by defining testable and reproducible parameters. Through the development of EcoFABs for microbiomes of interest, scientists will be able to develop principles for microbiome assembly and structure, understand the functions of genes, microbes, and metabolomes, and predict microbiome health and trajectory. These EcoFABs would bring together communities of scientists working on shared systems, enabling more effective knowledge transfer and the ability to build upon previous findings. By expanding our understanding of the assembly, structure, and functions of microbiomes, significant scientific and technical advances will be made in biomedical and environmental health, agriculture, energy, and nutrient cycling.