Model Ecosystems to Advance Microbiome Science

Fabricated Ecosystems (EcoFABs)

2017 EcoFAB Report

Fabricated ecosystems, or EcoFABs, hold promise for replicating important ecosystem dynamics while simultaneously streamlining studies by defining testable and reproducible parameters. Used with microbiomes, scientists will be able to define principles for community assembly and structure, understand the functions of genes, microbes, and metabolomes, and predict microbiome health and trajectory. EcoFABs have the potential to 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 studies of biomedical technologies, environmental health, agriculture, energy, and nutrient cycling.

In recent years, our understanding of microbiomes has grown dramatically. They are important in soils for nutrient cycling and sustainable agriculture, in the human gut for maintaining health, and in aquatic systems for nutrient cycling. One major challenge in understanding complex environmental communities is a lack of controlled, reproducible, and standardized study systems. Many existing approaches are focused on examination of extremely simple lab consortia or very complex natural microbiomes. Consortia are advantageous for characterizing constituent isolates (in most cases) independently and for genetic manipulation to determine causal mechanisms; however, the validity of extrapolating these finding to authentic communities is unclear. Studies of natural communities are so unconstrained that it is difficult to establish causation without large meta-analysis to adequately constrain for numerous experimental variables. While model systems exist for some microbiomes and their ecosystems (e.g. gut microbiomes), there is a lack of consensus and standardization for many other microbiomes. Here, we demonstrate the design and utility of EcoFAB systems for standardized and reproducible microbiome analysis in our lab at the Joint Genome Institute (LBNL).