Microbiomes play essential roles in the natural processes that keep the planet and our bodies healthy, so it’s not surprising that scientists’ investigations into these diverse microbial communities are leading to advances in medicine, sustainable agriculture, cheap water purification methods, and environmental clean-up technology, just to name a few. However, trying to determine which microbes contribute to an important geochemical or physiological reaction is both incredibly challenging and slow-going, because the task involves analyzing enormous datasets of genetic and metabolic information to match the compounds mediating a process to the microbes that produced them.
EcoFABs: Fabricated Microbial Ecosystem Models to Advance Microbiome Research
Biosciences’ Trent Northen and Ben Brown, along with collaborators from more than a dozen institutions, co-authored a paper published in Nature Methods that outlines a vision for fabricated model microbial ecosystems (EcoFABs) and their potential impact on microbiome science.
Moving Beyond the Lab Bench
When researchers report developing a more efficient solar cell, or a technique that improves drug delivery, one of the inevitable follow-up questions they face is, “When will this be available to consumers?” In recent years, attempts to bridge the distance from lab bench to market have been promoted for researchers committed to seeing their work be applied to real world situations at universities, national laboratories and other institutions.
One such program is Fed Tech, launched in 2013 as part of the National Science Foundation’s Innovation Corps (I-Corps) program. Trent Northen and Peter Andeer, scientists in the Biosciences Area’s Environmental Genomics & Systems Biology (EGSB) Division at Lawrence Berkeley National Laboratory (Berkeley Lab), were part of the Fall 2018 cohort of Fed Tech Start-Up Studio, which culminated with a Pitch Day in late November. With entrepreneurs Rick Kjellberg and Jayan Rammohan, they were among 20 teams that participated in the eight-week program.
Biosciences Area FY18 LDRD Projects
The projects of 13 Biosciences Area scientists and engineers received funding through the FY18 Laboratory Directed Research and Development (LDRD) program. These projects span a diverse array of topics and approaches including the study of microbiomes in relation to patterns of mutualism, crop productivity, and gut health; synthetic biology for engineering biosurfactant production and energy conversion pathways; and the application of technologies such as machine learning, high-resolution optical microscopy, and single-cell transcriptomics. Together, these efforts account for 18.75 percent of the $20 million allocated. Lab-wide, 74 projects were selected from a field of 215.
Northen Lab Publishes Video Protocol for Building EcoFABs
Scientists in Trent Northen’s groups in Environmental Genomics and Systems Biology (EGSB) and Metabolomics Technology at the DOE Joint Genome Institute (JGI) have published detailed video protocols for creating fabricated ecosystems, or EcoFABs, in the Journal of Visualized Experiments (JOVE). These laboratory-scale controlled habitats, constructed using widely available 3D printing technologies, enable mechanistic studies of plant-microbe interactions within specific environmental conditions. The published protocols serve as a starting point for other researchers, ideally helping to create standardized experimental systems for investigating plant-microbe interactions. The video component of this article can be found here.
Was this page useful?
Send
