Innovation and Partnerships Office

Identifying Organism Interactions with High Throughput Enrichment Culturing 2016-132


Microbial community engineering to

  • Improve agricultural yields
  • Design probiotic applications in humans or livestock
  • Engineer increased industrial fermentor yields


  • Simultaneously evaluates all possible interactions from a mixed consortia
  • High throughput
  • Accurate


Adam Arkin and Nicholas Justice of Berkeley Lab have developed a technology to determine the specific microbial taxa, within a complex consortia of mixed taxa, that are interacting with each other within an environment of interest. By determining pairs of taxa positively or negatively interacting within a microbial community in a given cultivation condition, the Berkeley Lab technology enables the design and management of microbial communities used in health, industrial or agricultural processes.

In the Berkeley Lab technology, an environmental sample is inoculated into a large number of separate enrichment cultures and cultivated under conditions appropriate to detect interactions of interests so that each enrichment culture represents a small fraction of the original community complexity. Then DNA is extracted and taxonomic information is acquired from each culture. Presence / absence data on each taxon is used to determine taxa that occur together in significantly non-random patterns across all enrichment cultures. Compared to a bottom-up, one-by-one comparison of several species of interest, this top-down approach quickly queries potential interactions among assemblages of co-occurring microorganisms.

There are very few tools for evaluating and understanding multi-species processes. Current methods to predict organism interactions can be limited by the accuracy of gene annotations and metabolic models on which they are based. Other methods, such as computational modeling, may fail to capture cultivability information. Classical methods of coincubation of organisms are low throughput and do not simultaneously evaluate all possible interactions from a mixed consortia in a given cultivation condition. The Berkeley Lab technology overcomes these limitations to bring the field of microbial community engineering to the forefront and benefit industry users.

DEVELOPMENT STAGE: Proven principle

STATUS: Available for licensing or collaborative research.