Elementary Flux Mode Analysis predicts co-culture stability in continuous bioprocesses

Cell phenotype and metabolism adaptation are common in
natural and human-controlled biological processes. Whereas in
nature, it usually translates into extended strain fitness, within
industrial bioprocessing, it usually results in a loss in process
productivity. This problem is more relevant for new-generation
bioproducts which require more controlled and specialized
bioprocesses. This is the case of the production of specialized
compounds by microbial consortia, where the challenge is to
constrain populations with specific metabolic functionalities
into a designed threshold of productivity. Assessing metabolic
distributions is critical for accurately controlling the functionality of these complex and specialized continuous co-culture bioprocesses. In this work, we use Elementary Flux Mode Analysis
as a metabolic state profiling tool to characterize the metabolic
distributions in bacteria-yeast co-culture couples and establish
diverse strategies for their control. The consumption and production yield analysis ,composed from the microorganisms central metabolism network, resulted in a mixed cybernetic model,
which described the population and metabolic flux distributions phenomena during co-culture. Yield analysis showed that
the higher the degree of separation between substrate consumption capabilities, the more extensive the stability range
of the microorganism pair. While the cybernetic model also
suggested that dynamic interplay between two different substrates helps alleviate competition by enabling each strain to
dominate in different substrate niches, even when both strains
are capable of their utilization. An online control of alternate
substrate pulsing strategy was then used in a proof-of-concept
bioprocess to optimize e production of p-coumaric acid in a
continuous co-culture