In vitro fermentation test bed for evaluation of engineered probiotics in polymicrobial communities.

In vitro fermentation systems offer significant opportunity for deconvoluting complex metabolic dynamics within polymicrobial communities, particularly those associated with the human gut microbiome. In vitro gut models have broad experimental capacity allowing rapid evaluation of multiple parameters, generating knowledge to inform design of subsequent in vivo studies. Here, our method describes an in vitro fermentation test bed to provide a physiologically-relevant assessment of engineered probiotics circuit design functions. Typically, engineered probiotics are evaluated under pristine, mono- or co-culture conditions and transitioned directly into animal or human studies, commonly resulting in a loss of desired function when introduced to complex gut communities. Our method encompasses a systematic workflow entailing fermentation, molecular and functional characterization, and statistical analyses to validate an engineered probiotic's persistence, plasmid stability and reporter response. To demonstrate the workflow, simplified polymicrobial communities of human gut microbial commensals were utilized to investigate the probiotic Escherichia coli Nissle 1917 engineered to produce a fluorescent reporter protein. Commensals were assembled with increasing complexity to produce a mock community based on nutrient utilization. The method assesses engineered probiotic persistence in a competitive growth environment, reporter production and function, effect of engineering on organism growth and influence on commensal composition. The in vitro test bed represents a new element within the Design-Build-Test-Learn paradigm, providing physiologically-relevant feedback for circuit re-design and experimental validation for transition of engineered probiotics to higher fidelity animal or human studies.

Engineering probiotics for therapeutic applications: recent examples and translational outlook.

Engineered probiotics are the next generation of live biotherapeutics that have been genetically modified to target specific diseases. With the advancements in synthetic biology, the engineering of probiotics has become increasingly sophisticated which has led to the development of therapies for treating cancer, infection, metabolic disorders and inflammation, as well as for diagnosing and preventing them. Herein, we review some of the recent examples of probiotics which have been engineered to target such diseases. Although there are numerous examples of engineered probiotics showing efficacy in animal models, there are no approved products on the market with very few in clinical trials. Therefore, we also discuss a set of features that may be incorporated into engineered probiotics to aid in clinical translation and ultimately, realizing the potential of these biotherapeutics.