Syntrophic co-culture amplification of production phenotype for high-throughput screening of microbial strain libraries.

Microbes can be engineered to synthesize a wide array of bioproducts, yet production phenotype evaluation remains a frequent bottleneck in the design-build-test cycle where strain development requires iterative rounds of library construction and testing. Here, we present Syntrophic Co-culture Amplification of Production phenotype (SnoCAP). Through a metabolic cross-feeding circuit, the production level of a target molecule is translated into highly distinguishable co-culture growth characteristics, which amplifies differences in production into highly distinguishable growth phenotypes. We demonstrate SnoCAP with the screening of Escherichia coli strains for production of two target molecules: 2-ketoisovalerate, a precursor of the drop-in biofuel isobutanol, and L-tryptophan. The dynamic range of the screening can be tuned by employing an inhibitory analog of the target molecule. Screening based on this framework requires compartmentalization of individual producers with the sensor strain. We explore three formats of implementation with increasing throughput capability: confinement in microtiter plates (102-104 assays/experiment), spatial separation on agar plates (104-105 assays/experiment), and encapsulation in microdroplets (105-107 assays/experiment). Using SnoCAP, we identified an efficient isobutanol production strain from a random mutagenesis library, reaching a final titer that is 5-fold higher than that of the parent strain. The framework can also be extended to screening for secondary metabolite production using a push-pull strategy. We expect that SnoCAP can be readily adapted to the screening of various microbial species, to improve production of a wide range of target molecules.

Microdroplet co-cultivation and interaction characterization of human vaginal bacteria.

The human vaginal microbiome (HVM) plays a fundamental role in women's reproductive health. For instance, bacterial vaginosis (BV) is characterized by a depletion of lactobacilli and an overgrowth of strict anaerobes. Women with BV may have an increased risk of acquiring sexually transmitted diseases and adverse pregnancy outcomes. Although the HVM is important, the ecological roles of many vaginal species remain unclear and current approaches for investigating them have severe limitations. We previously developed a new high-throughput technology based on the co-cultivation of bacteria in microdroplets to dissect inter-species interactions in microbial communities. Here, we adapted and extended this technology to investigate the HVM and tested it using pairwise model systems. In one case, Lactobacillus jensenii JV-V16, a lactic acid bacterium, and Gardnerella vaginalis ATCC 49145, a bacterium associated with BV, were cultured in microdroplets as pure cultures and co-cultures. Two assays were developed to analyze their growth in microdroplets. First, qPCR was used to quantify the bacteria in pooled microdroplets. Second, cells in individual microdroplets were plated and enumerated on agar media. The results showed that growth of G. vaginalis was severely inhibited by L. jensenii, which recapitulated previous findings of studies conducted in flask batch cultures. Additionally, we validated the general applicability of our technology pipeline with a second co-culture model system by observing that Enterococcus faecalis, another bacterium from the urogenital tract, was also inhibited by L. jensenii. Our results show that co-cultivation and characterization of bacteria in microdroplets provides an effective way to study inter-species interactions in microbial ecosystems.