Co-cultivation is a powerful approach to produce a robust functionally designed synthetic consortium as a live biotherapeutic product (LBP)

ABSTRACT

The success of fecal microbiota transplants (FMT) has provided the necessary proof-of-concept for microbiome therapeutics. Yet, feces-based therapies have many associated risks and uncertainties, and hence defined microbial consortia that modify the microbiome in a targeted manner have emerged as a promising safer alternative to FMT. The development of such live biotherapeutic products has important challenges, including the selection of appropriate strains and the controlled production of the consortia at scale. Here, we report on an ecology- and biotechnology-based approach to microbial consortium construction that overcomes these issues. We selected nine strains that form a consortium to emulate the central metabolic pathways of carbohydrate fermentation in the healthy human gut microbiota. Continuous co-culturing of the bacteria produces a stable and reproducible consortium whose growth and metabolic activity are distinct from an equivalent mix of individually cultured strains. Further, we showed that our function-based consortium is as effective as FMT in counteracting dysbiosis in a dextran sodium sulfate mouse model of acute colitis, while an equivalent mix of strains failed to match FMT. Finally, we showed robustness and general applicability of our approach by designing and producing additional stable consortia of controlled composition. We propose that combining a bottom-up functional design with continuous co-cultivation is a powerful strategy to produce robust functionally designed synthetic consortia for therapeutic use.

KEYWORDS:

• Microbiome therapeutics
• consortium design
• anaerobic carbohydrate metabolism
• division of labor
• continuous co-cultivation
• live biotherapeutic products (LBP)

Acknowledgments

We thank Christophe Chassard for support with the strain selection.

Disclosure statement

F.K., G.E.L., L.A., P.R.v.B., C.M., M.M., F.R., M.R., and T.W. are or were employees of PharmaBiome. T.W., G.R., and C.L. are founders of PharmaBiome. F.K., L.A., M.M., M.R. and F.R. are co-founders of PharmaBiome. F.K., L.A., G.R., M.R.S., C.L., M.M., F.R., and T.W. are inventors on patent application number WO2018189284, entitled ‘Consortia of living bacteria useful for treatment of microbiome dysbiosis’. F.K., C.L., F.R., and T.W. are inventors on patent application WO2020079026, entitled ‘A method of manufacturing a consortium of bacterial strains’. PharmaBiome provided financial support.

Data availability

All data analyzed during this study are included in this published article and its supplementary information files, and deposited in the ETH Research Collection (20.500.11850/576817).

Author contributions

F.K., L.A., M.R.S., G.R., C.L., and T.W. conceptualized the project. F.K., G.E.L., F.R., M.R.S., G.R., C.L., T.W., planned the experiments. F.K, L.A., F.R., and T.W. developed methods. M.R.S. planned and performed mouse experiments. F.K. and L.A. assisted with mouse experiments. F.K, C.M., M.R., and M.R.S. performed analyses. G.E.L. and P.R.v.B. analyzed and curated data. M.M. contributed to choosing the primers for the strains and developed software used in parts of the analysis. T.W., C.L., and G.E.L. supervised the work. F.K., G.E.L., C.L., and T.W. wrote the original draft. All authors reviewed and edited the manuscript.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/19490976.2023.2177486

Additional information

Funding

PharmaBiome AG and ETH Zurich provided infrastructure and financial support, and were supported by Innosuisse Innovation Projects 20713.1 IP-LS and 27873_1 PFLS-LS.