Synthetic Colonic Mucus Enables the Development of Modular Microbiome Organoids

The human colon is home to more than a trillion microorganisms that modulate diverse gastrointestinal processes and pathophysiologies. Our understanding of how this gut ecosystem impacts human health, although evolving, is still in its nascent stages and has been slowed by the lack of accessible and scalable tools suitable to studying complex host-mucus-microbe interactions. In this work, we report a synthetic gel-like material capable of recapitulating the varied structural, mechanical, and biochemical profiles of native human colonic mucus to develop compositionally simple microbiome screening platforms with broad utility in microbiology and drug discovery. The viscous fibrillar material is realized through the templated assembly of a fluorine-rich amino acid at liquid-liquid phase separated interfaces. The fluorine-assisted mucus surrogate (FAMS) can be decorated with various mucins to serve as a habitat for microbial colonization and be integrated with human colorectal epithelial cells to generate multicellular artificial mucosae, which we refer to as a microbiome organoid. Notably, FAMS are made with inexpensive and commercially available materials, and can be generated using simple protocols and standard laboratory hardware. As a result, this platform can be broadly incorporated into various laboratory settings to advance our understanding of probiotic biology and inform in vivo approaches. If implemented into high throughput screening approaches, FAMS may represent a valuable tool in drug discovery to study compound metabolism and gut permeability, with an exemplary demonstration of this utility presented here.