Microfluidic encapsulation of the human gut microbiota-a tool for research and beyond

Over the past few decades, the importance of the human gut microbiota has been cast into the limelight. A growing number of studies are attempting to detangle the complex functions of the gut microbiota for human health; however, one existing shortcoming is an incomplete understanding of the microbiota community composition. Up to 70% of bacteria colonizing the human gastrointestinal tract are estimated to lack complete genomic or functional characterization due to their low abundance within the gastrointestinal tract or challenge to culture. As traditional culture methods often favour fast-growing or easily cultured species, alternative strategies are needed to access the broader gut microbial diversity. Here, we propose a novel approach to improve the growth of difficult-to-culture gut bacteria through single-cell microencapsulation, which will allow for in vitro manipulation. This work provides evidence of high biocompatibility of four-arm poly(ethylene glycol) maleimide (PEG4MAL) for gastrointestinal microbial culture and significant anaerobic gut bacteria proliferation in PEG4MAL microbeads generated via microfluidics. Specifically, we varied the concentration of PEG4MAL and the presence of Arg-Gly-Asp peptide motifs to tune the mechanical properties and porosity of the microbeads, and examined their impact on bacterial viability, confluency, and colony formation.