Enhancing cultivable microbial diversity from mouse gut microbiome using droplet microfluidics

To comprehend the complex dynamics of the gut microbiome and its influence on host health, it is essential to cultivate and isolate gut microorganisms. However, traditional culturing methods often struggle to capture the full diversity of gut microbiota, especially when it comes to rare and slow-growing species (1, 2). In this study, we introduce a droplet microfluidic platform as an efficient and high-throughput approach for cultivating and isolating microorganisms from mouse gut. Miniaturized droplets with volume ranging from few picoliters to nanoliters are generated at kilohertz frequencies targeting confinement of single gut bacteria per droplet (3–5). Millions of these droplets are incubated in parallel, with homogenous incubation conditions. We cultivated and isolated a diverse range of gut microorganisms from mouse fecal pellets. A comparative analysis with conventional agar plating techniques showed that our droplet cultivation method yielded a greater number of unique isolates, highlighting its superior ability to capture the cultivable fraction of the gut microbiome. Additionally, 16S rRNA amplicon sequencing demonstrated that our system reflects changes in microbial diversity. Droplet microfluidics serves as an innovative solution for expanding the cultivable fraction of the gut microbiota.

References

L. Mahler et al., Elife. 10, 1–23 (2021).D. K. Chaudhary, A. Khulan, J. Kim, Sci. Rep. 9, 6666 (2019).S. Hengoju, M. Tovar, D. K. W. Man, S. Buchheim, M. A. Rosenbaum, in Microfluidics in Biotechnology (2020), pp. 129–157.W. J. Watterson et al., Elife. 9, 1–22 (2020).T. Moragues et al., Nat. Rev. Methods Prim. 3, 32 (2023).