Droplet microfluidics-based iX-seq uncovers cross-feeding interactions between Phascolarctobacterium faecium and Eubacterium limosum in the gut microbiota

Droplet microfluidics is an innovative technology with notable potential for high-throughput separation and cultivation of bacterial isolates from complex microbial communities such as the gut microbiota. In this study, we utilized droplet microfluidics in tandem with 16S rRNA amplicon sequencing to screen for cross-feeding bacteria, hereafter referred to as iX-seq, in a human fecal sample. We identified Phascolarctobacterium faecium and Eubacterium limosum as unidirectional cross-feeders, wherein P. faecium growth appeared to be dependent on E. limosum-derived 2-oxoglutarate for survival when co-cultured in modified YCFA medium. As a key intermediate in the succinate metabolic pathway, 2-oxoglutarate was likely utilized as a nutrient source by the succinate-metabolizing P. faecium. Furthermore, P. faecium failed to colonize the intestines of germ-free mice without co-inoculation with E. limosum, further evidencing their cross-feeding relationship. These findings demonstrate the utility of droplet microfluidics for uncovering the mechanisms of microbial interactions within the complex gut environment.