Single-cell omics for complex microbial communities

Abstract

Despite over a decade of effort, microbial single-cell genomics and transcriptomics remain a challenge, especially for complex communities such as the human microbiome. Here we report a solution based on the Laser-Induced Forward Transfer (LIFT) technology, which circumvent the need for droplet microfluidics and complex barcoding, and allow selective amplification of the genome and the transcriptome of commensal bacteria from complex samples. We capture the diverse oral microbiome, and elucidate the single-cell transcriptome in sporulation. This single-cell method is both scalable and precise, and enables investigation into tissue samples. The approach shows great promise for elucidating the single-cell fate of microbial populations and the native environment of the host-associated microbiome.