Single-cell genome sequencing of fecal microbiomes in inulin-fed mice.
a Workflow for SAG-gel-based single-cell genome sequencing of bacterial cells in a complex microbial community. Individual bacterial cells are randomly captured in picoliter-sized gel beads and processed by in-gel lysis and whole-genome amplification (WGA). Single-cell amplified genomes (SAGs) in the gel are fluorescently detected and sorted into well plates as a SAG library. The SAGs are re-amplified for further analysis by NGS, amplicon sequencing, and storage. b–f Assembly qualities of 324 SAGs, excluding short fragments (length < 100 kb) and contaminated samples (contamination > 10%). b Completeness and contamination statistics for 302 SAGs (IMSAGs) and 22 composite SAGs (IMSAGCs). c–f The number of contigs, N50 values, number of tRNAs, and 16S rRNA gene lengths for 324 SAGs.