[eLife] Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from comp
Metagenomics and single-cell genomics have enabled genome discovery from unknown branches of life. However, extracting novel genomes from complex mixtures of metagenomic data can still be challenging and represents an ill-posed problem which is generally approached with ad hoc methods. Here we present a microfluidic-based mini-metagenomic method which offers a statistically rigorous approach to extract novel microbial genomes while preserving single-cell resolution. We used this approach to analyze two hot spring samples from Yellowstone National Park and extracted 29 new genomes, including three deeply branching lineages. The single-cell resolution enabled accurate quantification of genome function and abundance, down to 1% in relative abundance. Our analyses of genome level SNP distributions also revealed low to moderate environmental selection. The scale, resolution, and statistical power of microfluidic-based mini-metagenomics make it a powerful tool to dissect the genomic structure of microbial communities while effectively preserving the fundamental unit of biology, the single cell.
Feiqiao Brian Yu Paul C Blainey Frederik Schulz Tanja Woyke Mark A Horowitz Stephen R Quake Is a corresponding author Stanford University, United States MIT Department of Biological Engineering and Broad Institute of Harvard and MIT, United States Department of Energy Joint Genome Institute, United States Chan Zuckerberg Biohub, United States