Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples
Author(s)
Yu, Feiqiao Brian; Schulz, Frederik; Woyke, Tanja; Horowitz, Mark A; Quake, Stephen R; Blainey, Paul C; ... Show more Show less
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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.
Date issued
2017-07Department
Massachusetts Institute of Technology. Department of Biological EngineeringJournal
eLife
Publisher
eLife Sciences Publications, Ltd
Citation
Yu, Feiqiao Brian et al. “Microfluidic-Based Mini-Metagenomics Enables Discovery of Novel Microbial Lineages from Complex Environmental Samples.” eLife 6 (July 2017): e26580 © 2017 Yu et al
Version: Final published version
ISSN
2050-084X