High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome

Characterizing complex microbial communities with single-cell resolution has been a long-standing goal of microbiology. We present Microbe-seq, a high-throughput method that yields the genomes of individual microbes from complex microbial communities. We encapsulate individual microbes in droplets with microfluidics and liberate their DNA, which we then amplify, tag with droplet-specific barcodes, and sequence. We explore the human gut microbiome, sequencing more than 20,000 microbial single-amplified genomes (SAGs) from a single human donor and coassembling genomes of almost 100 bacterial species, including several with multiple subspecies strains. We use these genomes to probe microbial interactions,…

• NS
  National Science Foundation

  Awards: DMR-1708729, 1708729, 2011754, DMR-2011754
• UD
  U.S. Department of Energy
• NA
  National Aeronautics and Space Administration

  Award: NNX13AQ48G
• HU
  Harvard University

  Award: DMR-2011754
• NS
  Nuclear Safety and Security Commission
• NI
  National Institutes of Health

  Award: P01HL120839
• MR
  Materials Research Science and Engineering Center, Harvard University

  Awards: DMR-2011754, 2011754
• DO
  Division of Materials Research

  Awards: DMR-2011754, 1708729, 2011754, DMR-1708729