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Detailed resolution of microbial communities

Microbes live in, on, and around us, most often in complex communities that impact both biomedical and environmental well-being. Our ability to understand the functions of these communities requires detailed resolution and comprehensive characterization of each community member. Other sequencing methods are often limited by short reads and/or bias, which can result in incomplete genome assembly, limited functional insight, and lack of species-level identification.

Defining microbial community form and function

PacBio Systems offer comprehensive microbial community characterization, including complete genome assembly and the identification of mobile elements, phage, and epigenomic data. Single Molecule, Real-Time (SMRT) Sequencing is ideal for either full-length 16S rRNA sequencing or whole genome shotgun metagenomics, both of which benefit from long reads to achieve deeper strain-level resolution or complete, high-accuracy genome assembly. With this sequencing technology, you have the ability to:

  • Resolve community composition and phylogeny using full-length 16S rRNA sequences
  • Discover novel genes and gene clusters from longer reads and assembled contigs
  • Identify and assign functions to community members with improved genome assemblies
  • Leverage epigenomic data to associate contigs and plasmids from closely related strains

spotlight-microbiology-icon

Workflow: from DNA to resolved microbial communities

  • SMRT Sequencing with PacBio Systems
    • Take advantage of the Sequel System to reduce project costs and generate 7X more reads compared with the PacBio RS II
    • Achieve ~10 kb average read lengths, with some reads as long as 60 kb
    • Scalable throughput based on project needs
      • 100X coverage to resolve 16S rRNA sequences
      • 50X coverage per genome for de novo metagenomic assembly
    • Profile metagenomic communities with single-molecule reads using circular consensus sequencing
    • Simultaneously capture epigenetic information

Featured research: achieve species-level resolution with full-length 16s rRNA sequencing

Characterize_Microbial_Communities.Spotlight2.Full_length_16s_rRNA_Sequencing
Scientists used full-length 16S rRNA SMRT Sequencing to characterize the microbial communities in cecum, water, and soil. They detected the community members with genus/major taxa and species-level resolution1.

Explore this research further.

To learn more about how to fully resolve your microbial community, contact us.

Reference

  1. Bowman, B. et al. (2015) Long-read, Single Molecule, Real-Time (SMRT) DNA sequencing for metagenomic applications. Izzard, J. and Rivera, M. C. (ed.) Metagenomics for Microbiology. Oxford: Academic Press. 25–38.

Selected Resources