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Resolving complexity

Generating new insights into how microbial communities function requires improved approaches. Long-read sequencing enables species-level resolution and drives functional insights with full-length 16S rDNA and shotgun sequencing for metagenomic profiling and assemblies.

See the microbial world in high resolution

Single Molecule, Real-Time (SMRT) Sequencing for metagenomics pairs long reads with high accuracy, enabling you to:

  • Understand key community functions by sequencing complete operons at 99.9% accuracy with long-insert metagenomic profiling – no assembly required
  • Identify microbial community members with strain-level resolution using full-length 16S rDNA or shotgun sequencing
  • Discover novel genes and gene clusters by reconstructing multi-kilobase long contigs with whole genome shotgun metagenomic assembly
  • Leverage epigenomic data to associate contigs and plasmids from closely related strains

Workflow: from DNA to resolved microbial communities

 

Library & Sample Preparation
Prepare targeted sequences or shotgun libraries to characterize your microbial community.

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Sequencing
Choose sequencing parameters to achieve 250-500K high-accuracy reads per SMRT Cell 1M on the Sequel System, depending on your library size.

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Data Analysis
Make discoveries using bioinformatics tools in SMRT Analysis or PacBio DevNet.

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Spotlight: Strain-level identification of bacterial communities with the unprecedented accuracy of PacBio full-length 16S sequencing

Using DADA2 software, all copies of the 16S housekeeping gene can be recovered from microbial communities. 16S sequence variants from the same strain appear in the data in integer ratios that reflect their copy number in each genome. In some cases, for example E. coli O157:H7 in the Zymo mock community, this high-resolution information can be used to unambiguously identify not only the species but the strain present. Explore this research further:

Callahan, B. J.,  et al. (2018). High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. BioRxiv, Preprint.

Long reads and methylation profiles enable binning of metagenome assembly contigs and plasmids

SMRT Sequencing of metagenomes enables highly contiguous assemblies of community members, but leveraging the associated methylation information further allows those contigs to be associated into near-complete genome bins. Plasmids of sufficient size can also be associated with hosts via their methylation fingerprints. Explore this research further:

Beaulaurier, J., et al. (2017). Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation. Nature Biotechnology, 36(1), 61–69.

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

Selected Resources