Long Reads Versus More Reads: Comparing Two Sequencing Tools for Evaluating Live Biotherapeutics as Microbiome Interventions

A longstanding challenge in microbiome research has been achieving the taxonomic resolution needed to generate testable hypotheses about how the gut microbiome impacts human health and disease, and to assess the mechanism and efficacy of specific microbiome interventions. Short read whole genome shotgun metagenomic sequencing provides high taxonomic resolution plus functional information but is expensive for large cohort studies. Because of its lower cost, short-read sequencing of the bacterial 16S rRNA gene has become the standard for microbiome profiling, despite its limitations.

Recently, HiFi sequencing with PacBio has offered an alternative to both short-read shotgun metagenomics and partial 16S gene sequencing, providing richer information from shotgun data and higher taxonomic resolution from full length 16S sequences. Here, we use 12 human microbiome samples from 6 donors enrolled in a Phase 1b trial of a live biotherapeutic product to compare the utility and cost effectiveness of long-read and short-read sequencing methods for evaluating microbiome interventions using both 16S StrainID from Shoreline Biome and PacBio HiFi sequencing shotgun datasets.

Watch this webinar to understand how:

16S sequencing with Shoreline Biome and PacBio allows for strain-level identification and tracking of bacteria in fecal samples
Less PacBio HiFi shotgun data is needed to generate the same level of functional profiling information, because unlike with short read data, nearly every read has at least one, and typically multiple, functional annotations
PacBio HiFi data generates multiple single contig MAGs from fecal samples when multiplexed at 3 samples per SMRT Cell 8M, outperforming other sequencing alternatives

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Speakers

Meredith Ashby, PhD

Associate Director, Segment Marketing
PacBio

Jeanette Gehrig, PhD

Senior Scientist
Siolta Therapeutics

Democratizing Genome Assembly and Annotation

Ted Kalbfleisch, Ph.D., Associate Professor, University of Kentucky

Molecular Genetic Applications Enabled by Platinum Quality Reference Genome Assemblies in Octoploid Strawberry

Mitchell Feldmann, Ph.D., Postdoctoral Fellow, University of California, Davis.

Democratizing Genome Assembly and Annotation

Ted Kalbfleisch, Ph.D., Associate Professor, University of Kentucky

Molecular Genetic Applications Enabled by Platinum Quality Reference Genome Assemblies in Octoploid Strawberry

Mitchell Feldmann, Ph.D., Postdoctoral Fellow, University of California, Davis.