Shoreline Biome Microbiome Sequencing Kits

Microbiome Sequencing Kits

Shoreline Biome’s easy end-to-end workflow provide significant improvement over many of the standard protocols that are known to miss microbes or provide biased results. All aspects of the systems are designed from the ground up to work together on the industry leading long-read PacBio and Oxford Nanopore sequencing platforms as well as the short-read Illumina sequencing platform.

PCR Sequencing Targets

Based on your experimental needs and the availability of sequencing platforms, Shoreline Biome kits offer optimized PCR choices for parallel sequencing of over 100s to 1000s of samples leveraging either variable regions of the 16S rRNA gene, the entire 16S region or the 16S gene plus the highly variable internally transcribed  spacer region depending on the taxa classification needs of the experiment.

The kits take the guesswork out of which target sequences to choose, what polymerase to use, and the level of primer degeneracy. They are designed and validated with multiplex primers for sequencing many samples simultaneously in a single sequencing run. The PCR conditions are optimized for sequencing a simple or a complex microbiome community and ensure conditions that result in correct microbial profiles.

The assay kits for the PacBio Sequel system contain prearrayed PCR wells for lysis, DNA purification beads, and prearrayed PCR wells containing dual-ended  barcoded primers targeting either the entire 16S rRNA gene or the extended 16S-ITS-23S gene region. Following PCR amplification, amplicons are pooled and ready for the addition of PacBio SMRTbell adaptors followed by sequencing on the PacBio Sequel System.  96-sample and 16-sample kits can be combined for a total of 112 barcodes or run separately. Utilization of barcoded SMRT bell adaptors also allow further multiplexing of 100s to 1000s of samples on a single SMRT cell.

The assay kits for the Oxford Nanopore Technologies platform contain prearrayed PCR wells for lysis, DNA purification beads, and prearrayed PCR wells containing dual ended  barcoded primers targeting the extended 16S-ITS-23S gene region. Following PCR amplification, amplicons are pooled and ready for Oxford Nanopore ligation adaptors followed by sequencing. 96-sample and 16-sample kits can be combined for a total of 112 barcodes or run separately.

The assay kits for the Illumina sequencing platform contain prearrayed PCR wells for lysis, DNA purification beads, and prearrayed PCR wells containing dual-ended barcoded primers targeting either the V1-V3 or V4 region of the 16S rRNA gene.  Following PCR amplification, multiple amplicons already containing the Illumina sequencing adaptor are pooled, purified, and ready for sequencing.

2 Kit Configurations Available

  • Shoreline Complete kits include the lysis, DNA purification, and PCR reagents needed to easily and quickly lyse and prepare amplicons for sequencing.
  • Shoreline Wave kits provide the same PCR reagents for customers with already prepared high-quality DNA.

Data Analysis

Shoreline Biome SBanalyzer software for long-read amplicon data generated either from the PacBio or Oxford Nanopore sequencers, sorts samples by barcode and allows tracking by user-selected sample names. Each sample’s reads are mapped using the Athena Microbial Reference Database to determine phylogenetic identity.

Output can be transferred to a spreadsheet to compare results between individual samples or combine samples into virtual groups for comparison at the phylum, strain, or other taxonomic levels.

Mapping allows investigators to quickly test hypotheses about variations in microbial types between microbiome cases and controls. Reads can also be used for custom analysis, as desired.

Shoreline Biome Workflow

you need any help?

Please contact:

Dr. Sieke Schaepe

Tel. +49 (0) 6221 71415 16 info@biocat.com