Shoreline Biome Software Update Enables High-Throughput Microbiome Profiling of Known and Unknown Microbial Strains

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Version 3.0 adds classification improvements, faster speed, downstream tool support

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Shoreline Biome, a microbiome research company with multi-platform, easy to use, ‘Sample-to-Answer’ products for characterizing microbiome populations down to the strain level, announces a significant update to its SBanalyzer software.

Shoreline Biome’s SBanalyzer software enables discovery of never before detected species and strains from microbiome samples. In addition, SBanalyzer simplifies taxonomic assignment from the Shoreline Biome long amplicon kits using the proprietary Athena™ database built from curated contiguous 16S-ITS-23S sequences. Shoreline Biome’s ‘Expert User Protocol’ details the exact steps needed in conjunction with DADA2 for ASV inference/database-independent identification and tracking of novel sequences or strains within and across experiments.

Version 3.0 of the ‘point and click’ SBanalyzer software features improvements to classification capability, including ‘intelligent’ mapping of reads from unknown strains, faster processing speeds, recovery of reads with common sequencing artifacts for improved data yield, an expanded Athena 16S-ITS-23S bacterial database, update to include SILVA v138 database, and support for the downstream informatics tools DADA2 and QIIME 2. A full list of updates appears below.

"We take input from our customers seriously," said Tom Jarvie, Ph.D., Shoreline Biome's co-founder and Chief Marketing Officer. "SBanalyzer version 3.0 is a response to the requests for enhanced capabilities we've heard from our customers, who want SBanalyzer to enable rapid, point and click mapping of strain-level data to known bacterial sequences in the Athena and SILVA databases, but also want output that enables high-resolution of unknown strains not in any database, as well as outputs that plug directly into popular analysis tools like QIIME2 and DADA2. This update will further enable them to discover and track never-before-detected species and strains from microbiome samples with and across experiments."

"It is exciting to see Shoreline Biome pushing the envelope of the resolution that is possible from amplicon profiling of complex microbial communities by combining long - - read amplicon ASVs with their long read database” said Benjamin Callahan, Ph.D, Assistant Professor, Microbiomes and Complex Microbial Communities, North Carolina State University.

The SBanalyzer version 3.0 features:

  • Improved classification of unknowns by scanning poorly mapping novel reads without close matches in any database against highly conserved portions of the long amplicons
  • Ten-fold faster processing speed with multi-core enabled for processing on 6 or 8-core laptops/desktops, so investigators do not require computer core facilities to analyze data
  • Sequencing platform ‘artifact aware’ read processing for greater data yield per sequencing run
  • Expanded Athena database of highly curated reference genome targets: ~20K genomes & 66K 16S-ITS-23S regions
  • Updated SILVA v138 update included in GUI drop-down menu for mapping
  • Options for output files that enable the use of the downstream informatics tools DADA2 and QIIME 2

Jonas Korlach, Chief Scientific Officer of Pacific Biosciences commented, "We are pleased that Shoreline Biome’s new software in conjunction with our highly accurate HiFi sequencing can precisely identify and classify both known and unknown bacterial strains in any microbiome sample. The combination of the Shoreline Complete StrainID kit with the SBanalyzer software and Athena database generates previously unattainable strain-level resolution from 16S sequencing technology and makes it easily accessible to the typical microbiome researcher.”

About Shoreline Biome:
Characterizing the human microbiome and analyzing its role in human health and disease are priority goals for researchers around the world. Shoreline Biome accelerates breakthroughs in microbiome research by developing transformative discovery tools that characterize microbiome populations down to the strain level. With Shoreline Biome products, all it takes is three easy steps: lyse, purify, and amplify. Shoreline Biome’s easy-to-use companion analysis software and comprehensive reference database enables straightforward strain-level identification and quantitation of all bacteria in the sample. To learn more, visit

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