Frequently Asked Questions

Please read our FAQ. If you still have a question, email us using the contact form.

What is Shoreline Biome?

Shoreline Biome is an early-stage company developing leading-edge microbiome technologies and products designed to advance microbiome research. Shoreline Biome provides easy-to-use, cost-effective tools and reagents that support end-to-end microbiome analysis.

Shoreline Biome has developed the first comprehensive and easy-to-use solution for all-in-one microbe lysis, nucleic acid extraction, and 16S PCR amplification from complex samples for sequencing on both the Illumina and PacBio sequencing platforms.

Since its inception, Shoreline Biome’s goal has been to create products that allow researchers to get to their science faster with more complete and comprehensive data. Researchers at the forefront of microbiome research are using Shoreline Biome kits to generate the highest-quality and most-complete data sets without added time and expense.

Where is Shoreline Biome located?

Shoreline Biome is located in Farmington, Connecticut, at the University of Connecticut Technology Incubator Program (UConn TIP). The UConn TIP is within walking distance of the University of Connecticut Health Center and The Jackson Laboratory for Genomic Medicine.

How do I purchase a Shoreline Biome assay kit?

Shoreline Biome assay kits can be purchased via credit card or purchase order from our secure online store. For quotes and larger orders, please contact Karen Woodward, VP of Business Development, at karen.woodward@shorelinebiome.com.

What is included in Shoreline Biome assay kits?

Each Shoreline Biome assay kit includes the reagents and barcoded primers needed to easily and quickly prepare amplicons for 16S sequencing.

The assay kits for the Illumina sequencing platform contain one 96-well plate for lysis, one tube of DNA purification beads, and one 96-well PCR plate containing 96 barcoded primers targeting either the V1–V3 or V4 region of the 16S rRNA gene. Following PCR amplification, the amplicons containing the Illumina sequencing adaptor are pooled, purified, and are ready for sequencing.

The assay kits for the PacBio sequencing platform contain one 96-well plate for lysis, one tube of DNA purification beads, and one 96-well PCR plate containing 96 barcoded primers targeting either the full 16S rRNA gene or the 16S-ITS-23S region. Following PCR amplification, the amplicons are pooled and ready for the PacBio SMRTbell reaction.

Why are Shoreline Biome assay kits better than others on the market?

Shoreline Biome kits provide the most-complete and easy-to-use microbiome sequencing solution on the market. Experienced and novice microbiome researchers alike trust Shoreline Biome assay kits for fast, comprehensive data results. Shoreline Biome kits allow researchers to quickly generate the amplicons required for their short- or long-read sequencing data.

The kits provide the highest-quality 16S amplicon preps available, prepared for pooling and sequencing on either the Illumina or PacBio sequencing platform. In head-to-head comparisons, Shoreline Biome’s proprietary technology has identified organisms that other kits could not. It is not necessary to weigh samples prior to starting the process.

The kits allow for simple lysis of up to 96 samples with comprehensive representation of Gram-positive Firmicutes and other difficult-to-lyse microbes in under 35 minutes. They are configured in a 96-well plate format that provides a seamless transition to single-step PCR.

Unique, dual-matched barcode designs cover known PCR primer variants while limiting PCR bias and maintaining proportional representation.

When used with the PacBio platform, Shoreline Biome's intuitive analysis software and specially-curated Athena database allow a straightforward analysis of the sequence data with superior high-resolution readouts.

I use an Illumina sequencing platform. Are Shoreline Biome assay kits right for me?

Shoreline Biome has two kits for purchase that support Illumina 16S sequencing.

The Shoreline Complete V1-V3 Kit provides reagents for sequencing the V1–V3 region of 16S.

The Shoreline Complete V4 kit provides PCR reagents for sequencing the V4 region of 16S.

Both kits include Illumina sequencing adaptors which are added to the amplicons during the PCR step. Additionally, both kits output 96 barcode-labeled amplicons ready for Illumina sequencing.

I use a PacBio or other long-read sequencing platform. Are Shoreline Biome assay kits right for me?

Shoreline Biome has two kits for purchase that support PacBio sequencing.

The Shoreline Complete V1-V9 Kit supports full-length 16S. This kit yields SMRTbell-ready amplicons of approximately 1,500 bp. The full-length 16S amplicon generally leads to identification of microbes at the species level.

The Shoreline Complete StrainID Kit supports 16S-ITS-23S. This kit yields SMRTbell-ready amplicons of approximately 2,500 bp. The StrainID amplicon allows identification of microbes at the strain level.

Tell me more about your Athena database.

The Shoreline Biome StrainID kit is a unique long amplicon that requires mapping to our specially curated Athena database. Athena is built from RefSeq genomes, and contains comprehensive, integrated, non-redundant, well-annotated genomes. Many of these genomes overlap with other databases (i.e., homd, etc). Currently, the database contains 18,566 genomes and 77,212 16S-23S regions.

Do your primers cover all bacteria?

To build our primer sets, we performed a search of the SILVA database (hundreds of thousands of complete and partial 16S gene), the Riken database (2,275 complete and 5,664 draft genome sequences including the Human Microbiome Project (HMP) genome sequences data from NCBI), and the Athena database (18,566 fully assembled genomes from RefSeq database, Dec 2018). The databases include organisms from many different sources including human oral, fecal, skin, model organisms, environment, etc. Our design includes all known (sequenced) variants and prospective unknown primer variants based on the rRNA gene structure. We also have a novel primer design that limits the effects of potential primer depletion or competition.

What is the advantage of using the V1V9 kit?

We developed the V1V9 kit for customers who have existing data on the full 16S gene but also want the technological benefits of our Shoreline Biome lysis and primers. In addition, there are a few organisms that cannot be detected with the StrainID kit because the primer targets are not located near one another within the genome. Notably, Helicobacter pylori and Deinococcus radiodurans.

Can I pool barcodes together in a single sequencing run?
The following can be pooled together in a single sequencing run. For any other combination, please contact technical support hello@shorelinebiome.com.
Kit             These sets can be pooled
V4              Set A,B,C
V1V3          Set A,B 
V1V9          Set Z,A
StrainID      Set Z,A
 
 
Are there any restrictions on the use of Shoreline Biome assay kits?

Shoreline Biome kits are currently available for research use only and are not for redistribution. If you are interested in using Shoreline Biome kits for diagnostic assay development, please contact us at hello@shorelinebiome.com.

I ordered a Shoreline Biome assay kit. When will I receive it?

Most orders are shipped within 2–3 working days of order placement. Each customer is provided an estimate of delivery at time of order. Orders placed on Friday will not be shipped until the following Monday.

Do you ship kits internationally?

We have distribution agreements with a number of companies outside the United States. For more information, please contact our business development team at hello@shorelinebiome.com.

If you are interested in international distribution, please contact our business development team at hello@shorelinebiome.com.

I am interested in collaborating on a research project. Who should I contact?

Please contact us via email at hello@shorelinebiome.com.

I would like to purchase kits in bulk. How do I request a quote for a bulk order?

Please contact Karen Woodward, VP of Business Development, for a quote. Her email is karen.woodward@shorelinebiome.com.

How is Athena database different from other publicly available databases?

Strain-level taxonomic differentiation of bacteria using 16S databases (SILVA, RDP, Riken, HOMD, etc) is typically not possible, regardless of how many reads are in the database, because the 16S gene does not contain sufficient variability to differentiate many species/strains. Mapping to 16S databases will typically assign taxonomy at the genus level at best because the information about the spacer-region sequence is not included. For the same reason, identification of novel strains is typically not possible. The spacer-region sequences between the genes are a rich source of variability crucial for differentiating closely related bacterial strains. The Athena database contains contiguous 16S-23S gene sequences from comprehensive, integrated, non-redundant, well-annotated genomes allowing strain level identification.

What are the additional materials I need to purchase that are not included in the kit?

A magnet for handling the magnetic beads is required (Invitrogen Dyna Mag 96 side magnetic rack, #12331D or Magnetic stand-96 #AM10027). Please note that we strongly recommend the Invitrogen Dyna Mag 96 magnet. We’ve found that users have had the most success with this type of magnet. The Magnetic stand-96 (Thermo Fisher #AM10027) is the only other approved magnet. Plate magnets that have a 'well' type magnet rather than a 'bar' or 'post' will result in low DNA yield. For post PCR clean up the Qiagen MinElute® PCR Purification Kit (Cat. No. 28004) is needed. We do not recommend using SPRI beads during this step. The other required items are common to most labs and are listed in the protocol.

What is the recommended sequencing coverage for Illumina and PacBio for Shoreline Biome Complete kits?

Coverage is very dependent on experimental design and goals so each project can have different requirements. Illumina suggests 100,000 reads/sample for 16S analysis. Many researchers have done much lower reads with good results. We have multiplexed 288 samples using Shoreline Biome V4 kits, and sequenced on MiSeq with sufficient coverage. For PacBio sequencing with the StrainID kit we suggest running ~96 samples on one SMRT cell. This gives sufficient reads/sample to identify bacterial strains present at 1% with reasonable confidence on the Sequel I. In general, more reads will yield greater depth per sample, enabling identification of bacteria present at lower levels in the sample. For highly diverse samples where representation below 1% is needed, more than one Sequel I SMRT cell or a single Sequel II SMRTcell may be advisable.

Send us an email

Send us an email using the form below.