BenchMark Microbial Amplicon Sequencing

BenchMark™ is our approach to amplicon sequencing for microbiome profiling. Amplicon sequencing uses primers that match the conserved areas of marker genes, such as the 16S ribosomal RNA gene of bacteria (16S rRNA) or the internal transcribed spacer region 2 of fungi (ITS2).

Optimized Amplicon Sequencing

We pair our low-bias amplification method with an optimal closed-reference alignment to provide you with highly accurate data.

We offer BenchMark™ sequencing that targets the variable region 4 of the bacterial 16S rRNA gene, the fungal ITS2 region, and custom marker genes of your choice.

Eliminate Taxonomic Dropout

BenchMark™ combines real-time PCR sample quantification, dual-indexed multiplexing, and optimized enzymatic and PCR conditions to eliminate most of the taxonomic dropout that is observed with standard amplicon sequencing methods.

In 2016, our BenchMark™ approach was published in Nature Biotechnology by ​our founders,​ Daryl Gohl, Dan Knights and Kenny Beckman [1].

BenchMark™ suppresses chimera formation and minimizes PCR error, resulting in greater accuracy when tested head-to-head against other amplicon sequencing methods in the analysis of defined mock community standards.

In the plot below, the dotted line represents the expected percent abundance of each community member in a mock community. The BenchMark™ low-bias approach is highlighted in yellow.

Sample Types Suited for BenchMark™

Shotgun metagenomic sequencing is highly accurate, but isn’t best suited for all sample types.

Samples with low microbial loads benefit from the approach of amplifying and sequencing just a small portion of the microbial genome.

BenchMark™, our amplicon sequencing approach, is recommended for samples that have low biomass, including environmental samples such as soil and surface swabs.

We also recommend amplicon sequencing for samples with high amount of host DNA, such as skin swabs or biopsy samples.

BenchMark™ Basics


Starts at $89/sample.

Minimum order:

88 samples for 3-week turnaround, 24 samples for 6-week turnaround.


Adaptor-removed and filtered sequencing data (fastq), stitched and combined sequences file (fasta), annotated taxonomy and function tables, quality-control dashboard, and a full Core Analysis report. Review example report.


BenchMark™ sequencing is performed in a CLIA-certified laboratory.

The following are included in your BenchMark™ project:

  • Initial quality control check on all samples
  • QC report returned for review
  • Amplification and library preparation using our optimized approach
  • Core Analysis Report
    • Taxonomic assignments via fully optimal gapped DNA sequence alignment to a curated reference database
    • Functional predictions (16S) via alignment to a curated reference database
    • Sequencing quality-control dashboard
    • Interactive visualizations that leverage your sample metadata
  • Fastqs: adaptor-trimmed and quality-filtered sequencing data
  • Fasta: trimmed, stitched and combined DNA sequences in QIIME-ready

Review example report.

BenchMark™ sequencing starts at $89 a sample.
To ensure data of the highest quality, we require a minimum number of 24 samples per project.

The standard turnaround time for a BenchMark™ project is 3 weeks from DNA generation, but we can expedite your results. Find out how by reviewing our FAQ document.

Large projects beyond 1,000 samples may require additional time. Contact us ​with questions.

To ensure your BenchMark™ samples return the best data, we recommend performing your ​DNA extraction​ at CoreBiome.

Input DNA quality and quantity can have dramatic impacts on the microbial profile generated for your samples.

By allowing the experts at CoreBiome to extract and prepare your DNA, we can ensure the best quality library preparations for amplicon sequencing.

CoreBiome accepts primary samples, such as swabs, fecal samples, and soil, as well as pre-extracted DNA.

For more information regarding sample preparation and shipment, check out our ​sample guidelines​.

All we need to know are some quick details regarding the types of samples you have, how many, and how they are stored.

From there, our team of experts can recommend the best approach for generating your microbiome data and discoveries.

Request a quote or contact us with questions.​

For research purposes only.

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