BoosterShot®Shallow Shotgun Metagenomic Sequencing

BoosterShot is our highly-accurate approach to shallow shotgun sequencing that makes full species-level resolution and functional profiling attainable for large scale studies.

Shallow shotgun sequencing can profile down to 0.05% of a microbial community, without the need for standard deep sequencing.  BoosterShot gives you access to information that is just not reachable with amplicon sequencing.

Every BoosterShot project includes a Core Analysis™ Report which provides fully annotated data tables, interactive visualizations and all the raw data delivered through our customer portal.  

Benefits of Shallow Sequencing

We developed algorithms of unparalleled sensitivity to unlock maximum information from sequencing depths of just 2 million reads per sample. This gives you more sensitivity and statistical power than you would get with amplicon sequencing.

BoosterShot can profile down to 0.05% of a community, allowing researchers to obtain information about complex microbiome communities, otherwise unreachable without deep sequencing depths. Each BoosterShot project includes species-level taxonomic profiling and functional profiling of biological pathways present in your samples.

See an example of a Core Analysis report with taxonomy and function tables, a quality-control dashboard, and interactive profile plots.

Scalable Big Data

With BoosterShot, researchers can unlock more information about their microbiome samples and thus, examine their data in new ways. Shallow shotgun sequencing allows you to increase your study size, allowing for time-series sampling and multiple pre- and post-treatment collections. More samples equals more power.

When robust studies are paired with the highly-accurate species and functional profiles that shotgun metagenomic sequencing returns, unlocking signals in your data is easy. 

One example of this approach was employed in the academic lab of one of our founders, Dan Knights. Dense time series collection of participants was done with daily collections for 17 days [Johnson et al., 2019, Cell Host & Microbe 25, 789–802]. When linked with daily dietary data, Johnson et al were able to find patterns in microbiome stability and diversity correlated with dietary intake.

Collection of participants for 17 days plotted.

Studies like this aren’t feasible at the price of traditional deep sequencing, whereas our approach enables the mix of sensitivity and power.

Want to unlock more information from your samples? Contact us to find out how we can help enrich your studies.

Sample Types Suited for Shallow Shotgun Sequencing

Ideal samples are high-biomass samples with less than 50% host DNA contamination. Samples containing microbes that are well represented in whole-genome reference databases work well with BoosterShot.

Some examples include human fecal and oral samples, as well as, fecal samples from model organisms. Although a high amount of host-DNA can decrease the percentage of reads that will contribute to your microbiome profile, host contamination can be overcome with additional sequencing depth.

Shallow shotgun sequencing is a powerful sequencing tool – we recommend it for many projects – but isn’t best suited for all sample types. In our experience samples with low microbial loads or a high proportion of host genome contamination benefit from using BenchMark™ amplicon sequencing for DeepSeq™ deep shotgun sequencing.

Contact us to find the right balance of depth and data for your project.

BoosterShot Shallow Shotgun Sequencing Basics

Suggested Sample Types

BoosterShot is particularly useful for high biomass, low host contamination samples containing microbes that are well represented in whole-genome reference databases. Examples are human stool and oral samples or fecal samples from model organisims. For more information regarding sample preparation and shipment, check out our sample guidelines.

We have experience working with a wide array of samples types, some of the most common types that are suitable for shallow shotgun are listed below. Contact us if your sample of interest is not represented here.

  • Primary Samples (ex. stool, saliva)
  • Mixed microbial communities and microbial consortia
  • Swabs (ex. vaginal, oral, rectal)
  • pre-extracted DNA (for the best data quality, please allow us to perform the extraction)


Every BoosterShot project Includes

  • Initial quality control check on all samples
  • QC report returned for review
  • Amplification and library preparation using our optimized approach
  • Sequencing starting at 2 million reads per sample
  • Core Analysis Report
    • Strain-level and species-level taxonomic assignments via fully-optimal gapped
      DNA sequence alignment to a curated reference database
    • Direct functional profiling via alignment to a curated reference database, reported as KEGG orthology groups, modules, and pathways
    • Strain coverage tables
    • Sequencing quality-control dashboard
    • Interactive visualizations that leverage your sample metadata
    • Fastqs: adaptor-trimmed and quality-filtered sequencing data
    • Fasta: trimmed and combined DNA sequences in QIIME-ready format

Review example report.


Turnaround Times:

Project turnaround times can be adjusted to meet your needs.

In general, our turnaround times are 4-6 weeks depending on the size of your project.


Diversigen provides services and generates data for research purposes only.  Not all services are available in all regions.