Shotgun Metagenomic Sequencing Service

Unbiased Microbe Detection

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Quick Turnaround Time

Receive shotgun metagenomic sequencing results in as little as 2 weeks

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High-Quality Comprehensive Data

Microbiome standards included in every run

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Strain-level identification for bacterial discovery

Sequencing Accuracy and Consistency

Our cutting-edge data analysis algorithms dramatically reduce false positives in taxonomy assignment and our workflow has been validated at each step to optimize against inaccuracies. Combined with ultraclean reagents to minimize ‘kit-ome’ background noise, our Shotgun Metagenomic Sequencing Service provides high confidence accuracy for sample profiling.

Comprehensive Bioinformatics Analysis

The Shotgun Metagenomic Sequencing Service includes taxonomy analysis, alpha diversity bar plots, beta diversity analysis, gene family profiling, metabolic pathway analysis, antibiotics resistance gene and virulence gene profiling, and LEfSe biomarker discovery.

View Sample Report

Highly Accurate Taxonomic Identification

Multi-Kingdom Strain Level Resolution

Bacteria icon Bacteria Fungi icon Fungi Virus icon Viruses Protist icon Protists

The Zymo Research database contains over 77,000 reference strains across all kingdoms (Bacteria, Archaea, Eukaryote and DNA Viruses). Proprietary algorithm eliminates the risks of false positives in taxonomy assignment.

Providing the Highest Quality

  • Strain-Level Identification with Superior Resolution

  • Microbiome standards included in every run

  • Proprietary algorithm eliminates the risks of false positives

  • Unique dual indexes prevent index swapping

  • Functional Profiling allows identification of antibiotic resistance, virulence factors, and metabolic pathways

See how Zymo’s cutting edge data analysis algorithms dramatically reduce inaccuracies, giving you results you can trust!

Data analysis chart

Results of two bioinformatic pipelines analyzing the same raw shotgun metagenomic sequence data derived from a vaginal swab sample

Shotgun Metagenomic Sequencing Service Made Simple

How our Straightforward, User-Friendly Service Works

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Inquire Below

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Send Us Your Samples

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Receive A User-Friendly
Analysis Report

Multiple Payment Options Available

Trusted by Industry Leaders

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You need a forward-thinking, flexible company guided by deep scientific understanding to drive custom manufacturing success. With over 27 years of experience, Zymo Research has provided top-tier innovation, quality, and customer service to meet the needs of its partners & collaborators in the field of life sciences.

Shotgun Metagenomic Sequencing Technical Specifications

Sequencing Platform Illumina NovaSeq 6000™, NextSeq 2000™, NovaSeq X™
Sample Collection Raw Sample

Various sample collection devices provided upon request

DNA sample (> 1 ng/μl by Fluorescence DNA quantification)

Please ensure it is PCR inhibitor-free

Read Length 2 x 150 bp
Taxonomy Resolution

Bacteria and Archaea: strain-level

Fungi and Viruses: species-level

Accepted Sample Types Extracted Genomic DNA, or raw samples
DNA Extraction

ZymoBIOMICS 96 Magbead DNA (D4308)

ZymoBIOMICS DNA Miniprep (D4300)

Library Prep

Illumina DNA Prep (Formerly Nextera Flex)

Unique Dual Indexing (UDI) included

Sequencing Analysis Kmer signature based analysis using Sourmash with antimicrobial resistance using Diamond and functional pathway analysis using Humann3
Reference Database

We use pre-built databases supported by the SourMash development group covering Prokaryote, Eukaryote, Archaea, and Viral genomes compatible with GTDB and NCBI taxonomies.

Data Visualization

Taxonomy Profiling

Taxa abundance bar plot and heatmap

Alpha diversity boxplot

Beta diversity PCoA plot

Functional Profiling

Antibiotics resistance identification

Virulence gene identification

Gene family profiling (UniRef)

Metabolic pathway profiling (Metacyc)

Statistical Analysis

LEfSe analysis uncovers taxa/traits that are differentially distributed among defined sample groups.

Example Report Our sample shotgun metagenomic sequencing service report can be viewed here
Data Storage

Raw sequencing data and analysis report are stored for up to 3 months

Frequently Asked Questions

There is no sample minimum required in order to submit to our Metagenomic Shotgun Sequencing Service

We recommend sending 200-500 mg for solid samples or 500-1mL of liquid samples in general. This may vary depending on the specific sample type.

The minimum volume of DNA required is 30 µl with a recommended concentration of 10-50 ng/µl. If the concentration is lower, we can often still successfully sequence as our pipeline is quite robust.

We have processed a wide variety of sample types, from human tissue samples, environmental samples, to food samples. If you have questions or concerns, please feel free to fill out an inquiry or contact us.

Because of our included quality control standard, it is possible to batch samples over time and have confidence that the samples were processed in the same way. We recently completed a project that had a total of >2,000 samples processed over a period of 6 months. By comparing the results from the standard for each group of samples, we had confidence that the results from different batches could be compared together.

Tell Us About Your Shotgun Metagenomic Sequencing Project

Please describe your project and one of our scientists will reach out to assist you.

The Benefits of Metagenomics

Shotgun metagenomic sequencing has widely been used to characterize an assortment of microbiome samples, including those derived from human/animal body sites and environmental samples (e.g. soil, sediments, sludge, water, air, etc.).

The use of shotgun sequencing for metagenomics, rather than a targeted microbiome profiling (e.g. 16S/ITS), enables more information to be obtained from a sample. This includes cross-kingdom microbial identification, metabolic function profiling, strain-level differentiation, detection of virulence genes and antibiotic resistance genes.

The workflow of shotgun metagenomic sequencing is complex with multiple steps where improper handling can cause bias that can significantly alter the results. A well-established workflow with extensive validation is crucial to the success of a metagenomic sequencing project.

Zymo Research is a well-known pioneer as a reagent and kit provider for microbiome research. Our innovative microbiome products include DNA/RNA Shield for unbiased sample collection, ZymoBIOMICS DNA kits for unbiased lysis, and microbiome standards to ensure superior process quality control.

Building on the top of these innovative products, we have established a shotgun metagenomic sequencing service that was optimized thoroughly and validated to ensure unbiased microbiome profiling.

Our shotgun metagenomic sequencing service also includes a comprehensive bioinformatics report that includes strain-level taxonomy profiling, metabolic gene family and metabolic pathway profiling, virulence gene and antibiotics resistance gene identification, statistical analysis, etc. Innovations on the taxonomy assignment algorithm enable us to dramatically reduce the false positives in microbial identification, a common issue that most existing metagenomics tools and most service providers suffer from.

Academic researchers and industrial clients alike trust our shotgun metagenomic sequencing service. This includes high-throughput direct-to-consumer testing companies that also enjoy our fast turn-around time and the complete workflow from sample collection to bioinformatic analysis.

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