Shotgun Metagenomics

As the name indicates, shotgun metagenomics is an attempt to capture fragments of eDNA dispersed at random within a microbial community, similar to the spray of a shotgun shell. The acquired DNA is expected to represent the microbial community surveyed and provides an opportunity to assemble whole microbial genomes, capture viral or pathogen interactions that may be missed by 16S/ITS studies, and collect information regarding the abundance of genes within a microbial community to determine putative metabolic activities. While the interpretation of 16S/ITS data is accessible to most, metagenomics poses a more complex challenge. Fortunately, many tutorials exist to help answer most metagenomics questions and represent the diversity of questions that can be addressed with a complex dataset.

At SeqCenter, we utilize our Illumina DNA Library Prep pipeline to perform Illumina shotgun WGS of your entire metagenomic sample. In our data analysis, we provide a basic community composition analysis and an annotated assembly of microbial genomes to help make the data more accessible to the greater scientific community. Shotgun metagenomics can be more costly than the 16S approach but can potentially offer more specific identification, functional gene information, and analytical possibilities for the user. For an example version of our shotgun metagenomics analysis methods, click here, and for an example of the analysis output, click here.

Sample Requirements:

  • Total volume of 30 µL or more
  • Sample eluted into water or dilute Tris/TE buffer
  • Sample concentration greater than:
    • 10 ng/µL measured by Qubit
    • 20 ng/µL measured by Nanodrop

What you will receive:

  • Two fastq files (2 x 151bp) for each sample
  • Sequencing stats summary
  • Materials and methods summary
  • Data shared via Box folder within 2 weeks
  • Shotgun metagenomics analysis includes:
    • Metagenomic Assembly
    • Assembly Annotation
    • Taxonomic Assignment

Packages & Pricing

Sequencing Package
(Minimum Read Count Per Sample)
Small Metagenome
Minimum of 6.5M Illumina Reads (1Gbp) with Analysis
Medium Metagenome
Minimum of 32M Illumina Reads (5Gbp) with Analysis
Large Metagenome
Minimum 65M Illumina Reads (10Gbp) with Analysis
Extra Large Metagenome
Minimum of 165M Illumina Reads (25Gbp) with Analysis
*Orders >48 Samples receive 5% discount

We offer convenient DNA extraction services using ZymoBIOMICS DNA extraction kits. This protocol can extract DNA even from tough-to-lyse cells using a bead bashing tube for consistent mechanical lysis. We are able to accommodate all organisms up to BSL2+ and do not accept BSL3 or higher classified organisms for extraction services. We cannot accept soil samples from outside of the US.

Samples requiring DNA extraction can be submitted as aspirated cell pellets shipped frozen on dry ice. A minimum of 109 cells is recommended for all microbial DNA isolation submissions. We cannot culture samples; we encourage you to ensure that there is adequate growth before shipping.

Please note that while this kit is broadly applicable to many sample types, we cannot guarantee its efficacy for a given organism. More information about the ZymoBIOMICS kit can be found here.

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