Metagenomics can leverage next generation sequencing to rapidly analyze the diversity of microbial communities and elucidate the role of constituent species. We offer a suite of metagenomics solutions ranging from targeted assays (16S for prokaryotes and ITS2 for fungi) to whole genome analysis. Learn more below to see which service best fits your needs.

Check out our latest webinar “Uncovering Hidden Microbial Diversity with NGS Technology” to learn more about our latest capabilities.


Service Options

Fungal Identification
Whole Genome Metagenomics

 Microbes Targeted

Bacteria and Archaea Fungi All

 Taxon Level

Genus/Species Genus/Species Sub-species
Genomic Loci Sequenced 16s rRNA gene
(V3 and V4 regions)
Internal Transcribed
Spacer 2 (ITS2)
Whole Genomes
Purpose of Assay  Taxon Identification
  • Taxon identification
  • Functional analysis
  • Variant discovery
Benefits Enhanced sensitivity outperforms
V4-only assays
High variation in ITS2
region allows differentiation
between closely related species
  • Most comprehensive assay - identify over 53,000 microbes
  • Phylogenetic and functional analysis
  • Ideal for organisms with poorly annotated 16S genes
Available Reports
  • Rank-abundance curve
  • Taxonomic classification
  • Rarefaction curve
  • Principal coordinate analysis
  • Hierarchical clustering
  • Taxonomic classification of reads across all ranks
  • Microbial abundance estimation across all ranks
  • Cross-sample comparisons across all ranks
  • Dynamic, visual exploration of microbial taxonomy
  • Interactive, searchable data tables
  • Functional analysis

Coming soon! Full-length 16S sequencing for sub-species resolution. Please inquire for more details.


Webinar: Uncovering Hidden Microbial Diversity with NGS Technology

This webinar outlines the role and importance of microorganisms in our everyday world, how to classify and identify them, and the next generation sequencing techniques that work best for these tasks. We touch on the wide array of areas that microbial genomics can be applied to and the NGS case studies that have helped scientists thrive in various research areas.

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Example Report: 16S-EZ Metagenomics Bioinformatics Analysis

With the addition of the new, enhanced bioinformatics analysis and report, 16S-EZ delivers industry-leading analysis of microbiome diversity and composition. This improved report takes the tedium out of dendrogram and graph creation, allowing you to analyze your data faster. An example report is available for viewing by clicking the button below.

The enhanced report includes the following information:

  • Rank-abundance curve
  • Taxonomic classification
  • Rarefaction curve
  • Principal coordinate analysis
  • Hierarchical clustering
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Case Study

Tech Note: 16S MetaVx™ Environmental Detects Greater Prokaryotic Diversity Than Traditional 16S Assay

We compared GENEWIZ’s 16S MetaVx Environmental service against a traditional V4-only assay. 16S MetaVx Environmental consistently detected a greater number of bacteria and archaea, demonstrating its superior sensitivity and specificity.

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Please inquire for more details. (

Sample Submission Guidelines

GENEWIZ accepts a variety of starting materials for Metagenomics projects. For detailed sample submission requirements please visit our Sample Submission Guidelines page.



All customers receive their raw data as FASTQ files. MetaVx2.0™ provides an enhanced report through analysis with the QIIME software suite. This optional, enhanced report includes figures such as rank-abundance curves, taxonomic classification, rarefaction curves, principal coordinate analysis and hierarchical clustering analysis. An interactive taxonomic viewer detailing different taxa and their relative abundance in each sample is also available by request.

NGS Platforms

GENEWIZ is a certified service provider for Illumina and Life Technology NGS platforms. For information on our NGS platforms as well as recommended configurations for your projects, please visit the NGS Platforms page. GENEWIZ does not guarantee data output or quality for sequencing only projects.

How To Order

Email | Phone (1-877-GENEWIZ (436-3949), Ext. 1) | Live Chat