Metagenomic Sequencing


Metagenomic sequencing uses next generation sequencing (NGS) to rapidly analyze microbial community diversity and understand the role of constituent species. Our metagenomic sequencing solutions range from targeted assays, such as 16S for prokaryotes and ITS2 for fungi, to shotgun sequencing and metagenomic analysis. Explore below which service best fits your needs, or check out our webinar, “Uncovering Hidden Microbial Diversity with NGS Technology,” to learn more about our capabilities.

What is metagenomic sequencing?

Metagenomic sequencing is the collective analysis of all genomic material present in a sample (containing mixed microorganism communities), thus eliminating the need for isolating and cultivating individual organisms.


What is metagenomics vs. genomics?

Both metagenomics and genomics are fields of study within molecular biology, but the difference is in scope. While genomics is focused on the genome of a single organism, metagenomics encompasses all genomes of various microorganisms within a single given sample, providing a broad overview of an ecosystem’s composition.


Metagenome Sequencing Service Options

  16S-EZ 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
  • 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 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


Digital PCR (dPCR)

Detect your target sequences with unmatched accuracy

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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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. (
Case Study

Webinar | Understanding biological mechanisms to better predict the evolution of antibiotic resistance

The rapid and wide-spread evolution of antibiotic resistance is threatening global health. In this webinar, presented by Dr. Mato Lagator, Wellcome Trust, Royal Society Sir Henry Dale Fellow, University of Manchester, you will learn about different approaches to study evolutionary processes that underpin the emergence of resistance. Special focus is given on how these methods can be utilized to improve drug development and longevity.

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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.


For information on our NGS platforms as well as recommended configurations of your projects, please visit the NGS Platforms page. Azenta does not guarantee data output or quality for sequencing-only projects.

10x Genomics

How To Order

Email | Phone 1-877-436-3949, Ext. 1