Sequence thousands of organisms in parallel

Comprehensively sample all genes in all organisms present in a complex sample

Shotgun Metagenomic Sequencing

Shotgun metagenomic sequencing allows researchers to comprehensively sample all genes in all organisms present in a given complex sample. The method enables microbiologists to evaluate bacterial diversity and detect the abundance of microbes in various environments. Shotgun metagenomics also provides a means to study unculturable microorganisms that are otherwise difficult or impossible to analyze.

Unlike capillary sequencing or PCR-based approaches, next-generation sequencing (NGS) allows researchers to sequence thousands of organisms in parallel. With the ability to combine many samples in a single sequencing run and obtain high sequence coverage per sample, NGS-based metagenomic sequencing can detect very low abundance members of the microbial community that may be missed or are too expensive to identify using other methods.

16S rRNA Sequencing is another method used for metagenomics studies.

There are multiple ways to perform these experiments, but these are some suggested products for each step of the workflow.

Click on the below to view products for each workflow step.

Nextera XT Library Prep Kit

Prepare sequencing-ready libraries for small genomes (bacteria, archaea, viruses), amplicons, and plasmids in less than 90 minutes.

TruSeq DNA PCR-Free Library Preparation Kits

Simple, all-inclusive library preparation for whole-genome sequencing applications. Researchers can sequence a wide variety of organisms, from small genomes such as bacteria to whole-human genomes.

Desktop Sequencing Systems

MiSeq System

Speed, accuracy and simplicity for far reaching applications in microbiology.

MiSeq v3 Reagents Kits

Improved chemistry to increase cluster density and read length. Enables up to 15 Gb of output.

MiSeq v2 Reagents Kits

Ideal for sequencing microbial transcripts in less than 6 hours. Micro and nano formats available for low-throughput applications.

NextSeq Series

Flexible desktop sequencer for exome, transcriptome, and whole-genome sequencing.

NextSeq 500/550 v2 Kits

Enhanced clustering chemistry yields even higher data quality. Provides 130 or 400 million reads and up to 120 Gb output per run.

High-Throughput Sequencing Systems
Power for shotgun metagenomics and flexibility to scale based on your project or workflow needs.

HiSeq 2500 System

Power and efficiency for large-scale genomics.

HiSeq 2500 Reagent Kits

Clustering and sequencing reagents for up to 600 Gb of output.


HiSeq 3000/HiSeq 4000 Systems

Maximum throughput, lowest cost for production-scale genomics.

HiSeq 3000/4000 SBS Kit and PE Cluster Kit

Leverage patterned flow cell technology to generate up to 1500 Gb (1.5 Tb) of output per dual flow cell run.

BaseSpace Apps for k-mer alignments and taxonomic classification

Kraken Metagenomics

Assigns taxonomic labels to short DNA sequences with high sensitivity and speed using exact alignments of k-mers and a novel classification algorithm.

One Codex

Enables metagenomics analysis by rapidly assessing your samples from BaseSpace Sequence Hub with a fast, comprehensive, accurate data platform

GENIUS Metagenomics: Know Now

Uses CosmosID's curated genome database and high performance algorithms to provide rapid, accurate, and actionable bacterial identification at the species, subspecies, and strain level.

Interested in receiving newsletters, case studies, and information on microbial genomics? Enter your email address.
Lungs, Germs and Metabolites: A Cystic Fibrosis Story
Lungs, Germs and Metabolites: A Cystic Fibrosis Story

Overview of Illumina next generation sequencing platforms and relevant applications and use cases for food pathogen testing.

View Video
Metagenomic Analysis of Environmental Water Samples
Metagenomic Analysis of Environmental Water Samples

Shotgun metagenomic sequencing with the NextSeq 500 System provides insight into microbial responses to environmental changes in a water reservoir.

Access PDF
Metagenomics Research Review
Metagenomics Research Review

See selected publications using sequencing to better understand microbial populations.

Access PDF
HiSeq and Shotgun Metagenomics
HiSeq and Shotgun Metagenomics

The HiSeq sequencer is ideal for high-throughput metagenomic sequencing.

Learn More
NGS to Discover New Virus Types on Skin
NGS to Discover New Virus Types on Skin

Illumina sequencers offer deep coverage to identify novel HPV types correlated with non-melanoma skin cancers.

Read Article
Metagenomics to Map Ocean Biodiversity
Metagenomics to Map Ocean Biodiversity

An epic ocean expedition sequenced salt water samples from around the globe to survey plankton diversity in marine ecosystems.

Read Interview