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.

Shotgun Metagenomics Methods Guide
Shotgun Metagenomics Methods Guide

Sequence complex microbial samples to identify emerging diseases or gain insight into microbial community biodiversity and function.

Download Guide

Metagenomic Sequencing Research Stories

NGS is Revealing the Mysterious World of Microbes
The Mysterious World of Microbes

Phil Hugenholtz, PhD explains how shotgun metagenomic sequencing with NGS has made a difference in his research.

Read Interview
How Microbiome Multi-Omics Can Bolster Human Health
How Microbiome Multi-Omics Can Bolster Human Health

Sequencing technologies are enabling a deeper analysis of the gut microbiome and how it contributes to, or protects from, disease.

Read Article
The Time is Now for Microbiome Studies
The Time is Now for Microbiome Studies

Whole-genome shotgun sequencing and transcriptomics provide researchers and pharmaceutical companies with data to refine drug discovery and development.

Read Interview

The Explify Platform is a fully supported NGS-based, clinical metagenomics technology suite for clinical laboratories. Watch this video for a virtual tour to understand how the Explify Platform can help your lab streamline processes, improve results, and much, much more.

Watch Video
IDbyDNA's Explify Platform Delivers Advanced Insights
Microbes and Metagenomics Research Review

Metagenomics is one of the fastest-growing scientific disciplines. This document highlights peer-reviewed publications that apply Illumina sequencing technologies to metagenomics research.

Read Review
Microbes and Metagenomics Research Review

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

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

Illumina DNA Prep

A fast, integrated workflow for a wide range of applications, from human whole-genome sequencing to amplicons, plasmids, and microbial species.

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.

Benchtop Sequencing

MiSeq System

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

NextSeq 1000 and 2000 Systems

Groundbreaking benchtop sequencers allow you to explore new discoveries across a variety of current and emerging applications, with higher efficiency and fewer restraints.

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

NovaSeq 6000 System

High throughput, low cost for production-scale genomics.

BaseSpace Apps for k-mer alignments and taxonomic classification

DRAGEN Enrichment

The DRAGEN Enrichment App aligns and optionally variant calls FASTQ, BAM or CRAM files, outputting a BAM, VCF, or both.

One Codex

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

Frequently Purchased Together

Infectious Disease Surveillance
Crowd of people

NGS supports effective strategies to track infectious disease transmission. Metagenomics can help scientists identify novel pathogens and study zoonotic reservoirs to help predict and prevent outbreaks.

Learn More
COVID-19 Host Risk and Response
T cells

Studies of host genetic variation and immune responses may reveal COVID-19 therapeutic targets. Metagenomics can help researchers analyze microbiome differences between individuals with severe or mild COVID-19.

Learn More
COVID-19 Sequencing Solutions

Find solutions to detect and characterize SARS-CoV2, track transmission routes, study co-infection, and investigate viral evolution. Compare shotgun metagenomics with other pathogen NGS methods. 

Learn More
COVID-19 Solutions
Soil Microbiome Profiling
Soil Sample

This metagenomic shotgun sequencing workflow offers fully automated soil sample preparation, sequencing, and analysis, to help researchers characterize soil microbial communities.

Read Article
Shotgun Sequencing of eDNA
School of Fish

Environmental DNA (eDNA) sequencing is an emerging method for biodiversity and ecosystem studies, used to analyze species that are likely abundant in a sample (such as bacteria or small eukaryotes).

Learn More
Interested in receiving newsletters, case studies, and information on microbial genomics? Enter your email address.
Person listening to podcast
Clinical Metagenomics and COVID-19

Robert Schlaberg and Lauge Farnaes from IDbyDNA discuss applications of metagenomics to infectious diseases in the clinical realm.

Listen to Podcast
Metagenomic Analysis of Environmental Water Samples
Metagenomic Analysis of Environmental Samples

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

Access PDF
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
Nextera DNA Flex Library Prep for Soil Shotgun Metagenomics
Soil Metagenomics Workflow

Explore taxonomic and functional diversity of soil microbial communities with this comprehensive shotgun metagenomics workflow.

Learn More
NovaSeq and Shotgun Metagenomic Sequencing
NovaSeq and Metagenomic Sequencing

Microbial metagenomic sequencing and assembly with the NovaSeq SP 2x251.

Access PDF
Metagenomics and Emerging Pathogens

IDbyDNA experts discuss use of metagenomics in facing the threat of emerging pathogens.

Listen to Podcast