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.

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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.

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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.

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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.

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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.

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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.

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Microbes and Metagenomics Research Review
NovaSeq Reagent Kits
NovaSeq Reagent Kits

Reagent kits for the NovaSeq 6000 System provide ready-to-use cartridge-based reagents for cluster generation and SBS.

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MiSeq System and Reagents
MiSeq System and Reagents

The MiSeq benchtop sequencer enables targeted and microbial genome applications, with high-quality sequencing, simple data analysis, and cloud storage.

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NextSeq 2000 System
NextSeq 2000 System

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

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Nextera XT DNA
Nextera XT DNA

Prepare sequencing libraries for small genomes, amplicons, plasmids, and other applications.

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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.

Nextera DNA Flex Library Prep Kit

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 2000 System

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

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

Driving Insights Through Microbiome Profiling

This metagenomic shotgun sequencing workflow featuring the Nextera DNA Flex Library Prep Kit and the NextSeq 550 System enables accurate DNA detection from soil.

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Alt Name

Environmental DNA (eDNA) sequencing is a rapidly emerging method for studying biodiversity and monitoring ecosystem changes. Shotgun sequencing of environmental DNA is helpful for studying species that are likely abundant in a sample, such as bacteria or small eukaryotes.

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Shotgun Sequencing of eDNA
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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.

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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.

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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.

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Nextera DNA Flex Library Prep for Soil Shotgun Metagenomics
Nextera DNA Flex for Soil Shotgun Metagenomics

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

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NovaSeq and Shotgun Metagenomic Sequencing
NovaSeq and Shotgun Metagenomic Sequencing

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

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