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.
Phil Hugenholtz, PhD explains how shotgun metagenomic sequencing with NGS has made a difference in his research.Read Interview
Shotgun metagenomics methods are enabling a deeper analysis of the gut microbiome and how it contributes to, or protects from, disease.Read Article
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
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
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.
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.
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 SequencingMiSeq 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.
Power for shotgun metagenomics and flexibility to scale based on your project or workflow needs.
High throughput, low cost for production-scale genomics.
BaseSpace Apps for k-mer alignments and taxonomic classificationKraken Metagenomics
Assigns taxonomic labels to short DNA sequences with high sensitivity and speed using exact alignments of k-mers and a novel classification algorithm.
Enables metagenomic analysis by rapidly assessing your samples from BaseSpace Sequence Hub with a fast, comprehensive, accurate data platform
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
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
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
This metagenomic shotgun sequencing workflow offers fully automated soil sample preparation, sequencing, and analysis, to help researchers characterize soil microbial communities.Read Article
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