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
Michael Bunce, PhD uses shotgun sequencing and NGS metabarcoding to study biodiversity in environmental samples.Read Interview
An epic ocean expedition sequenced salt water samples from around the globe to survey plankton diversity in marine ecosystems.Read Interview
Metagenomics is one of the fastest-growing scientific disciplines. This document highlights peer-reviewed publications that apply Illumina sequencing technologies to metagenomics research.Access PDF
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 550 System
Flexible desktop sequencer for exome, transcriptome, and whole-genome sequencing.
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 platformGENIUS 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.
This metagenomic shotgun sequencing workflow featuring the Nextera DNA Flex Library Prep Kit and the NextSeq 550 System enables accurate DNA detection from soil.Read Article
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.Learn More