Accelerate microbial breakthroughs

Microbial Genomics

Characterize un-culturable organisms. Discover entirely new viruses. Develop new strategies to control outbreaks. Monitor host-pathogen interactions.

Next-generation sequencing (NGS) is opening new doors in microbial genomics, revealing fresh insight into how microbes impact humans and the environment.

  • See how  NGS enables a broad range of microbial genomics studies. View Video.
  • Explore how NGS is transforming infectious disease surveillance, characterization, and outbreak responses.  Learn More.
  • Learn how Dr. Ramunas Stepanauskas uses single-cell sequencing on Illumina systems to uncover hidden diversity and biogeographic variability in marine microorganisms. Read Case Study (PDF).

Through the power and high resolution of Illumina technology, you can now understand the genetic makeup of organisms that were previously impossible to study—helping you examine microbial biological functions, track genetic changes, rapidly respond to outbreaks, monitor food sources, and more.

See the bigger picture by examining the smallest details in the tiniest organisms with NGS. Learn more about how NGS can change your approach to microbiology.
Read Brochure (PDF).

COVID-19 Sequencing

Next-generation sequencing is uniquely positioned in an infectious disease surveillance and outbreak model. Explore methods and find solutions to detect and characterize SARS-CoV-2 and other respiratory pathogens, track transmission routes, study co-infection, and investigate viral evolution. 

Learn More
COVID-19 Solutions
Podcast stories explore unusual and surprising applications of genomics
Podcast stories explore unusual and surprising applications of genomics

Illumina partners with Naked Genetics to engage audiences in the world of next-generation sequencing

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
Reaching new heights in data quality and throughput on a benchtop sequencer
Reaching new heights in data quality and throughput on a benchtop sequencer

At AGBT 2024, Illumina presented several studies, highlighting improvements to NextSeq Systems and more

Read article
icon DNA

NGS Workflow Finder

Take the guesswork out of your next workflow. The NGS Workflow Finder provides personalized solution recommendations and resources so you can sequence with confidence.

Find your NGS workflow today
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.

View Product
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.

Learn More
Nextera XT and Nextera DNA Flex
Nextera XT and Nextera DNA Flex

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

View Product

Dr Brian Hedlund uses genomics to study the microbes that populate hot springs. He is discovering new classes of organisms, learning how to culture microbes that would not have been culturable without genomic information, and learning new insights about microbial life.

View Video
In Hot Water with Extremophiles

Educational Resources

Beginner's Guide to NGS

These educational resources cover key topics in next-generation sequencing designed for beginners. Learn the basics of NGS and find tips for getting started.

Learn More

Illumina Resources & Tools

Find education and assistance for your genomics workflow, from start to finish. Find tools to glean insight from the data, then purchase what you need and get access to support.

Learn More

Interested in receiving newsletters, case studies, and information on microbial genomics? Enter your email address.
CMOS Tech Note
CMOS Chip and One-Channel SBS Chemistry

CMOS technology and innovative one-channel SBS chemistry combine for highly accurate data.

Access PDF
MiSeq, 16S rRNA Sequencing and the American Gut Project
The MiSeq System and the American Gut Project

This "citizen science" project uses NGS to help people examine their own microbiomes.

View Video
Overview: NGS for Microbiology
Overview: NGS for Microbiology

View an introduction to NGS and its applications for microbiology.

Read Introduction
Library Prep and Array Kit Selector
Library Prep and Array Kit Selector

Find the right sequencing library prep kit or microarray for your needs. Compare similar kits or view further details.

Find the Right Kit
Automated Methods for Metagenomic Analyses
Automated Methods for Metagenomic Analyses

Dr Russ Carmical discusses the benefits of using automated 16S rRNA and whole-genome sequencing methods for microbial genomics.

View Webinar
New Technologies for Microbial Genomics
NGS for HIV Tropism Studies

Deep sequencing enables microbiology researchers to study HIV tropism and how it changes during infection.

Read Interview
TELL-Seq: Bringing Speed and Accuracy to Long-Range Sequencing
TELL-Seq: Bringing Speed and Accuracy to Long-Range Sequencing

TELL-Seq technology is a simple library prep solution which enables Illumina NGS systems to generate highly accurate and economical long-range sequencing information.

Read Application Note