Sequence hundreds of organisms with the power of multiplexing

Generate accurate reference genomes and perform comparative genomic studies

Microbial Whole-Genome Sequencing

Microbial whole-genome sequencing is an important tool for mapping genomes of novel organisms, finishing genomes of known organisms, or comparing genomes across multiple samples. Sequencing the entire microbial genome is important for generating accurate reference genomes, for microbial identification, and other comparative genomic studies.

Unlike capillary sequencing or PCR-based approaches, next-generation sequencing (NGS) allows microbiology researchers to sequence hundreds of organisms with the power of multiplexing. Unlike traditional methods, NGS-based microbial genome sequencing doesn’t rely on labor-intensive cloning steps, saving time and simplifying the workflow. NGS can identify low frequency variants and genome rearrangements that may be missed or are too expensive to identify using other methods.

De novo whole-genome sequencing involves assembling a genome without the use of a genomic reference and is often used to sequence novel microbial genomes. Illumina sequencers provide unparalleled raw read accuracy, read length and read depth for high-quality draft and complete microbial genome assemblies.

Get the Nextera DNA Flex Advantage

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

View Product

Microbial whole-genome resequencing involves sequencing the entire genome of a bacteria, virus, or other microbe, and comparing the sequence to that of a known reference. Generating rapid and accurate microbial genome sequence information is critical for detecting low frequency mutations, finding key deletions and insertions, and discovering other genetic changes among microbial strains.

In Hot Water with Extremophiles

Dr Brian Hedlund uses genomics to study the microbes that populate hot springs. His work has uncovered new classes of organisms.

View Video
Can Applying NGS Lead to Better Beer?

An international group of scientists, yeast producers, and brewers sequenced 96 yeast strains to learn how genetics can influence the flavor of beer. Their findings, published in Cell, could help brewers make better beers.

Read Article
Can Applying NGS Lead to Better Beer?

There are multiple ways to perform these 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 Mate Pair Library Prep Kit

A gel-free method for preparing up to 12 kb mate pair libraries with a low DNA input requirement. It is an ideal approach for de novo sequencing, genome finishing, and the detection of structural variation.

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 with shortened gel-free workflows, the ability to sequence the most challenging regions, and the power to identify the greatest number of variants for whole-genome sequencing applications.

Benchtop Sequencing Systems

iSeq System

Affordable, fast, and accessible sequencing power for targeted or small genome sequencing in any lab.

MiniSeq System

Supports a broad range of targeted DNA and RNA applications.

MiSeq System

Several kit configurations, including a 500 cycle kit for efficient mapping of small genomes. Micro and nano formats available for cost-efficient sequencing of 1-4 samples.

NextSeq 550 System

Flexible desktop sequencer for exome, transcriptome, and whole-genome sequencing.

High-Throughput Sequencing Systems
Power for high-throughput microbial whole-genome sequencing and flexibility to scale based on your project or workflow needs.

HiSeq 4000 System

Maximum throughput, lowest cost for production-scale genomics.

NovaSeq 6000 System

Scalable throughput and flexibility for virtually any genome, sequencing method, and scale of project.

BaseSpace Apps for de novo assemblies or mapping of contigs and scaffolds

Velvet de novo Assembly

De novo assembly of bacteria using the Velvet assembler with a focus on Nextera Mate Pair data.

String Graph Assembler

Performs a contig assembly, builds scaffolds, removes mate pair adapter sequences, and calculates assembly quality metrics.

SPAdes Genome Assembler

Online bioinformatics tool for assembling microbial genome sequences.

Prokka Genome Annotation

Rapidly annotates genes and identifies coding sequences in prokaryotic genomes, from de novo assembly sequences.


Improves scaffolding in bacterial de novo assemblies by removing assembly errors and closing gaps in the consensus sequence.

Interested in receiving newsletters, case studies, and information on microbial genomics? Enter your email address.
De Novo Bacterial Sequencing
De Novo Bacterial Sequencing

Learn how high-quality paired-end reads on MiSeq ensure superior assembly.

Access PDF
Nextera Mate Pair Library Prep
Nextera Mate Pair Library Prep

Optimized method for long-insert libraries for de novo assemblies.

Access PDF
Microbiology: Spotlight on Food Pathogen Testing
Microbiology: Spotlight on Food Pathogen Testing

Overview of Illumina next-generation sequencing platforms and relevant applications and use cases for food pathogen testing.

View Video
Push-Button De Novo Microbial Genome Sequence Assembly
Push-Button De Novo Microbial Genome Sequence Assembly

Perform de novo assembly of microbial genomes using DNAStar Seqman NGen.

Learn More
Assembly of the Saccharomyces cerevisiae Genome
Assembly of the Saccharomyces cerevisiae Genome

This application note describes a complete workflow for sequencing small genomes with MiSeq.

Access PDF
NGS for microbial genomes and infection control
NGS for Microbial Genomes and Infection Control

Global collaboration of researchers is using the MiSeq System to understand the evolution and spread of drug-resistant bacteria.

Read Interview