Microbial Sequencing

Microbial ID, strain sub-typing, and infectious disease research panels for targeted sequencing

Microbial sequencing application note
Targeted sequencing for infectious disease research flyer

The evolution of Ion Torrent™ next-generation sequencing has enabled researchers to take advantage of increased throughput, higher accuracy, and longer reads to produce rapid and accurate sequencing of microbes with streamlined sample preparation and a simple and optimized data analysis workflow. Ion Torrent sequencing has been critical in facilitating rapid research results from archived samples for disease surveillance, outbreak investigation, and disease etiology determination. Downstream of whole genome microbial sequencing, data analysis methods include de novo and reference-guided assembly and typing of microbial strains.

For targeted sequencing of a specific set of genes, such as 16S rRNA, Ion AmpliSeq™ technology delivers simple and fast library construction. Based on ultrahigh-multiplex PCR, Ion AmpliSeq technology requires as little as 1 ng of input DNA. Through the use of targeted sequencing, researchers can efficiently identify the microbes within a mixed population without the need to culture samples, perform research on retrospective outbreak samples, and discover mutations that may be associated with antibiotic resistance.

Whole-genome sequencing

Deep-coverage whole-genome sequencing of microbial organisms is the ultimate tool for discovering the full range of genetic variations, including SNPs, insertions, deletions, inversions and complex rearrangements. It is used to characterize and discover new organisms or to type specific bacterial and viral organisms.

Bacterial and viral typing research

Rapid and affordable bacterial and viral typing research during disease surveillance, using archived samples from outbreak investigations and disease etiology studies.

Targeted sequencing with Ion AmpliSeq technology

Through the use of targeted sequencing of specific genes, you can now identify the microbes within a mixed population, study potential virulence factors and transmission patterns, and discover mutations that may be associated with antibiotic resistance.

Workflow for microbial analysis

1 Select
targets

• Ion 16S Metagenomics Kit
• Ion AmpliSeq Ebola Research Panel
• Ion AmpliSeq TB Research Panel
• Ion AmpliSeq Targeted Custom Panels
• PathAmp Flua Reagents

2 Construct library

• Ion Xpress Plus Fragment Library Kit
• ThermoScientific MuSeek™ Library Preparation Kit
• ThermoScientific ClaSeek Library Preparation Kit

3 Prepare template

• Ion Chef system
• Ion OneTouch 2 System

4 Run sequence

• Ion S5 or S5 XL System
• Ion PGM System

5 Analyze
data

• Torrent Suite Software
• Torrent Browser Plugins
• Ion Reporter Software

See product selection guides for more detail:

Ion S5 System product selection guide
Ion PGM System product selection guide

New solutions for microbial analysis

600 bp sequencing chemistry for Ion S5 Systems

The Ion 520™ & Ion 530™ ExT Kit-Chef enables an automated workflow for long-read sequencing in less than 2 days, using the Ion Chef™ and Ion S5™ or Ion S5 XL Systems.

Sequencing chemistry for Ion PGM System

When sequencing with Ion PGM™ Hi-Q View™ sequencing chemistry, you can now see the success of your templating using colored Ion Sphere Particles (ISPs) and see increased coverage in GC regions.

Fast template prep for Ion PGM System using isothermal amplification

When a few hours can make all the difference, the Ion PGM™ Template IA Kit helps reduce the time required for template preparation by half, when compared to other template prep workflows for Ion PGM System, enabling the fastest workflow for microbial sequencing.

The diversity of microbes

After decades of analyses and hundreds of studies, we’ve learned the diversity of microbes is even greater than imagined. And the diversity of these species can tell us about the well-being of an ecosystem or how their interactions may be linked to diseases such as Inflammatory bowel disease, obesity, and chronic wounds. Hear how Dr. George Watts and Dr. Charles Li are using Ion 16S™ sequencing in their clinical and environmental research applications.