From microbial ID to variant sub-typing research
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New system for microbial sequencing

Adopting next-generation sequencing (NGS) in your lab is now simpler than ever before with the Ion S5™ System’s industry-leading speed and affordability, and the flexibility to do multiple sequencing applications on a single system.

Bacterial & Viral Typing Research

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


Ion 16s™ Metagenomics Kit

Rapid, comprehensive, and broad-range research analysis of microbial populations using Ion Torrent™ Sequencing System.


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. In addition, the Ion PGM™ System has been critical for facilitating rapid research results from archived samples for disease surveillance, outbreak investigation, and disease etiology determination.* Downstream of microbial sequencing, data analysis methods include de novo and reference-guided assembly and multi-locus sequence typing (MLST) for bacterial identification tests or typing of microbial strains.

Application Notes & Publications

Read application notes and peer-reviewed publications to learn how the Ion PGM System has empowered advances in microbes sequencing.

Data Set

Download a data set generated on the Ion PGM System, and see the results for yourself.


Customer Videos

Learn how Ion Torrent™ sequencing has enabled customers in their microbiology research.


Microbial sequencing literature & publications


The Ion PGM™ System is cited in more than 400 peer-reviewed publications on small genome sequencing, making it the leading system for de novo assembly of small genomes.

Petrof, E., et al. (2013). Stool substitute transplant therapy for the eradication of Clostridium difficile infection: 'RePOOPulating' the gut Microbiome 2013, 1:3. DOI: 10.1186/2049-2618-1-3

Hassan, S. S., et al. (2012). Complete genome sequence of Corynebacterium pseudotuberculosis biovar ovis strain P54B96 isolated from antelope in South Africa obtained by rapid next generation sequencing technology Stand Genomic Sci 7(2): 189-199. DOI: 10.4056/sigs.3066455

Yergeau, E., et al. (2012). Next-generation sequencing of microbial communities in the Athabasca River and its tributaries in relation to oil sands mining activities Appl Environ Microbiol 78(21): 7626-7637. DOI: 10.1128/AEM.02036-12

View additional publications ›

Microbial sequencing videos

Small Genome Sequencing

Learn how Ion Torrent™ sequencing has enabled customers in their microbiology research


*Mellmann A, Harmsen D, Cummings CA et al. (2011) Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS One 6, e22751; Rohde H, Qin J, Cui Y et al. (2011) Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med 365, 718-724; Sherry NL, Porter JL, Seemann T et al. (2013) Outbreak investigation using high-throughput genome sequencing within a diagnostic microbiology laboratory. J Clin Microbiol. 2013 Feb 13. [Epub ahead of print ]