Microbial Sequencing

The evolution of Ion semiconductor 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 a rapid response during disease surveillance, investigating outbreaks, and determining disease etiology.* Downstream of microbial sequencing, data analysis methods include de novo and reference-guided assembly and multi-locus sequence typing (MLST) for identification or typing of microbial strains.

Microbial Sequencing Application Notes & Publications

Application Notes

Discover how German scientists leveraged the Ion PGM™ Sequencer to get answers when faced with a serious public health outbreak (shiga toxin-producing E. coli outbreak in northern Germany)

The Ion PGM™ System, with 400-base read length chemistry, enables routine high-quality de novo assembly of small genomes

Ion PGM™ System and PathAmp™ FluA Reagents—Influenza A whole-genome sequencing

Publications

The Ion PGM™ System is cited in more than 40 peer-reviewed publications about 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

Antwerpen, M., et al. (2012). Draft genome sequence of Bacillus anthracis BF-1, isolated from Bavarian cattle
J Bacteriol 194(22): 6360-6361. DOI: 10.1128/JB.01676-12

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

*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 ]

†The content provided herein may relate to products that have not been officially released and is subject to change without notice.
Ion Chef™ System is expected to be available for quotation and purchase in Q1 2013 and is expected to begin shipping in the first half of 2013.

For Research Use Only. Not for use in diagnostic procedures.