Rapid & Accurate Sequencing of Microbes
Next-generation sequencing technologies have been indispensable in the characterization of micro organisms; including bacteria, viruses, fungi & algae.
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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.
Read application notes and peer-reviewed publications to learn how the Ion PGM™ System has empowered advances in microbes sequencing.
Download a data set generated on the Ion PGM™ System, and see the results for yourself.
Learn about microbial sequencing informatics solutions for the fastest way to get to your biological results.
Microbial Sequencing Application Notes & 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
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.
The Ion Plus Fragment Library Kit or Ion Xpress™ Plus Fragment Library Kit provide low-cost sample preparation in as little as 2 hours for gDNA and amplicon libraries.
The Ion Chef™ System† provides simple, high-throughput template preparation with only minutes of hands-on time. The Ion OneTouch™ 2 System provides simple, 15-minute template preparation for 400 bp and 200 bp sequencing runs.
The Ion PGM™ Sequencer enables rapid de novo sequencing with 400 bp or 200 bp sequencing. Runs are completed in just 3.7 hours and 7.3 hours for the Ion 314™ Chip and Ion 318™ Chip, respectively.
Primary data analysis is performed using Torrent Suite Software. The DNAStar® SeqMan NGen® software package provides an easy-to-use interface for genome assembly.
Fast, affordable viral typing is now possible using Ion PGM™ System and the PathAmp™ FluA Reagents.
Read our application note to learn more.
Dunlap, C., et al. (2013). "Genomic analysis and secondary metabolite production in Bacillus amyloliquefaciens." Biological Control, 64(2), February 2013. DOI: 10.1016/j.biocontrol.2012.11.002
Adlakha, N., et al. (2013). "Draft Genome Sequence of the Paenibacillus sp. Strain ICGEB2008 (MTCC 5639) Isolated from the Gut of Helicoverpa armigera." Genome Announc 1(1). DOI: 10.1128/genomeA.00026-12
Agarwal, L. and H. J. Purohit (2013). "Genome Sequence of Rhizobium lupini HPC(L) Isolated from Saline Desert Soil, Kutch (Gujarat)." Genome Announc 1(1). DOI: 10.1128/ genomeA.00071-12
Planet, P., et al. (2013), "Bordetella holmesii: initial genomic analysis of an emerging opportunist." Pathogens and Disease. DOI: 10.1111/2049-632X.12028
Roy, A. S., et al. (2013). "Draft Genome Sequence of Pseudomonas aeruginosa Strain N002, Isolated from Crude Oil-Contaminated Soil from Geleky, Assam, India." Genome Announc 1(1). DOI: 10.1128/ genomeA.00104-12
Debroy, S., et al. (2013). "Draft Genome Sequence of the Nitrate- and Phosphate-Accumulating Bacillus sp. Strain MCC0008." Genome Announc 1(1). DOI: 10.1128/ genomeA.00189-12
Silva, A., et al. (2012). "Complete genome sequence of Corynebacterium pseudotuberculosis Cp31, isolated from an Egyptian buffalo." J Bacteriol 194(23): 6663-6664. DOI: 10.1128/ JB.01782-12
Manzoor, S., et al. (2013). "First Genome Sequence of a Syntrophic Acetate-Oxidizing Bacterium, Tepidanaerobacter acetatoxydans Strain Re1." Genome Announc 1(1). DOI: 10.1128/ genomeA.00213-12
Joshi, M. N., et al. (2013). "Draft Genome Sequence of the Halophilic Bacterium Halobacillus sp. Strain BAB-2008." Genome Announc 1(1). DOI: 10.1128/ genomeA.00222-12
Debroy, S., et al. (2013). "Draft Genome Sequence of a Phosphate-Accumulating Bacillus sp., WBUNB004." Genome Announc 1(1). DOI: 10.1128/ genomeA.00251-12
Debroy, S., et al. (2013). "Draft Genome Sequence of a Nitrate- and Phosphate-Removing Bacillus sp., WBUNB009." Genome Announc 1(1). DOI: 10.1128/ genomeA.00254-12