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

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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.

Automated and fast template preparation and sequencing of 400 to 600 base-read libraries using the Ion Chef™ System and the Ion S5™ and Ion S5™ XL Sequencing Systems is enabled using the Ion 520™ & Ion 530™ ExT Kit-Chef.

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

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.

Microbial sequencing literature & publications


Ion S5 infectious disease application note
Ion AmpliSeq Infectious Disease Research Panels flyer
New 16S flyer
16S algorithm application note
Bacterial typing application note
Strain-Typing and Antibiotic Resistance Profiling From Research Samples Using Highly Multiplexed Targeted Library Construction with High Throughput Semi-Conductor Based Sequencing
Ion PGM™ System and PathAmp™ FluA Reagents—Influenza A whole-genome sequencing


Ion Torrent sequencing is cited in more than 900 peer-reviewed publications on microbial genome and metagenome sequencing.

Bacterial whole genome sequencing and typing

Soni I, et al. (2015). Draft Genome Sequenci of Methicillin-Sensitive Staphylococcus aureus ATCC 29213, ATCC 29213 Genome Announc 3(5): e01095-15. DOI: 10.1128/genomeA.01095-15 

Mattos-Guaraldi AL, et al. (2015). Draft Genome Sequence of Corynebacterium striatum1961 BR-RJ/09, a Multidrug-Susceptible Strain Isolated from the Urine of a Hospitalized 37-Year-Old Female Patient 

Targeted sequencing

Gardner et al. Targeted amplification for enhanced detection of biothreat agents by next-generation sequencing BMC Research Notes (2015) 8:682.DOI: 10.1186/s13104-015-1530-0 

Ferrario, et al. A genome-based identification approach for members of the genus Bifidobacterium.FEMS Microbiol Ecol. 2015 Mar;91(3). pii: fiv009. DOI: 10.1093/femsec/fiv009. Epub 2015 

Viral sequencing

Santiago-Rodriguez TM, et al. (2015) The human urine virome in association with urinary tract infections. Front. Microbiol. 6:14 DOI: 10.3389/fmicb.2015.00014 

Kosoy Ol, et al. Novel Thogotovirus Associated with Febrile Illness and Death, United States, 2014. Emerg Infect Dis 2015 May. http://dx.doi.org/10.3201/eid2105.150150 

Zhang Y, et al. Isolation and characterization of H7N9 avian influenza A virus from humans with respiratory diseases in Zhejiang, China. Virus Res. 2014 Aug 30; 189:158-64.  DOI:10.1016/j.virusres.2014.05.002 

16S and metagenome sequencing

Cuervo A, et al. Phenolic compounds from red wine and coffee are associated with specific intestinal microorganisms in allergic subjects. Food funct., 2016, Advance Article, DOI: 10.1039 

Saarenheimo, J, et al. In press. Bacterial community response to changes in a tri-trophic cascade during a whole-lake fish manipulation. Ecology. http://dx.doi.org/10.1890/15-1052.1 

Candon S, et al. (2015) Antibiotics in Early Life Alter the Gut Microbiome and Increase Disease Incidence in a Spontaneous Mouse Model of Autoimmune Insulin-Dependent Diabetes. PLoS ONE 10(5): e0125448. doi:10.1371/journal.pone.0125448 

Shaw, JLA, et al. Using amplicon sequencing to characterize and monitor bacterial diversity in drinking water distribution systems. Appl. Environ. Microbiol. AEM.01297-15 

Kommedal O, et al. Massive Parallel Sequencing Provides New Perspectives on Bacterial Brain Abscesses. J. Clin. Microbiol. June 2014 vol. 52 no. 6 1990-1997 

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