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

The need for faster results and better outcomes in disease research has resulted in a migration from traditional pathogen identification techniques, such as culture assays and rapid biochemical methods, to molecular-based methods like next-generation sequencing (NGS).

The evolution of Ion Torrent NGS 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, antimicrobial resistance detection, 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

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, you can now perform targeted sequencing of specific genes to 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
select target
Construct library
Construct library
ion s5 grey
select target
Construct library
Construct library
ion s5 grey

See product selection guide for more details:

Ion GeneStudio System product selection guide

New solutions for microbial analysis

Ion AmpliSeq Community Panels for Ion GeneStudio S5 Systems

New Ion AmpliSeq Pan-Bacterial and Ion AmpliSeq Antimicrobial Resistance community panels offer fast and easy microbial identification and AMR analysis in mixed samples.

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 two days using the Ion Chef Instrument and the Ion GeneStudio S5, S5 Plus, or S5 Prime System.

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.

Customer experience video: The diversity of microbes

Using Ion 16S sequencing for clinical and environmental research applications

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 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. 

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. 

Candon S, et al. (2015) Antibiotics in Early Life Alter the Gut Microbiome and Increase Disease Incidence in a Spontaneous Mouse Model. 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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