Comprehensive Microbial Applications for NGS

From microbial whole genome sequencing using 16S metagenomics to microbiome profiling for human health research to infectious disease research and pathogen identification using targeted sequencing

The need for faster results and better outcomes in disease research has resulted in a migration from traditional molecular biology techniques such as Sanger sequencing, PCR, and culture assays to targeted commensal bacterial species profiling and pathogen identification using 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 and disease etiology determination. Downstream of whole genome microbial and targeted microbiome 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 samples, and discover mutations that may be associated with antibiotic resistance.

Characterize the gut microbiome for health research


The gut microbiome has emerged as an important biomarker in research into the potential efficacy of immune-modulatory drugs. Using an Ion AmpliSeq highly multiplexed PCR approach enables an efficient and affordable means for conducting extensive analyses of the human microbiome and has applications in the study of phenotypic variability as it relates to disease, emergent resistance mechanisms, and potential future therapies.

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Infectious disease research

Bacterial and viral typing

Rapid and affordable bacterial and viral typing research during disease surveillance, using archived samples from investigations and disease etiology studies, such as studies of SARS-CoV-2, MERS, H1N1, and Ebola.

Whole-genome sequencing

16S metagenomics

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.

Targeted sequencing

AmpliSeq panels (microbiome health)

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.

Our newest panel, the Ion AmpliSeq Microbiome Health Research Panel, enables robust charactization of bacterial microbes relevant to human diseases at a species level with 100% specificity and sensitivity.

NGS workflow for microbial analysis and infectious disease research

Featured solutions

select target

Infectious disease research

Whole genome sequencing

Order ready-made gene panels or custom design your own at

Construct library
Construct library
ion s5 grey

Featured solutions

select target

Infectious disease research

Whole genome sequencing

Order ready-made gene panels or custom design your own at

Construct library
Construct library
ion s5 grey

See product selection guide for more details:

Ion GeneStudio System product selection guide

The latest infectious disease and microbial research solutions

Ion AmpliSeq SARS-CoV-2 Research Panel

The Ion AmpliSeq SARS-CoV-2 Research Panel is designed to cover more than 99% of the SARS-CoV-2 genome for complete genome sequencing and variant detection for epidemiological studies. Deliver highly accurate coronavirus typing in under a day.

Ion AmpliSeq Microbiome Health Research Kit

The Ion AmpliSeq Microbiome Health Research Kit is a targeted NGS assay for characterizing the human gut microbiome, which has been implicated in research of human disease such as cancer, immunological, and gastrointestinal (GI)

disorder The panels provides the highest species level resolution for the comprehensive profiling of microbial diversity in the human gut microbiome.

Customer videos

What's in our gut effects our health

Hugo Roume of the French National Institute for Agricultural Research discusses the role of the microbiome in human health.

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 16S metagenomics, commensal and dysbiosis microbiome for human health research, and microbial genome 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 

View additional publications

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