Cost-effective, species-level microbiome profiling

The Ion AmpliSeq Microbiome Health Research Kit is a next-generation sequencing (NGS) assay that allows for cost-effective yet comprehensive profiling of microbial diversity in the human gut microbiome. This new assay offers increased resolution and specificity of species-level detection compared with traditional 16S rRNA sequencing for key organisms associated with cancer, as well as immunological and gastrointestinal (GI) disorder research.

Request project costs

Currently, most 16S panels target only 2–4 hypervariable (HV) regions of the 16S rRNA gene, while the panel included in the Ion AmpliSeq Microbiome Health Research Kit targets 8 out of the 9 HV regions for highly comprehensive and sensitive microbial profiling.

Combined with a set of high-resolution markers for increased species-level identification and fully integrated data analysis tools, a complete end-to-end solution is available to help simplify your research (Figure 1).

Figure 1. Workflow using the Ion AmpliSeq Microbiome Health Research Kit
  • Targeted sequencing—with comprehensive content that has 100% sensitivity and specificity at a species level at standard thresholds
  • Panel targeting 8 out of 9 HV regions—the most comprehensive 16S rRNA gene panel
  • Species-level resolution—detection of 73 key bacterial species associated with immuno-oncology as well as immunological and GI disorder research
While shotgun metagenomics offers higher functional resolution, it comes at a higher cost and takes more time. The Ion AmpliSeq Microbiome Health Research panel offers a cost-effective solution with species-level specificity for research of immuno-oncology and key gut-related disorders as well as autoimmune diseases (Figure 2).

 Click to enlarge
Figure 2. Stacked bar plot and relative abundance table showing high sensitivity and specificity at the species level.

Both the 16S panel as well as the highly curated species-specific panel allow for 100% specificity and sensitivity. Using stool samples, we show high reproducibility from experiment to experiment (Figure 3).

 Click to enlarge
Figure 3. Intra-sample abundance identification in stool samples showing high correlation at both 16S and species level.

The Ion AmpliSeq Microbiome Health Research Kit aoffers a complete end-to-end solution with the Ion AmpliSeq Microbiome Health Analysis plug-in within Torrent Suite Software. In addition, an analysis tool within Ion Reporter Software is optimized for microbiome health research and allows for multi-sample analysis, with additional visualization options to come.


1. Routy B, et al. Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors. Science. 2018 Jan 5;359(6371):91-97.
2. Matson V, Fessler J, Bao R, Chongsuwat T, Zha Y, Alegre ML, Luke JJ, Gajewski TF. The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients. Science. 2018 Jan 5;359(6371):104-108.
3. Gopalakrishnan V, et al. Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients. Science. 2018 Jan 5;359(6371):97-103.