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.

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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

Webinar: Understanding the potential impact of the gut microbiome on SARS-CoV-2 research


This webinar explores research into the potential impact of the gut microbiome on host response to SARS-CoV-2 as well as the efficacy of various immune interventions such as future vaccines.

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Poster: Characterization of the gut microbiome associated with immune response using a targeted NGS assay


This poster introduces a first-of-its-kind targeted sequencing solution for a cohort of bacteria associated with immune responses to cancer immunotherapy, gastrointestinal/autoimmune disorders, and infectious diseases such as SARS-CoV-2 infection.

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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).

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).

Recently, the SARS-CoV-2 virus has highlighted the potential influence that the commensal gut microbiome has on infection as well as severity of infection.  There have been many studies looking at the possible impact that a disruption of gut dysbiosis has on SARS-CoV-2 infection and how diversity and abundance of key species may play a role in vaccine research and efficacy.  Targeted NGS utilizing the Ion AmpliSeq Microbiome Health Research Kit is a simple and pertinent tool to understand and characterize microbe mediation of SARS-CoV-2 infection as well as immune health and treatment research.

The Ion AmpliSeq Microbiome Health Research Kit offers a complete end-to-end solution with the launch of the Ion Reporter Software 5.14.  This analysis tool supports the kit by detecting bacterial species through the 16S rRNA gene and target species-specific amplicons. Ion Reporter Software provides full taxonomic profiling as well as species level resolution for selected key microbes associated with human health. Single and multi-sample comparisons are possible using a variety of common reference databases including SILVA and utilizing QIIME2 functionality.

Microbiome videos



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.