Cost-effective, species-level microbiome profiling

The Ion AmpliSeq Microbiome Health Research Assay (MHRA) 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 immunological response to cancer, diabetes and autoimmune diseases, gastrointestinal (GI) disorders, and infectious diseases.

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Most other commercially available 16S panels target two to four hypervariable (HV) regions of the 16S rRNA gene, while the panel included with the MHRA targets eight out of the nine HV regions in addition to a set of high-resolution markers for increased species-level identification for highly comprehensive and sensitive microbial profiling research.

This larger targeted NGS panel, combined with a fully integrated data analysis tools, create a complete end-to-end solution to help both expand and simplify your microbiome research. Two versions of the MHRA are available, one on the Ion GeneStudio System, and the other on the Ion Torrent Genexus System, and these two versions of the assay take advantage of the different benefits offered by each NGS platform.

  • Targeted sequencing—cost-effective approach to investigate the human gut microbiome diversity using the AmpliSeq protocol
  • Panel targeting 8 out of 9 HV regions—one of the most comprehensive 16S rRNA gene panels to detect and quantify all microbes of bacterial origin in the sample
  • Species-level resolution—detection of 73 key bacterial species associated with research in immuno-oncology as well as immunological, GI disorders, and infectious diseases

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 can offer some advantages over targeted NGS, such as higher functional resolution, it is more costly and time-consuming, and requires more complex bioinformatics tools, making this approach difficult to master, potentially causing issues with data reliability and reproducibility. The MHRA offers an easy to use, cost-effective, and rapid solution to detect and quantify microbes of bacterial origin in the sample by targeting 8 out of 9 hypervariable regions present in the 16S rRNA gene. The assay also provides species-level specificity to interrogate the presence of a curated list of 73 bacterial species (Table 1) that have strong scientific evidence to be implicated in immuno-oncology (I-O) response, gut health, and autoimmunity, as well as response to infection. This highly curated species-specific panel allows for 100% specificity and sensitivity (Figure 1).

Using stool samples, we show high reproducibility from experiment to experiment (Figure 2).

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 diversity 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 MHRA is a simple and pertinent tool to understand and characterize microbe mediation of infectious diseases as well as immune health and treatment research.

The MHRA also offers a complete end-to-end, nucleic acid-to-report solution, with an optimized analysis workflow using Ion Reporter Software for analysis of data generated with the Ion GeneStudio system or embedded in the Genexus Software when using the Genexus System. The analysis workflow enables multi-sample analysis and visualization, such as heatmap, PCoA, relative abundance, and diversity visualization. The analysis uses up-to-date reference databases such as the curated SILVA database, the Applied Biosystems MicroSeq database, Greengenes, and NCBI.

Microbiome videos


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