Ion AmpliSeq Microbiome Health Research Assay

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 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.

Most other commercially available 16S panels target two to four hypervariable (HV) regions of the 16S rRNA gene, while the MHRA panel 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 targeted NGS panel, combined with integrated data analysis tools, creates a complete end-to-end solution to help both expand and simplify your microbiome research. Two versions of the MHRA are available, one is a kitted assay on the Ion GeneStudio System, and the other is a custom Ion AmpliSeq panel on the Ion Torrent Genexus System. These two versions of the assay take advantage of the different benefits offered by each NGS platform.

Easy, rapid microbial detection with NGS

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).

 

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. 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.

Features of the Ion AmpliSeq Microbiome Health Research Assay

  • 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
Akkermansia muciniphila Campylobacter jejuni Fusobacterium nucleatum Parabacteroides distasonis
Anaerococcus vaginalis Campylobacter rectus Gardnerella vaginalis Parabacteroides merdae
Atopobium parvulum Chlamydia pneumoniae Gemmiger formicilis Parvimonas micra
Bacteroides fragilis Chlamydia trachomatis Helicobacter bilis Peptostreptococcus anaerobius
Bacteroides nordii Citrobacter rodentium Helicobacter bizzozeronii Peptostreptococcus stomatis
Bacteroides thetaiotaomicron Clostridium difficile Helicobacter hepaticus Phascolarctobacterium faecium
Bacteroides vulgatus Collinsella aerofaciens Helicobacter pylori Porphyromonas gingivalis
Barnesiella intestinihominis Collinsella stercoris Holdemania filiformis Prevotella copri
Bifidobacterium adolescentis Desulfovibrio alaskensis Klebsiella pneumoniae Prevotella histicola
Bifidobacterium animalis Dorea formicigenerans Lactobacillus acidophilus Propionibacterium acnes (Cutibacterium acnes)
Bifidobacterium bifidum Enterococcus faecalis Lactobacillus delbrueckii Proteus mirabilis
Bifidobacterium longum Enterococcus faecium Lactobacillus johnsonii Roseburia intestinalis
Blautia obeum Enterococcus gallinarum Lactobacillus murinus Ruminococcus bromii
Borrelia burgdorferi Enterococcus hirae Lactobacillus reuteri Ruminococcus gnavus
Campylobacter concisus Escherichia coli Lactobacillus rhamnosus Slackia exigua
Campylobacter curvus Eubacterium limosum Lactococcus lactis Streptococcus gallolyticus
Campylobacter gracilis Eubacterium rectale Mycoplasma fermentans Streptococcus infantarius
Campylobacter hominis Faecalibacterium prausnitzii Mycoplasma penetrans Veillonella parvula

Table 1. List of targeted bacterial species

 

 

Figure 1. Stacked bar plot and relative abundance tab showing high sensitivity and specificity at the species level.

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

 

Figure 2. Intra-sample abundance identification in stool samples showing high correlation at both 16S and species level.

NGS systems compatible with MHRA

MHRA Kit on the GeneStudio S5 System

The Ion GeneStudio S5 System is a flexible, scalable, targeted NGS workhorse with wide application breadth and throughput capability. It’s ideal for labs looking for a cost-efficient NGS solution. You can perform MHRA on up to 48 samples per Ion 550 chip or choose the chip that fits your needs with an end-to-end, nucleic acid-to-report turnaround time of approximately 48 hours.

Custom MHRA panel on the Genexus System

Running the custom Ion AmpliSeq Microbiome Health Research Assay panel on the Ion Torrent Genexus Integrated Sequencer is ideal for labs that are new to in-house NGS and want to leverage the highly automated workflow. Using the GX5 Chip, customers can run 20 samples in 2 lanes with as little as 10 minutes of hands-on time and a total turnaround time of approximately 30 hours.

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.

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.

Video: SITC 2020 - Ion AmpliSeq Microbiome Health Research Kit

Introduction to the new Ion AmpliSeq Microbiome Health Research kit- high resolution species level microbiome profiling.

Ordering information

If there are species or gene targets beyond what is covered within the MHRA panel, reach out to your sales representative to understand the customizable options available.

 

 

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

PMR: 001481