Ion AmpliSeq™ Microbiome Health Research Assay, Library Prep only reagents, 48 samples - FAQs

The Ion AmpliSeq Microbiome Health Research Kit, Ion 550 bundle (Cat. No. A46497) consists of the Ion AmpliSeq Microbiome Health Research - 16S rRNA Gene Pool, the Ion AmpliSeq Microbiome Health Research - Target Species Pool, the Ion AmpliSeq Library Kit Plus, the IonCode Barcode Adapters, the Ion 550 Kit - Chef, and the Ion 550 Chip Kit for the rapid preparation of barcoded sample libraries from bacterial DNA. Sufficient reagents are provided to prepare uniquely barcoded DNA libraries from 384 research samples.
Note: The Ion Library TaqMan Quantitation Kit (Cat. No. 4468802) must be purchased separately.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

The Ion AmpliSeq Microbiome Health Research Kit, Library bundle (Cat. No. A46495) consists of the Ion AmpliSeq Microbiome Health Research - 16S rRNA Gene Pool, the Ion AmpliSeq Microbiome Health Research - Target Species Pool, the Ion AmpliSeq Library Kit Plus, and the IonCode Barcode Adapters for the rapid preparation of barcoded sample libraries from bacterial DNA. Sufficient reagents are provided to prepare uniquely barcoded DNA libraries from 48 research samples.
Note: The Ion Library TaqMan Quantitation Kit (Cat. No. 4468802) must be purchased separately.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

The Torrent Suite AmpliSeq_Microbiome_Health_ Analysis plugin and Ion Reporter Software workflows were developed and validated exclusively for the Ion AmpliSeq Microbiome Health Research Kit. Open source analysis tools may be available for your custom solutions.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

Customization solutions are available through AmpliSeq custom designs (Ampliseq.com), where you can customize your own assays for any species of your interest. For details, please contact your local Field Applications Scientist (FAS).

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

Several scientific publications have demonstrated the key role played by the gut microbial community in infection susceptibility and severity, including for SARS-CoV-2. The Ion AmpliSeq Microbiome Health Research Kit targets 73 species known to be associated with immune-related diseases, including a large number of known bacterial species with antiviral or immune-modulating properties.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

The Ion AmpliSeq Microbiome Health Research Kit is a targeted next-generation sequencing (NGS) assay that enables the profiling of the human gut microbiome by targeting eight of nine 16S hypervariable regions of 16S rRNA gene (16S rRNA Gene Pool) and allows for the accurate detection of 73 key bacterial species associated with human disease (Target Species Pool). The assay was validated on the Ion Chef and Ion GeneStudio systems and is available in different configurations, with only primers, primers and library prep reagents, or library prep, templating, and sequencing bundles. Check with your local Sales Rep for the best configuration for your experimental needs.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

A microbiome is a community of microorganisms living together in a particular habitat, for example the gut.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

- The overall library concentration may have been too low. We recommend renormalizing the individual libraries to 50 pM concentration and combining into a new library pool.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

- The overall library concentration may have been too high. We recommend diluting the library pool to 50 pM concentration.
- The individual library concentrations may have been too high. We recommend diluting the individual libraries to 50 pM concentration.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

- The individual libraries may have been normalized to different concentrations. We recommend renormalizing the individual libraries to 50 pM concentration and combining into a new library pool.
- The individual libraries may have been misquantified. We recommend requantifying the individual libraries, then normalizing the individual libraries to 50 pM concentration and combining into a new library pool.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

The overall library input into templating may have been low. We recommend renormalizing the individual libraries to 50 pM concentration and combining into a new library pool.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

The sample DNA may have been misquantified. We recommend requantifying the sample DNA using the Qubit dsDNA HS Assay Kit and Qubit Fluorometer.
Note: Library yield is not indicative of quality.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

Here are possible causes and solutions:
-The sample DNA may have been misquantified. We recommend requantifying the sample DNA using the Qubit dsDNA HS Assay Kit and Qubit Fluorometer.
-The sample quality may have been low. We recommend reextracting the sample DNA using the MagMAX Microbiome Ultra Nucleic Acid Isolation Kit or adding more sample DNA to the amplification reaction.
-The PCR, digestion, or ligation reactions may have been inefficient. We recommend ensuring proper dispensing and mixing of viscous components at each step.
-The AMPure XP beads may have been overdried. We recommend not drying the AMPure XP beads for more than 5 mins.
Note: Library yield is not indicative of quality.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

Up to 96 paired libraries (48 samples) can be combined and loaded onto a single Ion 550 Chip.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

The Ion AmpliSeq Microbiome Health Research Kit, Ion 540 bundle (Cat. No. A46496) consists of the Ion AmpliSeq Microbiome Health Research - 16S rRNA Gene Pool, the Ion AmpliSeq Microbiome Health Research - Target Species Pool, the Ion AmpliSeq Library Kit Plus, IonCode Barcode Adapters, the Ion 540 Kit - Chef, and the Ion 540 Chip Kit for the rapid preparation of barcoded sample libraries from bacterial DNA. Sufficient reagents are provided to prepare uniquely barcoded DNA libraries from 256 research samples.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

The minimum sample input is 1 ng/pool for the Ion AmpliSeq Microbiome Health Research - 16S rRNA Gene Pool and 10 ng/pool for the Ion AmpliSeq Microbiome Health Research - Target Species Pool.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

The Ion AmpliSeq Microbiome Health Research Kit was validated using DNA isolated from human stool samples to generate libraries for templating and sequencing on the Ion Chef and Ion GeneStudio systems. Different sample types and platform configurations may work but need to be validated by each lab. Contact your local Field Applications Scientist for assistance.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

The Ion AmpliSeq Microbiome Health Research Kit, Ion 540 bundle (Cat. No. A46496) is a targeted next-generation sequencing (NGS) assay that enables the profiling of the human gut microbiome by targeting eight of nine 16S hypervariable regions of 16S rRNA gene (16S rRNA Gene Pool ) and allows for the accurate detection of 73 key bacterial species associated with human disease (Target Species Pool). This bundle allows templating and sequencing with the Ion 540 Chip to be done on the Ion Chef and Ion GeneStudio systems.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.