DeepChek® 16S+ITS

End-to-end NGS workflow support for intestinal microbiome profiling across bacterial and fungal communities, from library preparation planning through automated bioinformatic reporting.

Intestinal Microbiome

Bacterial and fungal profiling in one NGS workflow

MetagenomicsRUO

DeepChek® 16S+ITS is positioned for laboratories that need a coordinated microbiome workflow to evaluate gut microbial composition and diversity. Gut microbiome imbalance is widely studied in areas such as obesity, type II diabetes, and broader metabolic research, and this workflow helps profile bacteria and fungi together for a clearer research view of intestinal microbial communities.

16S V3-V4ITS2Gut microbiome25 ng DNA inputUp to 288 samplesBioinformatics

DeepChek 16S+ITS intestinal microbiome workflow

Assay And Workflow Features

Target Coverage

Profiles bacterial and fungal communities from one coordinated intestinal microbiome NGS workflow.
Amplifies bacterial 16S rRNA V3-V4 regions together with fungal ITS2 DNA targets.
Supports species-level classification when the target region can differentiate the organism and reference data is available.

Library Preparation

Covers library preparation, bioinformatic analysis, visualization, and report generation as a connected workflow.
Includes the required library preparation reagent set for the supported assay workflow.
Produces sequencing-ready libraries in under three hours, supporting faster laboratory turnaround planning.
Designed for bacterial and fungal community identification from DNA input as low as 25 ng.
Provides ITS2 primers as a flexible add-on so fungal profiling can be included when required.

Sequencing Setup

Uses dual-indexed libraries to enable multiplexed sequencing of up to 288 samples in a run.
Includes balanced heterogeneity spacers to support library complexity and sequencing quality.
Can be run without a PhiX spike-in under the validated workflow, helping preserve sequencing capacity.
Compatible with Illumina MiSeq and other platforms that support 250 bp or longer paired-end reads.
Supports sample pooling and sequencing run setup through MicrobeCalc-assisted planning.
Uses a kit format designed to reduce tube count and plastic use where possible.

Workflow Overview

Workflow Snapshot

Targets16S rRNA V3-V4 and ITS2

ApplicationHuman intestinal microbiome research

DNA InputAs low as 25 ng

Library TimingSequencing-ready libraries in under 3 hours

MultiplexingDual indexes for up to 288 samples per run

SequencingMiSeq and paired-end 250 bp compatible platforms

Bioinformatics And Reporting

Capability	What it supports
Automated processing	Sequencing results can be processed and reviewed through a microbiome analysis workflow built for result visualization and report preparation.
Microbial identification	Species-level classification of bacterial and fungal communities using validated databases such as SILVA for bacteria and UNITE for fungi.
Reference comparison	Major bacterial phyla can be reviewed against established healthy-range references for intestinal microbiome research interpretation.
Alpha-diversity	Within-sample species identification and abundance measurement help describe richness and composition in each sample.
Beta-diversity	Between-sample comparison supports review of microbial community differences across individuals or study groups.
PCoA plots	Principal Coordinate Analysis visualizations help compare microbiome similarity and separation patterns across samples.
Relative abundance charts	Chart outputs make it easier to review organism or group-level abundance patterns in individual samples.
Heatmaps	Cross-sample heatmaps support side-by-side comparison of taxa, abundance, and clustering patterns.
Report delivery	Customizable PDF reports and raw abundance tables can be used for downstream review, archiving, or further analysis.

Important Use Notes

The automated reference ranges and explanatory report content are intended for gut microbiome analysis.

For other sample types, including urine, vaginal fluid, or saliva, laboratories should confirm DNA quality, DNA quantity, and extraction protocol performance before use.

Species reporting depends on organisms being distinguishable through the targeted V3-V4 and ITS2 regions and represented in established databases.

Research use only. Not for use in diagnostic procedures.

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Product References

Product	Status	REF	Unit Size
16S Microbiome + ITS NGS Assay [16 rxn]	RUO	9-131-16	16 reactions
16S Microbiome + ITS NGS Assay [Set A]	RUO	9-131	96 reactions
16S Microbiome + ITS NGS Assay [Set B]	RUO	9-132	96 reactions
16S Microbiome + ITS NGS Assay [Set C]	RUO	9-133	96 reactions

Indexing And Run Setup

REF 9-131, 9-132, and 9-133 use different indexing primer sets.
The 16 reaction configuration uses indexes that overlap with REF 9-131 Set A.
For runs above 96 samples, combine kits with unique primer sets, such as Set A with Set B.
IFU and brochure documents can be shared during product discussion or quotation support.

Need help planning a microbiome workflow?

Genient can support assay selection, DNA input and quality discussions, pooling strategy, sequencing setup, validation planning, training, reporting workflow, demo report review and downstream bioinformatics discussions.

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