16S/ITS- Amplicon Metagenomics
What Is 16S/ITS- Amplicon Metagenomics?
16S and ITS amplicon metagenomics are targeted sequencing approaches used to profile microbial communities with high sensitivity and taxonomic resolution.
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16S rRNA gene sequencing focuses on the conserved and hypervariable regions of the bacterial 16S ribosomal RNA gene, allowing researchers to identify and classify bacteria down to the genus or species level.
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ITS (Internal Transcribed Spacer) sequencing targets the ITS1 and ITS2 regions between rRNA genes in fungi, enabling fungal community profiling with similar precision.
These methods rely on PCR amplification of the target regions followed by next-generation sequencing (NGS), generating millions of reads that are analyzed to determine microbial composition, diversity, and relative abundance.
Unlike culture-based methods, amplicon metagenomics detects a wide range of microbes—including those that are unculturable—directly from environmental or clinical samples. AUGenomics uses optimized primer sets and high-throughput Illumina sequencing to deliver accurate, reproducible microbial community data with minimal bias.
Advantages of 16S/ITS- Amplicon Metagenomics
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High Taxonomic Resolution: Accurately profiles bacteria and fungi at genus to species level.
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Culture-Independent: Detects both culturable and non-culturable organisms directly from DNA.
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Optimized Primer Sets: Minimizes amplification bias and ensures broad microbial coverage.
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Flexible Sample Types: Supports environmental, clinical, agricultural, and industrial samples.
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Quantitative Insights: Provides relative abundance and diversity metrics for each sample.
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Low Input Requirements: Generates high-quality data from low biomass samples.
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Customizable Panels: Option to target specific variable regions (V3–V4, V4, etc.) or fungal ITS1/ITS2 regions.
16S and ITS sequencing are essential tools for microbiome research across clinical, environmental, and industrial applications. Common uses include:
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Human Microbiome Studies: Characterizing gut, skin, oral, and other host-associated microbiota.
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Environmental Microbiology: Profiling microbial diversity in soil, water, air, and built environments.
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Agricultural Research: Investigating plant-associated microbiomes that influence crop yield and disease resistance.
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Food Safety and Fermentation: Monitoring microbial composition in food production and processing.
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Clinical Infectious Disease Research: Detecting bacterial or fungal pathogens in clinical samples.
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Industrial Applications: Assessing microbial communities in bioreactors, wastewater, and other systems.
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Biodiversity & Ecology: Exploring microbial diversity in natural ecosystems for conservation studies.
What is 16S/ITS- Amplicon Metagenomics Used For?
16S/ITS- Amplicon Metagenomics with AUGenomics
Sample Submission
Extracted microbial DNA (≥10 ng) or environmental samples (e.g., swabs, soil, water filters) can be submitted. Please ensure samples are free from inhibitors and contaminants. Environmental samples should be kept cold and shipped overnight on ice packs or dry ice.
Please refer to our Shipping Guidelines for project-specific guidance.
Turnaround Time
Typical turnaround for 16S/ITS sequencing projects is 10–14 business days from sample receipt. Expedited options are available depending on project scope and sequencing depth.
Frequently Asked Questions (FAQs)
Q: What kind of taxonomic resolution can I expect?
A: Depending on your target region and database, species- or genus-level resolution is typically achievable.
Q: What is the difference between 16S and ITS sequencing?
A: 16S targets bacterial and archaeal communities, while ITS targets fungal communities. Both use amplicon sequencing to classify organisms.
Q: How many reads per sample are required?
A: We typically recommend 50,000–100,000 reads per sample for robust diversity analysis, but this can be adjusted depending on sample complexity.
Q: Can you detect viruses with this method?
A: No. 16S and ITS target ribosomal gene regions and do not detect viruses. For viral metagenomics, we recommend shotgun sequencing.
Q: What types of samples are compatible?
A: We accept DNA from a wide range of sources including stool, swabs, soil, water, air filters, plant tissues, and more.
Got more questions? Contact our team and get a free consultation anytime. info@augenomics.com
Glossary of Terms
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16S rRNA gene: A conserved bacterial gene used for microbial identification
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ITS (Internal Transcribed Spacer): A genetic marker for fungal species
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Metagenomics: The study of genetic material recovered directly from environmental samples
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Amplicon sequencing: Targeted sequencing of PCR-amplified genetic regions
