Metagenomics
Explore microbial diversity and function with 16s, ITS, and shotgun metagenomics
What is Metagenomics and what is it used for?
Metagenomics, or shotgun metagenomic sequencing, is the comprehensive analysis of genetic material extracted directly from environmental samples. This field, also referred to as environmental genomics, ecogenomics, or community genomics, encompasses the characterization of complex microbial communities, enabling taxonomic profiling, functional potential assessment, and insights into ecological interactions without the need for prior cultivation. While traditional microbiology and microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often 16s rRNA gene) to produce a profile of diversity in a natural samples.
Metagenomic sequencing methods reveal the previously hidden diversity of microscopic life and offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world. As the cost of DNA Sequencing continues to fall, metagenomics now allows microbial ecology to be investigated at a much greater scale and detail than ever.
Metagenomics Solutions
Shotgun Metagenome sequencing
Whole-community sequencing that captures bacteria, viruses, fungi, archaea, and functional genes in one workflow. Commonly used in pathogen discovery, AMR gene detection, viral metagenomics, metabolic, and functional profiling for species/strain-level resolution.
ITS 1 ITS 2 sequencing
Targeted sequencing of internal transcribed spacer regions for fungal community characterization. Commonly used for mycobiome studies, fungal ecology, and fungal detection.
16s rRNA gene sequencing
Targeted, cost-effective bacterial community profiling using variable regions of the 16S rRNA gene to analyze bacteria in human, plant, animal, and the environmental microbiome.
Amplicon-sequencing
Amplicon-seq for metagenomics-based studies uses targeted gene regions to profile microbial diversity and taxonomy across human, plant, animal, and environmental samples.
Applications of Metagenomic Sequencing
Microbiome & taxonomic profiling
Characterize microbial communities and classify organisms in humans, animals, plants, or the environment to understand health, disease, and ecosystem dynamics
Pathogen detection
& surveillance
Identify and monitor bacteria, viruses, and other microorganisms in clinical, food, or environmental samples - enabling rapid detection of infectious agents
Antibiotic resistance & functional gene analysis
Detect resistance genes and other functional genetic elements in microbial populations, supporting research on antimicrobial resistance and novel therapeutic targets
Environmental &
industrial applications
Assess microbial diversity in soil, water, or industrial bioreactors to optimize processes, study ecological impact, or discover new enzymes and bioactive compounds
Frequently Asked Questions
Sending samples? See our DNA sample submission guidelines for best practices on sample preparation, packaging, and shipment for the highest quality results.
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16S/ITS targets specific marker regions to profile bacterial or fungal communities at a lower cost. Resolution is typically genus-level for 16S and species-level for many fungi using ITS.
Shotgun metagenomics sequences all DNA in a sample, enabling species/strain-level identification, functional profiling, AMR gene detection, and viral/fungal/bacterial community analysis in one assay.
If you're unsure which you need, our team helps scope the most appropriate option. -
We support a wide range of primer sets to align with your study goals.
16S rRNA: V1–V9, V3, V4, V5, and custom primer designs.
ITS: ITS1 and ITS2 for fungal community profiling.
Custom primer sets can be validated upon request.
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We support a wide range of sample types, including:
Stool, saliva, sputum, swabs
Blood (cfDNA), tissue (FF/FFPE)
Soil, water, environmental swabs
Food, fermentation, agricultural samples
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Our standard recommendation for 16S rRNA gene sequencing is 0.1 million paired-end reads (PE 2×300) per sample. This depth provides reliable bacterial community profiling, supports diversity analyses, and meets typical publication standards.
(We can adjust sequencing depth based on your sample type, cohort size, or resolution needs.)
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Our standard turnaround time is typically 15 business days, though this can vary depending on the sample type, project complexity, and required sequencing depth. Expedited services are available upon request. Please contact us for a detailed quote and timeline specific to your project.
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We provide comprehensive, ready-to-use data.
View our demo reports to get a feel for what you can expect when working with our team:
Get the Most out of Your Study
Maximize your project’s potential with advanced analysis solutions. Our team of expert bioinformaticians curate pipelines tailored to your project’s experimental design.
See Metagenomics in Action
Admera Health provides comprehensive support for all projects, and delivers publication-ready data. Discover how researchers are using Admera Health to advance their environmental studies.