Metabarcoding vs Metagenomics

Metabarcoding vs. Metagenomics: Two Ways to Decode Diets and Microbiomes

​Modern ecological research increasingly relies on DNA to discover what animals eat.

Two broad classes of DNA-based strategies—called DNA metabarcoding and metagenomics—can provide complementary data that provide insight into what animals eat and why it matters.

When should we select one versus the other (or try combining both)?

An Oxford Nanopore MinION is a portable sequencing platform for metabarcoding and metagenomic applications

At a Glance: “Meta” DNA Approaches for Diet Analysis

Metabarcoding

• Data source: Short DNA ‘barcode’ snippets from feces or gut contents
• Focus: Taxonomic composition of diet for comparison across many samples
• Resolution: Often species- or genus-level (depends on barcodes and reference libraries)
• Strengths: High sensitivity, cost-effective, scalable
• Limitations: PCR biases, broad-spectrum primers and reference libraries can be limited

Metagenomics

• Data source: Whole-genome shotgun sequencing of all DNA in a sample
• Focus: Comprehensive genetic content, including functional genes and off-target taxa
• Resolution: Sub-specific in some cases; captures functional potential
• Strengths: Taxonomic and functional insights; multiple communities resolved in one run (e.g., diet and microbiome)
• Limitations: Higher cost, lower throughput, computationally intensive, large data storage

What Is DNA Metabarcoding?

Dietary DNA metabarcoding uses PCR to amplify a short, standardized DNA region (barcode) from a mixed sample, then sequences it to identify taxa. This approach is widely used for diet studies and also for environmental biodiversity surveys and microbial community profiling.

Why it works well:

• Allows rapid identification of known taxa
• Can detect rare or low-abundance organisms
• Less computationally demanding than whole-genome approaches

Key limitation: Only the targeted DNA region is sequenced—and only from the targeted taxa. It cannot reliably detect and classify taxa that are outside the target group or absent from reference databases.
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🧬 Find out how we use dietary DNA metabarcoding in wildlife ecology

What Is Metagenomics?

Metagenomics is a strategy to sequence all DNA in a sample rather than targeting specific barcodes. It allows us to reconstruct community composition and the functional genes or pathways of species that exist in the community we are profiling. It can be used to discover DNA from dietary resources in a sample—these will be sequenced together with everything else.

Why metagenomics is transformative:

• Avoids primer bias, captures unexpected or novel taxa
• Enables insights into diet, microbiome function, and other communities (e.g., parasites)
• Can link organisms to ecological functions via gene content

Challenges:

• Requires more computational resources and bioinformatics expertise
• More expensive per sample
• Large data files can be challenging to store and manage

🔗 Metagenomics: A viable tool for reconstructing herbivore diet

The Essentials of How They Differ

Key distinction: Metabarcoding is ideal for targeted questions about community composition or diet. Metagenomics is ideal for broad ecological or functional questions, including detection of unknown or rare organisms.

Why This Comparison Matters

Choosing the right approach affects interpretation and ecological conclusions:

• DNA metabarcoding may miss unusual or novel taxa
• Metagenomics may identify many rare or unimportant signals
• Combining both can reveal “who is there” and “what they do”

This distinction is critical in conservation, microbiome research, and wildlife management, where decisions depend on both taxonomic and functional understanding.

Choosing the Right Approach

• Use metabarcoding for taxonomic surveys, diet snapshots, and high-throughput studies
• Use metagenomics for functional ecology, microbiome studies, or novel discovery
• Consider a combination: metabarcoding for broad screening, metagenomics for detailed profiling of selected samples

🔗 Strategies and protocols to plan dietary DNA studies for wildlife ecology

Explore More in This Series

• Metabarcoding vs Microhistology
• Metabarcoding vs Direct Observation
• Metabarcoding vs Stable Isotopes