DNA metabarcoding is a method for identifying the variety of species present in a single, complex sample by analyzing short, standardized segments of DNA from all organisms mixed together. The technique provides a broad-scale assessment of biodiversity, taking a “DNA snapshot” of an environment like a river, a patch of forest soil, or even the air. This approach allows for rapid data collection from materials containing genetic traces from many different life forms.
How DNA Metabarcoding Works
The process begins with the collection of a sample, which can be diverse, ranging from soil and water to fecal pellets, air captured on filters, or a trap full of insects. From this mixed sample, all the genetic material is chemically extracted, resulting in a pool of DNA from every organism present, whether it be a bacterium, a plant, a fungus, or an animal.
Next, scientists use Polymerase Chain Reaction (PCR) to make millions of copies of specific DNA regions known as “barcodes.” These barcodes are short, standardized gene segments that differ from one species to another, allowing for precise targeting. Commonly used barcode regions include cytochrome c oxidase I (COI) for many animals, the Internal Transcribed Spacer (ITS) region for fungi, and 16S ribosomal RNA (rRNA) for bacteria and archaea. Universal primers bind to these genes to initiate the copying process for many species at once.
Following amplification, these millions of barcode copies are read using high-throughput sequencing, often called next-generation sequencing (NGS). This technology can process a massive number of DNA sequences simultaneously, generating a vast dataset from a single sample.
The final stage is bioinformatic analysis. The raw sequences are first filtered to remove any low-quality reads. They are then grouped into clusters of similar sequences, often referred to as molecular operational taxonomic units (MOTUs) or amplicon sequence variants (ASVs), which act as proxies for species. These representative sequences are then compared against large, curated reference databases to assign them a taxonomic identity.
Applications Across Ecosystems
A primary application of DNA metabarcoding is the analysis of environmental DNA (eDNA), which is genetic material shed by organisms into their surroundings. By filtering water from a lake or river, researchers can identify the fish, amphibian, and invertebrate species that live there without ever seeing or capturing them. Similarly, DNA from soil or even air can reveal the presence of terrestrial mammals, plants, and fungi in a given area.
Diet analysis is another application. By analyzing the DNA found in fecal samples, stomach contents, or regurgitates, scientists can precisely determine what an animal has been eating. This non-invasive method reveals predator-prey interactions and foraging habits that are difficult to document through direct observation.
The method is also used for large-scale biodiversity assessments and ongoing monitoring programs. It allows for rapid surveys of species richness in habitats from tropical rainforests to the deep sea, establishing species baselines. These surveys can be repeated over time to track how biological communities respond to environmental changes, such as shifts in climate, pollution events, or habitat restoration efforts.
Metabarcoding is a tool for managing ecosystems by detecting elusive or invasive species. It can provide early warnings of a non-native species’ arrival, allowing for more effective control measures. It also helps locate rare or secretive organisms that are seldom seen, confirming their persistence in a habitat. Beyond natural ecosystems, the technique is used to ensure food authenticity by identifying the species present in processed products to detect fraudulent labeling.
Unique Insights from Metabarcoding
DNA metabarcoding provides information that is often impossible to obtain using traditional methods like visual surveys or morphological identification. The technique can detect a much wider spectrum of species from a single sample, including organisms that are microscopic, taxonomically ambiguous (cryptic), or exist in very low numbers.
This method also offers enhanced efficiency. The ability to process many samples and identify thousands of organisms simultaneously streamlines biodiversity research. What might have taken teams of taxonomic experts months or years to accomplish by identifying organisms one by one can now be done in a fraction of the time.
Instead of focusing on a single target species, metabarcoding characterizes entire biological communities at once. Analyzing a bulk insect trap, for example, reveals not just one type of beetle but the entire insect community present at that location. This holistic view allows scientists to study complex interactions, community-wide patterns, and the overall health of an ecosystem.
Practical Aspects of Metabarcoding
A primary consideration in metabarcoding studies is preventing and detecting contamination. Because the method amplifies trace amounts of DNA, even tiny amounts of foreign genetic material from the lab or field can lead to false positives. Researchers incorporate negative controls—samples with no expected DNA—throughout the process to monitor for any such contamination.
The accuracy of species identification is directly tied to the quality and completeness of DNA reference databases. A species can only be identified if its specific DNA barcode sequence exists in a database for comparison. If a sequence is not present, the organism may be unidentifiable or, in some cases, misidentified as a close relative. These global databases are continuously expanding as more species are sequenced.
The primers used to amplify the DNA barcodes can also introduce biases. While primers are designed to be “universal,” they may not amplify the DNA of all species with equal efficiency. Some primers might preferentially amplify DNA from certain taxonomic groups over others, which could skew the perceived abundance or even presence of some species in the final data. Scientists account for such biases by using multiple primer sets or adjusting their analyses.
Interpreting the data requires careful consideration, especially concerning species abundance. While metabarcoding is excellent at determining which species are present, using the number of DNA sequences to estimate the population size or biomass of those species is complex. Factors like how long DNA persists in the environment and differences in how much DNA different organisms shed mean that sequence counts do not always correlate directly with abundance. This is an area of ongoing research.