metabarcoding

Metabarcoding is a molecular method for assessing biodiversity by sequencing a standardized genetic marker from many organisms within an environmental sample. It merges DNA barcoding with high-throughput sequencing to identify multiple taxa in parallel, enabling rapid surveys of complex communities without isolating organisms.

Workflow involves collecting samples (bulk tissue or environmental DNA from water, soil, or air); extracting DNA; amplifying a barcode region with universal primers (examples: COI for animals; 16S for bacteria and archaea; ITS for fungi); sequencing amplicons on high-throughput platforms; and processing data with bioinformatics to filter reads, remove chimeras, and cluster into amplicon sequence variants (ASVs) or operational taxonomic units (OTUs). Taxonomic assignment uses reference databases such as BOLD, SILVA, GenBank, and UNITE.

Applications include biodiversity inventories, ecological monitoring, diet analysis from feces or gut contents, surveillance for invasive or endangered species, and studies of microbial, fungal, and eukaryotic communities in soil, water, and air.

Advantages of metabarcoding include speed, cost-effectiveness, and the ability to detect rare or cryptic taxa. Limitations include primer bias, incomplete reference databases, limited taxonomic resolution for some groups, and semi-quantitative interpretation due to copy-number variation and amplification biases. DNA from dead material or contamination can complicate interpretation, requiring careful controls and validation.

Related terms include DNA metabarcoding or metabarcoding of environmental DNA (eDNA); it is often contrasted with metagenomics, which sequences total DNA without targeted amplification.