Multi-species detection

Multi-species detection is where an inventory of all species present in a sample derived from the environment can potentially be obtained. This technology differs in that non species-specific PCR primers are developed which amplify a region of DNA that provides sufficient diversity that when sequenced, can be used to identify species that are present. This technology is known as ‘meta-barcoding’, as it uses bar-coding regions of DNA in addition to high-throughput, massively parallel DNA sequencing platforms and sophisticated bioinformatic pipelines to analyse the data.

In order for this technology to work, reference databases are essential so that the correct species identity can be obtained from DNA sequence data. There are several public databases that can provide DNA sequence information but there are still gaps that require additional targeted collection. It is also important to ensure the experimental design takes into account biases that can occur when using multiple primer sets for particular groups of species, and the numbers of DNA sequence reads required in order to detect low-abundant species.  Tools and technologies are now enabling this methodology to be used in situ, and without specialist DNA sequencing facilities but still require appropriate standards and guidelines for routine application.

Applications of multi-species detection;

• Biodiversity monitoring; meta-barcoding is becoming more routine as a monitoring tool for biodiversity assessment across a wide range of taxonomic groups such as macro-invertebrates, fish, micro-organisms, plants, terrestrial vertebrates etc.
• Diet analysis: samples such as gut contents and fecal material can be used to provide DNA for meta-barcoding for studies on diet. Traditional methods can often miss more easily digested species and many undigested fragments are very difficult to assign to a particular species. This method offers greater information to be derived from such samples.
• Biosecurity surveillance: this technology has potential to be used in standard biosecurity operations to detect the presence of unwanted organisms being imported into Australia. One such application is the ornamental fish trade, where a water sample could provide identity of both the fish as well as any potential pathogens in consignments.