Using DNA metabarcoding to study the diet composition of predatory flying squids paralarvae

Dr Fernando Á. Fernández-Álvarez

NUI Galway

“We have contracted AllGenetics for several DNA barcoding and metabarcoding projects, and my opinion about them could not be better. Besides their strong knowledge and skills helping you in genomic projects, they are extremely professional and provide an excellent service prior to, during, and after the development of the work. Highly recommendable!”


The research team was interested in unveiling the diet composition of flying squids paralarvae. Although the diet of adult specimens was well characterised, the diet of the early developmental stages remained unknown. Therefore, and given our previous success with other diet analyses by DNA metabarcoding, they contacted us and asked for advice.


Laser capture microdissection was coupled with DNA metabarcoding to study the diet of these paralarvae. The gut contents of the paralarvae under study were microdissected by the research team in an ancient DNA laboratory (MNCN / CSIC) and DNA was isolated from the samples using a commercial DNA isolation kit. The DNA samples were then shipped to AllGenetics, where eukaryotic 18S and prokaryotic 16S rRNA DNA metabarcoding libraries were prepared and sequenced in the MiSeq platform. Subsequently, we analysed the raw MiSeq data to obtain the species composition for each sample. Self-contaminant reads (i.e., reads coming from the host) were bioinformatically deleted.


The DNA metabarcoding results showed that the gut contents were mainly composed of fungi, plant, algal, and animal species of marine and terrestrial origin, as well as eukaryotic and prokaryotic microorganisms commonly found in fecal pellets and particulate organic matter. The research team concluded that the species detected in the gut contents were consistent with a diet based on detritus. This research has been published in the journal Scientific Reports.