Molecular biological approach to gut contents analysis for a foodweb study of a marine ecosystem

Abstract

Conventional stomach contents analysis methods by morphology are problematic. Many consumed organisms are digested partly and become unrecognizable. Unrecognizable consumed organism is hard to identify and lead to unclear results. For this reason, molecular biological methods using recovered DNA sequences from stomach contents were applied recently. Here we designed universal primers to amplify portion of the 18S and 28S rDNA sequences to examine stomach contents using PCR techniques. The stomach contents of sailfin sandfish (Arctoscopus japonicus) and pacific squid (Todarodes pacificus) were examined. In total, 11 families of prey were identified that the primer with 18S and 28S rDNA using the universal primers. The DNA sequence data indicated that the primer sets successfully amplified a wide spectrum of species and represented stomach contents in a relatively convenient way. We found that information in NCBI database was not yet sufficient to discriminate the species we isolated. In addition, technology for the separation of heterogeneous PCR products and better resolution and quantification protocols would help increase data accuracy.