Sample preparation and dietary DNA extraction
The digestive contents of the shrimps were dissected using
flame-sterilized tools in a PCR-free room to avoid contamination. Of the
116 samples, 15 had empty stomachs and were discarded. DNA extraction
was performed with the NucleoSpin Tissue Kit (Macherey-Nagel), following
the manufacturer’s instructions, with filter tips under a sterile hood.
The largest samples were first crushed and mixed using sterile glass
beads and a Fastprep instrument (MP Biomedicals, Eschwege, Germany) and
approximatively 0.2 g of homogenized sample was used for DNA extraction.
Samples were processed in batches of 24, using aerosol (empty tubes kept
open) and extraction negative controls.