Our goal was to provide a description of the skin mucus bacteriome of the common carp (Cyprinus carpio) through shotgun metagenomics. 8 common carp skin mucus sample were taken from two ponds (4-4 each) at a fish farm in Hungary. Samples were taken from the lateral line region of the fish while great care was taken not to contaminate them. Plastic tools and sterile tubes were used for the sample collection. Additionally, water samples were taken from each ponds. Paired-end shotgun metagenome sequencing on Illumina platfrom was perfomed on the samples based on the following protocol: DNA purifications from the carp skin mucus samples were performed in triplicates, the resulting total DNA extracts were pooled together. All extractions were carried out using ZymoBIOMICS DNA/RNA miniprep kits (R2002, Zymo Research, Irvine, USA). For efficient lysis of the mucus samples bead homogenisation was performed using a Vortex Genie 2 with a bead size of 0.1 mm, a homogenisation time of 15 min at maximum speed, then the Zymo Research kits DNA purification protocol was followed. Total DNA qualities were assessed with an Agilent 2200 TapeStation instrument (Agilent Technologies, Santa Clara, USA) and DNA quantities were measured using a Qubit Flex Fluorometer. We closely followed all manufacturer recommendations when preparing sequencing libraries for Illumina sequencing platform (Illumina Inc., San Diego, USA). Pooled total DNA samples were used to construct libraries using the NEBNext Ultra II Library Prep Kit (NEB, Ipswich, MA, USA). Paired-end shotgun metagenome sequencing was performed on an NextSeq 550 (Illumina) sequencer using the NextSeq High Output Kit v2 sequencing reagent kit. Primary data analysis (i.e., base-calling) was performed using bcl2fastq software (version 2.17.1.14, Illumina).
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