16S rRNA Metagenomics Data on the Bacterial Communities in Integrated Poultry-Fish Farm Ponds
Description
The data include bacterial taxonomic profile and abundance in pond water samples collected from a farm practicing an integrated poultry farming system, in South-West, Nigeria. The data was generated from the amplification and sequencing of the V3-V4 region of the rRNA gene using the Miseq Illumina sequencing platform and different bioinformatic tools.
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Steps to reproduce
Water samples were collected from two integrated ponds and one unintegrated pond constructed on an IPF farm during two sampling visits. DNA was extracted from the samples using ZymoBIOMICS®-96 MagBead DNA Kit and subjected to Miseq Illumina sequencing platform using a 500 cycles v3 sequencing kit (2 x 250 bp paired-end reads). Distinctive or unique amplicon sequence variants obtained using the DADA2 pipeline was grouped into OTUs and taxonomy assignment was performed using QIIME v.1.9.1. Taxonomy with significant abundance within different groups was detected by LEfSe algorithm using default settings.