ITS2 rDNA nemabiome metabarcoding of gastrointestinal nematodes in Australian livestock utilising the FECPAKG2 platform

A new diagnostic approach to identify GINs that integrates a modern, remote-location digital faecal egg count platform, FECPAKG2, with ITS2 nemabiome metabarcoding, was developed. The technique involves a quick and simple protocol to harvest concentrated strongyle eggs from the FECPAKG2 cassette utilising a repurposed pipette tip, followed by DNA isolation and Illumina next generation sequencing (NGS). We compared the GIN species compositions and alpha diversity generated by our FECPAKG2 egg identification approach to traditional morphological larval differentiation and ITS2 nemabiome metabarcoding of larval and faecal samples.