Beyond taxonomy: Validating functional inference approaches in the context of fish-farm impact assessments

The aim of this study was to evaluate the performance of three metabolic inference methods, namely PAPRICA, PICRUSt2 and TAX4FUN2, against metagenomics and environmental data, in the context of salmon farm benthic surveys. In particular, we were interested in: 1) comparing predictions and abundance correlations between 16S rRNA amplicon-based metabarcoding functional inference approaches (hereafter referred to as HSP methods) and shotgun metagenomics functional profiling, 2) contrasting the taxonomic and functional microbial diversity recovered from metabarcoding and metagenomics, and 3) assessing and comparing the sensitivity of functional communities derived from HSP methods and metagenomics with respect to microbial turnover and in correlation with environmental data.