Linking AMR Genes to Taxonomy in Soil Metagenomics

Question

[LuciaNhu]

Hi everyone,

I'm working with a shotgun metagenomic dataset from soil samples. I've used MEGARes and AMR++, v3.0 to successfully identify AMR genes and their resistance mechanisms through resistome analysis. Additionally, I've used Kraken2 to perform microbiome analysis and obtain taxonomic classifications for the organisms present.

My question is: how can I best link the identified AMR genes to their specific source organisms within the metagenomic data? While I have the resistome and taxonomic profiles, I'm looking for recommendations on methods to connect these datasets and determine which organism harbors each AMR gene.

Thanks in advance for any advice!