Reference-based metagenomics is the approach that aims at characterising metagenomes based on existing genome sequences that are used as reference. This approach is meaningful when the microbial community under study is well known, such as the human microbiome, or when a reference MAG catalogue has been generated from a subset of samples under analysis. When the genome catalogue used as a reference has not been generated from the same environment (e.g., using human gut microorganisms as reference for vulture gut microbiomes), there are two major risks. The first one is that some of the microorganisms present in the studied environment might not be represented in the reference catalogue, which results in diversity underestimations. The second one is that the microorganisms present in the reference catalogue are similar but not identical to the ones in the target sample, which might result in incorrect taxonomic and functional inferences. It is therefore important to keep these caveats in mind when performing reference-based metagenomic analyses, mainly when dealing with non-model host organisms.