As outlined above, metagenomes derived from the same or similar environments, often supplemented with protein sequences from repositories (e.g., Homo sapiens entries in UniProt for human microbiome studies), are typically used as databases for protein identification. These metagenomes are usually assembled, genes are predicted (gene calling), and frequently, metagenome-assembled genomes (MAGs) are constructed to define sample-specific taxonomic units. For microbial effectors, tools such as PATHOFact (for virulence factors and antimicrobial resistance) , antiSMASH (for secondary metabolite biosynthesis) or Macrel (for predicting antimicrobial peptides) can be employed to annotate genes and their associated proteins (e.g., polyketide synthases or resistance genes). Furthermore, VirHostMatcher , phageAI , What the Phage and PHASTEST can be used to identify potential bacteriophage hosts and target structures.