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A metapangenome is a method for evaluating multiple genomes by considering both the gene clusters they possess, similar to a pangenome, and their occurrences in various environments or samples through metagenomic read recruitment.

Metapangenome describes the result obtained from analyzing pangenomes in association with the environment. The abundance and prevalence of gene clusters and genomes are retrieved through shotgun metagenomes. The integration of metagenomes with pangenomes, known as "metapangenomics," unveils the outcomes of habitat-specific filtering applied to the pangenomic gene pool at a population level.