Abstract Background Sponges, the oldest metazoans on the planet, have an evolutionary history shaped by symbiotic associations with microorganisms. Although well studied in marine sponges, these associations are poorly understood in freshwater species. This study explored the taxonomic diversity and functional potential of the microbiome of the freshwater sponge Metania sp. and its distinction from the surrounding water, using a metagenomic approach. The samples were collected in the Brazilian C