The microbiome is the set of genomes (genetic material) included in the microbiota, which is the set of microorganisms that co-inhabit the same niche. This community of microorganisms is composed of bacteria, fungi, archaea and viruses.
Almost any niche has a microbiota associated and the study of its microbiome can be achieved through the use of metagenomics. In other words, we can study entire communities of microorganisms by sequencing their genomes or part of them.