Microbiomes refers to all living organisms in a human or animal body, such as bacteria, yeast, fungi and viruses. It consists of both beneficial as well as (potentially) harmful microbes, but most are symbiotic meaning that they have emerged together with their host during evolution. Over the years, the microbiota (bacteria of the microbiome) has gained more and more attention due to its potential role in both health maintenance as well as in disease development. In addition, beneficial microorganisms (probiotics) and their growth stimulators (prebiotics) have been associated with health benefits upon consumption. Highly developing sequencing techniques such as Illumina and shotgun metagenomics, as well as genome sequencing and transcriptomics, are nowadays being applied broadly in order to define detailed composition, function and potential of the microbiome and its modulators.