Our bodies are colonized with trillions of microorganisms, comprising bacteria, fungi, micro-eukaryotes, and viruses, which are collectively named “microbiome” [1–3]. Several human body sites are colonized by different and distinct microbiomes, for example, the skin [4], the oral cavity [5], the gastrointestinal tract [6], and the urogenital tract [7]. Microbiomes have been shown to play crucial roles linked with our health and disease states [3, 4, 8, 9]. For example, it has been shown to train the immune systems in newborns [10], to digest important nutrients that otherwise we would not be able to process, and to produce health-promoting metabolites [11]. More in detail, it has been shown that gut bacteria help to break down complex carbohydrates [12] as well as absorb important vitamins and minerals present in the food [13]. For instance, they produce short-chain fatty acids (SCFAs) like butyrate, propionate, and acetate, by fermenting dietary fibers that reach the colon [14–17]. Additionally, commensal bacteria stimulate the production of mucus by the gut lining and compete for nutrients with pathogens and other harmful bacteria by occupying specific ecological niches in our digestive tract, thus preventing or limiting colonization [18, 19]. Certain bacteria can moreover produce antimicrobial compounds that can directly kill or inhibit the growth of pathogenic bacteria [20].