A microbiome is a collection of microorganisms (bacteria, viruses, and sometimes fungi) that live together in a particular environment. Humans actually have multiple microbiomes (on your skin, in your mouth, in your lungs – even your eyes have their own unique microbiome), but by far the largest and most important microbiome is the gut microbiome. The microorganisms that compose the gut microbiome can influence the health of their host in multiple ways such as helping us metabolize our food, produce vitamins and often most importantly train our innate immune system.
99% of genes isolated from human stool are from bacteria that originate from at least 150 distinct species that primarily belong to the phyla Firmicutes and Bacteroidetes. Fungi are far rarer in the gut than bacteria, but they are also far larger in size. Even in small numbers, emerging research suggests they can exhibit a significant effect. Unlike bacteria, the diversity of intestinal fungi is low, and most sequences can be assigned to a few genera, such as Saccharomyces, Malassezia, and Candida (Enaud et al. 2020 , Willis et al. 2020).