Gut microbiota refers to a complex network of microbes, which exerts a marked influenceon the host’s health. It is composed of bacteria, fungi, viruses, and helminths. Bacteria, or collectively,the bacteriome, comprises a significant proportion of the well-characterized microbiome. However,the other communities referred to as ‘dark matter’ of microbiomes such as viruses (virome), fungi(mycobiome), archaea (archaeome), and helminths have not been completely elucidated. Developmentof new and improved metagenomics methods has allowed the identification of complete genomesfrom the genetic material in the human gut, opening new perspectives on the understanding ofthe gut microbiome composition, their importance, and potential clinical applications. Here, wereview the recent evidence on the viruses, fungi, archaea, and helminths found in the mammalian gut,detailing their interactions with the resident bacterial microbiota and the host, to explore the potentialimpact of the microbiome on host’s health. The role of fecal virome transplantations, pre-, pro-, andsyn-biotic interventions in modulating the microbiome and their related concerns are also discussed
