Abstract
Free-living amoebae (FLA) are common in the environment, and some of them are pathogenic to animals and humans. The presence of FLA in the lower gastrointestinal tract and feces of vertebrates, and their role in the host organism, is a young field that requires further investigation. It is particularly important to determine the route of infection and the nature of interactions between FLAs and the host, as well as with other microorganisms constituting the gut microbiome. To this end, appropriate methods are needed. Earlier studies employed traditional methods, such as culture and microscopic observation, whereas more recent studies focus on molecular methods. This study determines the global prevalence and composition, genetic diversity, and taxonomic classification of FLA in the intestines and feces of vertebrates. It also reviews the methods used in the analyzed papers for FLA detection, identification, and pathogenicity assessment.