Javier del Campo, David Bass and Patrick J.Keeling,
Awareness of the role of microbes that live in humans and other animals has increased recently with the rise of the microbiome field. However, this interest has focused on bacteria and little is known about other microbes. Among those that have been ignored are the microbial eukaryotes, microscopic single cell organisms with a nucleus that are mostly familiar to us and the scientific community for being parasites, such as the malaria agent or the brain eating amoeba. Despite that notoriety, microbial eukaryotes are widespread and are known to be common inhabitants of animals, and most of the times are harmless. Nonetheless, microbial eukaryotes have an impact on the biology and lifestyle of the animals that host them, as well as on the populations of other microbes that live there such as bacteria. Beyond being parasites, microbial eukaryotes have many different roles in animals and very often positive or important ones, for example: they directly interact with the immune system in humans, they participate in cellulose degradation in termites and cockroaches, and they have an essential role in the survival of reef-building corals by providing them with food. Microbial eukaryotes have impacts at many levels, both positive and negative, from human health to conservation and aquaculture. Therefore, it is crucial to have a better understanding of their diversity and roles and we need to develop novel methodologies that can help us to increase and improve our knowledge of microbial eukaryotes living inside animals.