Are Human Intestinal Eukaryotes Beneficial or Commensals?

Since the advent of microbiology, it has been well known that each human body hosts a multitude of microbes. The magnitude of our microbial system is best reflected by the widely discussed ratio of one human cell to ten microbes. Indeed, humans and other mammals live in a consortium composed of vast arrays of viruses (these are typically called the virome), archaea and bacteria (i.e., the microbiome), along with fungi and other uniand multicellular eukaryotes (protists and helminths, respectively) historically thought of as “parasites.” It was the advent of next generation sequencing (NGS) that first allowed deeper insight not only into the composition of this “microbial zoo” but also its dynamics in relation to age, diet, health, sex, and geographic location of the host. Attention has focused primarily on the bacterial microbiome, which constitutes the most abundant and diverse segment of the human intestinal ecosystem. However, we argue that eukaryotes play important, but largely unrecognized roles and that there is much to gain by turning our attention to eukaryotic members of the gut ecosystem.