Microbial Eukaryotes: a Missing Link in Gut Microbiome Studies

Abstract

Human-associated microbial communities include prokaryotic and eukaryotic organisms across high-level clades of the tree of life. While advances in high-throughput sequencing technology allow for the study of diverse lineages, the vast majority of studies are limited to bacteria, and very little is known on how eukaryote microbes fit in the overall microbial ecology of the human gut. As recent studies consider eukaryotes in their surveys, it is becoming increasingly clear that eukaryotes play important ecological roles in the microbiome as well as in host health. In this perspective, we discuss new evidence on eukaryotes as fundamental species of the human gut and emphasize that future microbiome studies should characterize the multitrophic interactions between microeukaryotes, other microorganisms, and the host.

Keywords: Blastocystis; bacteria; eukaryotes; fungi; gut microbiome; immune system; interkingdom interactions; microbial ecology; prokaryotes; protozoan.

FIG 1

Proposed ecological role of Blastocystis sp. in the gut microbiota. In the absence of Blastocystis (left panel), a strong bacterial competitor dominates the community, which limits species richness and community evenness; when present (right panel), its predation on abundant bacterial taxa lowers the competition for nutrients and space, which leads to an increase in bacterial richness and community evenness. Without accounting for Blastocystis sp., the scenario in the right panel could be attributed to another variable.