Repertory of eukaryotes (eukaryome) in the human gastrointestinal tract: taxonomy and detection methods

Abstract

Eukaryotes are an important component of the human gut, and their relationship with the human host varies from parasitic to commensal. Understanding the diversity of human intestinal eukaryotes has important significance for human health. In the past few decades, most of the multitudes of techniques that are involved in the diagnosis of the eukaryotic population in the human intestinal tract were confined to pathological and parasitological aspects that mainly rely on traditionally based methods. However, development of culture-independent molecular techniques comprised of direct DNA extraction from faeces followed by sequencing, offer new opportunities to estimate the occurrence of eukaryotes in the human gut by providing data on the entire eukaryotic community, particularly not-yet-cultured or fastidious organisms. Further broad surveys of the eukaryotic communities in the gut based on high throughput tools such as next generation sequencing might lead to uncovering the real diversity of these ubiquitous organisms in the human intestinal tract and discovering the unrecognized roles of these eukaryotes in modulating the host immune system and inducing changes in host gut physiology and ecosystem.

The Host Microbiome Regulates and Maintains Human Health: A Primer and Perspective for Non-Microbiologists

“…In this area, present knowledge is based mostly on their roles as causative agents of disease; few studies have focused on healthy individuals or within a defined illness in a restricted number of individuals (29-33). Until recently, the focus on single disease agents also meant neglecting the reminder of the eukaryotic microbiome (34,35). …”

“…This work is dependent on a greater understanding of the true diversity in the population with the direct sequencing of large sample sets and/or large cohorts such as the Human Microbiome Project, MetaHIT, BioMarks, and future large scale projects (49-51). New resources are now attempting to bridge the different approaches and topics of detection across domains, such as the Human Pan-Microbe Community database (HPMCD) (34). The ability to isolate and sequence single cells offers the opportunity to deepen both our understanding of the genomic composition of taxonomic diversity, as well to put this diversity in context of its environment, microbial partners, biogeography, and host physiologic status both at the local and systemic levels (52-54).…”

Contrasting Strategies: Human Eukaryotic Versus Bacterial Microbiome Research

“…All the main eukaryotic supergroups have been detected in these human‐based investigations, even plants (Hamad et al. ; for discussion, see below). However, fungal microbiome (“mycobiome”) papers comprise more than 80% of the total human eukaryotic microbiome papers.…”

Microbiota, parasites and immunity

“…Two papers in this issue explore the relationship of the microbiome to gastrointestinal nematodes and protozoan infection . A third discusses what we know about the contribution of eukaryotes to the intestinal microbiome .…”

“…The term ‘microbiota’ refers to the population of microbes living among us and yet is rarely considered beyond prokaryotes. In the second paper of this highlight issue, Hamad, Raoult & Bittar consider the repertoire of eukaryotes in the human gastrointestinal tract. Eukaryotes including protozoa, fungi and helminths are known to stably inhabit the intestine, but little is known about their abundance and diversity in different humans or other host populations.…”