Kingdom-agnostic metagenomics and the importance of complete characterization of enteric microbial communities

Abstract

Advanced sequencing techniques have shown that bacteria are not the only complex and important microbes in the human intestine. Nonbacterial organisms, particularly the virome and the mycobiome, are important regulators of intestinal immunity and inflammation. The virome is mucosal and systemic; it can alter the host response to bacteria and interact with host genes and bacteria to contribute to disease pathogenesis. The human mycobiome is also complex and can contribute to intestinal inflammation. We review what has recently been learned about the nonbacterial and nonarchaeal microbes in the gastrointestinal tract, discussing their potential effects on health and disease and analytical approaches for their study. Studies of associations between the microbiome and intestinal pathology should incorporate kingdom-agnostic approaches if we are to fully understand intestinal health and disease.

Keywords: Metagenomics; Mycobiome; Virome.

Jason M. Norman

Scott A. Handley

Herbert W. Virgin

Figure 1

Model of trans-kingdom interactions between microbial taxa and the intestine. Trans-kingdom microbial interactions and environmental factors influence the composition of the intestinal flora. These microbes and microbial products interact with healthy hosts and those with disease and can gain access to new tissues and organs when the integrity of the epithelial barrier is compromised. Shifts in flora would lead to changes in host-microbe interactions.

Figure 2

Simplified taxonomic overview of meiofauna in the human GI tract. An overview of the common meiofauna present in the human intestine. Opisthokonta include animals, fungi, and many microbial eukaryotic organisms; Amoebozoa are unicellular amoeboid protozoa; Fornicata are unicellular flagellated protozoa; Alveolata contain eukaryotes such as the apicomplexa, ciliates, and dinoflagellates; and Stramenopiles are a major line of eukaryotes containing a wide range of species from algae to diatoms.