title: 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.
authors: Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri.
authors: Jason M
authors: JM
authors: Norman
authors: Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri.
authors: Scott A
authors: SA
authors: Handley
authors: Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri. Electronic address: virgin@wustl.edu.
authors: Herbert W
authors: HW
authors: Virgin
mesh_terms: D000818:Animals; D004198:Disease Susceptibility; D005658:Fungi / Q000145:classification / Q000235:genetics*; D005767:Gastrointestinal Diseases / Q000382:microbiology / Q000821:virology; D015966:Gene Expression Regulation, Fungal; D015967:Gene Expression Regulation, Viral; D006801:Humans; D007422:Intestines / Q000382:microbiology* / Q000821:virology*; D054892:Metagenome; D056186:Metagenomics / Q000379:methods; D064307:Microbiota; D014780:Viruses / Q000145:classification / Q000235:genetics*
keywords: Metagenomics; Mycobiome; Virome