title: Healthy human gut phageome.
abstract: The role of bacteriophages in influencing the structure and function of the healthy human gut microbiome is unknown. With few exceptions, previous studies have found a high level of heterogeneity in bacteriophages from healthy individuals. To better estimate and identify the shared phageome of humans, we analyzed a deep DNA sequence dataset of active bacteriophages and available metagenomic datasets of the gut bacteriophage community from healthy individuals. We found 23 shared bacteriophages in more than one-half of 64 healthy individuals from around the world. These shared bacteriophages were found in a significantly smaller percentage of individuals with gastrointestinal/irritable bowel disease. A network analysis identified 44 bacteriophage groups of which 9 (20%) were shared in more than one-half of all 64 individuals. These results provide strong evidence of a healthy gut phageome (HGP) in humans. The bacteriophage community in the human gut is a mixture of three classes: a set of core bacteriophages shared among more than one-half of all people, a common set of bacteriophages found in 20-50% of individuals, and a set of bacteriophages that are either rarely shared or unique to a person. We propose that the core and common bacteriophage communities are globally distributed and comprise the HGP, which plays an important role in maintaining gut microbiome structure/function and thereby contributes significantly to human health.
authors: Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717;
authors: Pilar
authors: P
authors: Manrique
authors: Department of Chemistry and Biochemistry Research, Montana State University, Bozeman, MT 59717;
authors: Benjamin
authors: B
authors: Bolduc
authors: Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717;
authors: Seth T
authors: ST
authors: Walk
authors: Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands;
authors: John
authors: J
authors: van der Oost
authors: Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands; Department of Bacteriology & Immunology, University of Helsinki, Haartmaninkatu 3, 00290, Finland;
authors: Willem M
authors: WM
authors: de Vos
authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717 myoung@montana.edu.
authors: Mark J
authors: MJ
authors: Young
mesh_terms: D001435:Bacteriophages / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D019295:Computational Biology; D005243:Feces / Q000382:microbiology; D000069196:Gastrointestinal Microbiome / Q000235:genetics*; D041981:Gastrointestinal Tract / Q000382:microbiology; D006801:Humans; D015212:Inflammatory Bowel Diseases / Q000235:genetics / Q000382:microbiology*; D056186:Metagenomics; D064307:Microbiota / Q000235:genetics
keywords: gut microbiome bacteriophage; gut microbiome viruses; human gut viral metagenome; shared microbiome viruses