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Nat Microbiol. 2018 Sep;3(9):1023-1031. doi: 10.1038/s41564-018-0210-y. Epub 2018 Jul 23.

Murine colitis reveals a disease-associated bacteriophage community.

Author information

1
Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA. breck.duerkop@ucdenver.edu.
2
Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA. manuel_kleiner@ncsu.edu.
3
Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.
4
Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
5
Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
6
Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA. lora.hooper@utsouthwestern.edu.
7
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA. lora.hooper@utsouthwestern.edu.

Abstract

The dysregulation of intestinal microbial communities is associated with inflammatory bowel diseases (IBD). Studies aimed at understanding the contribution of the microbiota to inflammatory diseases have primarily focused on bacteria, yet the intestine harbours a viral component dominated by prokaryotic viruses known as bacteriophages (phages). Phage numbers are elevated at the intestinal mucosal surface and phages increase in abundance during IBD, suggesting that phages play an unidentified role in IBD. We used a sequence-independent approach for the selection of viral contigs and then applied quantitative metagenomics to study intestinal phages in a mouse model of colitis. We discovered that during colitis the intestinal phage population is altered and transitions from an ordered state to a stochastic dysbiosis. We identified phages specific to pathobiotic hosts associated with intestinal disease, whose abundances are altered during colitis. Additionally, phage populations in healthy and diseased mice overlapped with phages from healthy humans and humans with IBD. Our findings indicate that intestinal phage communities are altered during inflammatory disease, establishing a platform for investigating phage involvement in IBD.

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