Few data exist on the role of intestinal bacteriophages in IBD. New findings reveal alterations of the phage population and elevation of phages that infect microbiota with pathogenic potential (pathobionts) in a mouse model of ulcerative colitis. Furthermore, the phageome of mice overlapped with that of humans in both healthy and diseased states.
In their study, Duerkop et al. examined the faecal metagenome of mice with chronic colonic inflammation induced by adoptive T cell transfer. Using a sequence-independent approach to identify virus contigs, the team created a virus-like particle (VLP) database of 1,104 contigs. Following induction of colitis, the phageome composition changed, resulting in a decrease in contig abundances and diversity after 42 days. Mapping VLP reads showed that phages of the Caudovirales families and those that infect Enterobacteriaceae and Enterococci were enriched in mice with colitis at day 42. Abundance of some phages correlated with that of their host bacteria, indicating a link of phages and pathobionts during IBD.
The team also mapped phage DNA sequencing reads from mice to phage contigs from healthy individuals and patients with IBD. Comparative analysis of contig read coverage from healthy individuals with those from healthy or colitic mice showed an overlap of 25%. Fewer contigs from healthy humans were mapped to those from mice with colitis and some mapped to healthy animals only. Contigs from patients with IBD had a 33% overlap with reads from healthy or colitic mice. Contig read coverage was better in mice with colitis than in healthy animals and some matched with those from diseased mice only. These data indicate that mouse colitis models can be useful tools to study phage–bacterial interactions.
Duerkop, B. A. et al. Murine colitis reveals a disease-associated bacteriophage community. Nat. Microbiol. https://doi.org/10.1038/s41564-018-0210-y (2018)
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Thoma, C. Bacteriophage virome in IBD. Nat Rev Gastroenterol Hepatol 15, 520 (2018). https://doi.org/10.1038/s41575-018-0056-z