Gut virome: New key players in the pathogenesis of inflammatory bowel disease

Table 1 Overview of the alteration in the gut phage ecosystem in patients with inflammatory bowel disease and animal models

Disease	No. of patients included in the study	Sample type	Interpretation of result	Ref.
CD	19	Biopsies	CD patients had considerably more VLPs than normal controls	[116]
CD	6	Ileal biopsies, colonic biopsies, gut wash samples	A significant excess of phages in biopsies and gut washes, Bacteroides phages (B10-8 and B124-14) were most predominant, and the composition of Mycobacterium phage differed between CD patients and controls in ileum tissue samples	[117]
CD	20	Stool samples, biopsies	Phage counts in stools were three times greater than in biopsies, CD patients had higher levels of Alteromonadales and Clostridiales phages	[114]
IBD	10	Colonic biopsies	Phages make up the bulk of the DNA viruses within the virome, about 50% of the phages were connected to the bacterial strains found in the colon specimens	[118]
UC and CD	(42 for UC) and (18 for CD)	Stool samples	Patients with IBD had a considerable increase in Caudovirales phages, and virome community in UC and CD patients were disease and cohort-specific	[31]
UC and CD	(5 pt. for UC) and (7 pt. for CD)	Stool samples	Caudovirales phage proportions in patients with IBD and normal controls were greater than Microviridae phage proportions. However, the Caudovirales phages were more prominent in CD than UC but not in controls. On the other hand, control persons had a larger diversity of Microviridae phages than CD patients, but not UC patients	[119]
UC	97	Rectal mucosa	Caudovirales phages were more abundant in UC cases compared to normal controls, but with lower richness, diversity, and balance, and UC patients’ mucosa had much more Enterobacteria and Escherichia phages than healthy controls	[113]
UC and CD	(42 pt. for UC) and (27 pt. for CD)	Stool samples	A stable virulent core virome is associated with a healthy gut and switched from a lysogenic to lytic cycle in temperate phages may be related to CD	[112]
CD	5	proximal and distal colonic wash samples	Considerable interpatient diversity and little, but significant, intrapatient variations between various regions	[120]
(VEO) IB	45	Stool samples	No detectable difference in the overall number of VLPs among VEO-IBD patients and normal controls, but the Caudovirales vs Microviridae ratio is larger in the VEO-IBD patients than in the controls	[121]
UC and CD	(38 pt. for UC) and (65 pt. for CD)	Stool samples	The prevalence of phages varied among patients with IBD and normal controls as well as the components of the temperate phage population were extremely distinctive to each individual. Moreover, compared to normal controls, active UC patients had a higher prevalence of temperate phages infecting Bacteroides thetaiotaomicron and Bacteroides uniformis	[122]
IBD	455	Stool samples	crAss-like phageome of the human gut has remained largely stable for 4 yr and individuals with IBD had lower levels of gut crAss-like phages	[65]
CD	19	Stool samples	CD patients had a considerably higher prevalence of crAss-like phages as well as no difference in the richness and evenness of the gut virome among CD patients and controls, but there was a substantial difference in the virome’s overall structure	[123]
Colitis	3 from C57BL/6 mice	Stool samples	The intestinal phage populations were altered and shifted to dysbiosis in the mice model, and a decrease in the variety of the phage community, such as Clostridiales phages during colitis	[124]

CD: Crohn’s disease; IBD: Inflammatory bowel disease; UC: Ulcerative colitis; VEO: Very early onset; VLPs: Virus-like particles.