Gut mucosal virome alterations in ulcerative colitis

Gut

Volumn 68, Issue 7, 2019, Pages 1169-1179

  Zuo, Tao ^a,b   Lu, Xiao Juan ^c   Zhang, Yu ^d   Cheung, Chun Pan ^a,b   Lam, Siu ^b   Zhang, Fen ^a,b   Tang, Whitney ^a   Ching, Jessica Y L ^a   Zhao, Risheng ^a,b   Chan, Paul K S ^a,b   Sung, Joseph J Y ^a,b   Yu, Jun ^a,b   Chan, Francis K L ^a   Cao, Qian ^d,e   Sheng, Jian Qiu ^c   Ng, Siew C ^a,b  

^a Prince of Wales Hospital   (Hong Kong)

^b CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

^c CHINESE PLA GENERAL HOSPITAL   (China)

^d ZHEJIANG UNIVERSITY   (China)

^e ZHEJIANG UNIVERSITY   (China)

Author keywords

Bacteria; Gut mucosa; Ulcerative colitis; Virome; Virome metacommunity

Indexed keywords

RNA 16S;

ALGORITHM; ARTICLE; BACTERIOPHAGE; CAUDOVIRALES; CHINA; CONTROLLED STUDY; DISEASE ASSOCIATION; ENTERITIS; ENTEROBACTERIA PHAGE; ESCHERICHIA PHAGE; GENE SEQUENCE; HUMAN; INTESTINE; MAJOR CLINICAL STUDY; METAGENOMICS; MICROBIAL COMMUNITY; MUCOSA; NONHUMAN; PATHOGENICITY; PRIORITY JOURNAL; RNA SEQUENCE; ULCERATIVE COLITIS; VIROME; VIRUS; VIRUS IDENTIFICATION; ADULT; CASE CONTROL STUDY; DYSBIOSIS; FEMALE; INTESTINE FLORA; INTESTINE MUCOSA; MALE; PATHOLOGY; RECTUM; VIROLOGY;

ADULT; CASE-CONTROL STUDIES; CHINA; COLITIS, ULCERATIVE; DYSBIOSIS; FEMALE; GASTROINTESTINAL MICROBIOME; HUMANS; INTESTINAL MUCOSA; MALE; RECTUM;

EID: 85062658723     PISSN: 00175749     EISSN: 14683288     Source Type: Journal    
DOI: 10.1136/gutjnl-2018-318131     Document Type: Article

References (55)

1. Kaistha A, Levine J. Inflammatory bowel disease: The classic gastrointestinal autoimmune disease. Curr Probl Pediatr Adolesc Health Care 2014;44:328-34.
2. Zuo T, Kamm MA, Colombel JF, et al. Urbanization and the gut microbiota in health and inflammatory bowel disease. Nat Rev Gastroenterol Hepatol 2018;15:440-52.
3. N g SC, Shi HY, Hamidi N, et al. Worldwide incidence and prevalence of inflammatory bowel disease in the 21st century: A systematic review of population-based studies. Lancet 2018;390.
4. Podolsky DK. Inflammatory bowel disease (1). N Engl J Med 1991;325:928-37.
5. Subramanian S, Blanton LV, Frese SA, et al. Cultivating healthy growth and nutrition through the gut microbiota. Cell 2015;161:36-48.
6. Zhao L, Zhang F, Ding X, et al. Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes. Science 2018;359:1151-6.
7. Marchesi JR, Adams DH, Fava F, et al. The gut microbiota and host health: A new clinical frontier. Gut 2016;65:330-9.
8. Subramanian S, Huq S, Yatsunenko T, et al. Persistent gut microbiota immaturity in malnourished Bangladeshi children. Nature 2014;510:417-21.
9. Zuo T, Ng SC. The Gut Microbiota in the Pathogenesis and Therapeutics of Inflammatory Bowel Disease. Front Microbiol 2018;9.
10. C adwell K. The virome in host health and disease. Immunity 2015;42:805-13.
11. Virgin HW. The virome in mammalian physiology and disease. Cell 2014;157:142-50.
12. Minot S, Bryson A, Chehoud C, et al. Rapid evolution of the human gut virome. Proc Natl Acad Sci USA 2013;110:12450-5.
13. Minot S, Grunberg S, Wu GD, Gd W, et al. Hypervariable loci in the human gut virome. Proc Natl Acad Sci USA 2012;109:3962-6.
14. R eyes A, Haynes M, Hanson N, et al. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 2010;466:334-8.
15. Waller AS, Yamada T, Kristensen DM, et al. Classification and quantification of bacteriophage taxa in human gut metagenomes. Isme J 2014;8:1391-402.
16. De Sordi L, Khanna V, Debarbieux L. The gut microbiota facilitates drifts in the genetic diversity and infectivity of bacterial viruses. Cell Host Microbe 2017;22:801-8.
17. N orman JM, Handley SA, Baldridge MT, et al. Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell 2015;160:447-60.
18. Duerkop BA, Kleiner M, Paez-Espino D, et al. Murine colitis reveals a diseaseassociated bacteriophage community. Nat Microbiol 2018;3:1023-31.
19. Yatsunenko T, Rey FE, Manary MJ, et al. Human gut microbiome viewed across age and geography. Nature 2012;486:222-7.
20. He Y, Wu W, Zheng HM, et al. Regional variation limits applications of healthy gut microbiome reference ranges and disease models. Nat Med 2018;24:1532-5.
21. Wessner DR. Discovery of the giant mimivirus. Nature Education 2010;3:61.
22. L a Scola B, Marrie TJ, Auffray JP, et al. Mimivirus in pneumonia patients. Emerg Infect Dis 2005;11:449-52.
23. L ong MD, Martin C, Sandler RS, et al. Increased risk of pneumonia among patients with inflammatory bowel disease. Am J Gastroenterol 2013;108:240-8.
24. A rumugam M, Raes J, Pelletier E, et al. Enterotypes of the human gut microbiome. Nature 2011;473:174-80.
25. C ostea PI, Hildebrand F, Arumugam M, et al. Enterotypes in the landscape of gut microbial community composition. Nat Microbiol 2018;3:8-16.
26. Manrique P, Bolduc B, Walk ST, et al. Healthy human gut phageome. Proc Natl Acad Sci USA 2016;113:10400-5.
27. Diard M, Bakkeren E, Cornuault JK, et al. Inflammation boosts bacteriophage transfer between Salmonella spp. Science 2017;355:1211-5.
28. Zuo T, Wong SH, Lam K, et al. Bacteriophage transfer during faecal microbiota transplantation in Clostridium difficile infection is associated with treatment outcome. Gut 2018;67:634-43.
29. C onceicaõ-Neto N, Deboutte W, Dierckx T, et al. Low eukaryotic viral richness is associated with faecal microbiota transplantation success in patients with UC. Gut 2018;67:1558-9.
30. Mirzaei MK, Maurice CF. Ménage à trois in the human gut: Interactions between host, bacteria and phages. Nat Rev Microbiol 2017;15:397-408.
31. Brüssow H, Canchaya C, Hardt WD. Phages and the evolution of bacterial pathogens: From genomic rearrangements to lysogenic conversion. Microbiol Mol Biol Rev 2004;68:560-602.
32. R eyes A, Wu M, McNulty NP, et al. Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut. Proc Natl Acad Sci USA 2013;110:20236-41.
33. Zhang Y, LeJeune JT. Transduction of bla(CMY-2), tet(A), tet(B) from Salmonella enterica subspecies enterica serovar Heidelberg to S. Typhimurium. Vet Microbiol 2008;129:418-25.
34. Maiques E, Ubeda C, Campoy S, et al. beta-lactam antibiotics induce the SOS response and horizontal transfer of virulence factors in Staphylococcus aureus. J Bacteriol 2006;188:2726-9.
35. Jerlström Hultqvist J, Warsi O, Söderholm A, et al. A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function. Nat Ecol Evol 2018;2:1321-30.
36. Kim MS, Bae JW. Spatial disturbances in altered mucosal and luminal gut viromes of diet-induced obese mice. Environ Microbiol 2016;18:1498-510.
37. Minot S, Sinha R, Chen J, et al. The human gut virome: Inter-individual variation and dynamic response to diet. Genome Res 2011;21:1616-25.
38. L im ES, Zhou Y, Zhao G, et al. Early life dynamics of the human gut virome and bacterial microbiome in infants. Nat Med 2015;21:1228-34.
39. Ogilvie LA, Jones BV. The human gut virome: A multifaceted majority. Front Microbiol 2015;6.
40. R eese TA, Bi K, Kambal A, et al. Sequential infection with common pathogens promotes human-like immune gene expression and altered vaccine response. Cell Host Microbe 2016;19:713-9.
41. T ao L, Reese TA. Making mouse models that reflect human immune responses. Trends Immunol 2017;38:181-93.
42. Beura LK, Hamilton SE, Bi K, et al. Normalizing the environment recapitulates adult human immune traits in laboratory mice. Nature 2016;532:512-16.
43. G ensollen T, Iyer SS, Kasper DL, et al. How colonization by microbiota in early life shapes the immune system. Science 2016;352:539-44.
44. Hayashi T, Hasegawa K, Ohta A, et al. Reduction of serum interferon (IFN)-gamma concentration and lupus development in NZBxNZWF(1)mice by lactic dehydrogenase virus infection. J Comp Pathol 2001;125:285-91.
45. Hayashi T, Noguchi Y, Kameyama Y. Suppression of development of anti-nuclear antibody and glomerulonephritis in NZB x NZWF1 mice by persistent infection with lactic dehydrogenase virus: Possible involvement of superoxide anion as a progressive effector. Int J Exp Pathol 1993;74:553.
46. I nada T, Mims CA. Infection of mice with lactic dehydrogenase virus prevents development of experimental allergic encephalomyelitis. J Neuroimmunol 1986;11:53-6.
47. N i J, Wu GD, Albenberg L, et al. Gut microbiota and IBD: Causation or correlation Nat Rev Gastroenterol Hepatol 2017;14.
48. L epage P, Häsler R, Spehlmann ME, et al. Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. Gastroenterology 2011;141:227-36.
49. Walker AW, Sanderson JD, Churcher C, et al. High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease. BMC Microbiol 2011;11:7.
50. Hansen R, Reiff C, Russell RK, et al. Colonic mucosal bacterial diversity of de novo extensive paediatric ulcerative colitis by next-generation sequencing. Gut 2011;60:A146-7.
51. Shah R, Cope JL, Nagy-Szakal D, et al. Composition and function of the pediatric colonic mucosal microbiome in untreated patients with ulcerative colitis. Gut Microbes 2016;7:384-96.
52. Sepehri S, Kotlowski R, Bernstein CN, et al. Microbial diversity of inflamed and noninflamed gut biopsy tissues in inflammatory bowel disease. Inflamm Bowel Dis 2007;13:675-83.
53. Forbes JD, Van Domselaar G, Bernstein CN. Microbiome survey of the inflamed and noninflamed gut at different compartments within the gastrointestinal tract of inflammatory bowel disease patients. Inflamm Bowel Dis 2016;22:817-25.
54. Yilmaz B, Juillerat P, ∅yås O, et al. Microbial network disturbances in relapsing refractory Crohn's disease. Nat Med 2019;25:323-36.
55. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012;9:357-9.