Stable core virome despite variable microbiome after fecal transfer

Gut Microbes

Volumn 8, Issue 3, 2017, Pages 214-220

  Broecker, Felix ^a,b,c   Russo, Giancarlo ^a   Klumpp, Jochen ^d   Moelling, Karin ^a,b  

^a UNIVERSITY OF ZURICH   (Switzerland)

^b MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^c MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^d ETH ZURICH   (Switzerland)

Author keywords

Clostridium difficile; core virome; fecal microbiota transplantation; long term analysis; microbiome; sequencing; virome

Indexed keywords

CONTIG; DOUBLE STRANDED DNA; RNA 16S;

AMINO ACID SEQUENCE; BACTERIAL FLORA; BACTERIOPHAGE; DYSBIOSIS; FECAL MICROBIOTA TRANSPLANTATION; GENE SEQUENCE; HUMAN; METAGENOMICS; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROBIOME; MYOVIRIDAE; NONHUMAN; OPEN READING FRAME; PODOVIRIDAE; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEOBACTERIA; REVIEW; SIPHOVIRIDAE; SPECIES RICHNESS; VIRUS CHARACTERIZATION; VIRUS GENOME; CLOSTRIDIUM INFECTION; FECES; HOST PATHOGEN INTERACTION; INTESTINE FLORA; ISOLATION AND PURIFICATION; MICROBIOLOGY; VIROLOGY; VIRUS;

CLOSTRIDIUM INFECTIONS; DYSBIOSIS; FECAL MICROBIOTA TRANSPLANTATION; FECES; GASTROINTESTINAL MICROBIOME; HOST-PATHOGEN INTERACTIONS; HUMANS; RNA, RIBOSOMAL, 16S; VIRUSES;

EID: 85020546063     PISSN: 19490976     EISSN: 19490984     Source Type: Journal    
DOI: 10.1080/19490976.2016.1265196     Document Type: Review

References (33)

1. Khoruts A, Sadowsky MJ. Understanding the mechanisms of faecal microbiota transplantation. Nat Rev Gastroenterol Hepatol 2016; 13:508-16; PMID:27329806; http://dx.doi.org/10.1038/nrgastro.2016.98
2. Xu MQ, Cao HL, Wang WQ, Wang S, Cao XC, Yan F, Wang BM. Fecal microbiota transplantation broadening its application beyond intestinal disorders. World J Gastroenterol 2015; 21:102-11; PMID:25574083; http://dx.doi.org/10.3748/wjg.v21.i1.102.
3. Seekatz AM, Young VB. Clostridium difficile and the microbiota. J Clin Invest 2014; 124:4182-9; PMID:25036699; http://dx.doi.org/10.1172/JCI72336
4. Broecker F, Klumpp J, Moelling K. Long-term microbiota and virome in a Zürich patient after fecal transplantation against Clostridium difficile infection. Ann N Y Acad Sci 2016; 1372:29-41; PMID:27286042; http://dx.doi.org/10.1111/nyas.13100
5. Savage DC., Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol 1977; 31:107-33; PMID:334036.
6. Scarpellini E, Ianiro G, Attili F, Bassanelli C, De Santis A, Gasbarrini A. The human gut microbiota and virome:Potential therapeutic implications. Dig Liver Dis 2015; 47:1007-12; PMID:26257129; http://dx.doi.org/10.1016/j.dld.2015.07.008
7. Dalmasso M, Hill C, Ross RP. Exploiting gut bacteriophages for human health. Trends Microbiol 2014; 22:399-405; PMID:24656964; http://dx.doi.org/10.1016/j.tim.2014.02.010
8. Chehoud C, Dryga A, Hwang Y, Nagy-Szakal D, Hollister EB, Luna RA, Versalovic J, Kellermayer R, Bushman FD. Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation. MBio 2016; 7:e00322; PMID:27025251; http://dx.doi.org/10.1128/mBio.00322-16.
9. Norman JM, Handley SA, Baldridge MT, Droit L, Liu CY, Keller BC, Kambal A, Monaco CL, Zhao G, Fleshner P, et al. Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell 2015; 160:447-60; PMID:25619688; http://dx.doi.org/10.1016/j.cell.2015.01.002
10. Lepage P, Colombet J, Marteau P, Sime-Ngando T, Doré, J, Leclerc M. Dysbiosis in inflammatory bowel disease:a role for bacteriophages? Gut 2008; 57:424-5; PMID:18268057; http://dx.doi.org/10.1136/gut.2007.134668
11. Minot S, Sinha R, Chen J, Li H, Keilbaugh SA, Wu GD, Lewis JD, Bushman FD. The human gut virome:inter-individual variation and dynamic response to diet. Genome Res 2011; 21:1616-25; PMID:21880779; http://dx.doi.org/10.1101/gr.122705.111
12. Broecker F, Kube M, Klumpp J, Schuppler M, Biedermann L, Hecht J, Hombach M, Keller PM, Rogler G, Moelling K. Analysis of the intestinal microbiome of a recovered Clostridium difficile patient after fecal transplantation. Digestion 2013; 88:243-51; PMID:24335204; http://dx.doi.org/10.1159/000355955
13. Lupp C, Robertson ML, Wickham ME, Sekirov I, Champion OL, Gaynor EC, Finlay BB. Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae. Cell Host Microbe 2007; 2:204; PMID:18030708.
14. Benson DA, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res 2015; 43(Database issue):D30-5; PMID:25414350; http://dx.doi.org/10.1093/nar/gku1216
15. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403-10; PMID:2231712
16. Miller ES, Kutter E, Mosig G, Arisaka F, Kunisawa T, Rüger W. Bacteriophage T4 genome. Microbiol Mol Biol Rev 2003; 67:86-156; PMID:12626685
17. Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, et al. The Pfam protein families database:towards a more sustainable future. Nucleic Acids Res 2016; 44(D1):D279-85; PMID:26673716; http://dx.doi.org/10.1093/nar/gkv1344
18. Meinicke P. UProC:tools for ultra-fast protein domain classification. Bioinformatics 2015; 31:1382-8; PMID:25540185; http://dx.doi.org/10.1093/bioinformatics/btu843
19. Ackermann HW. 5500 Phages examined in the electron microscope. Arch Virol 2007; 152:227-243; PMID:17051420; http://dx.doi.org/10.1007/s00705-006-0849-1
20. Minot S, Bryson A, Chehoud C, Wu GD, Lewis JD, Bushman FD. Rapid evolution of the human gut virome. Proc Natl Acad Sci U S A 2013; 110:12450-5; PMID:23836644; http://dx.doi.org/10.1073/pnas.1300833110
21. Dutilh BE, Cassman N, McNair K, Sanchez SE, Silva GG, Boling L, Barr JJ, Speth DR, Seguritan V, Aziz RK, et al. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat Commun 2014; 5:4498; PMID:25058116; http://dx.doi.org/10.1038/ncomms5498
22. Dutilh BE., Metagenomic ventures into outer sequence space. Bacteriophage 2014; 4:e979664; PMID:26458273; http://dx.doi.org/10.4161/21597081.2014.979664
23. Mokili JL, Rohwer F, Dutilh BE. Metagenomics and future perspectives in virus discovery. Curr Opin Virol 2012; 2:63-77; PMID:22440968; http://dx.doi.org/10.1016/j.coviro.2011.12.004
24. Ogilvie LA, Caplin J, Dedi C, Diston D, Cheek E, Bowler L, Taylor H, Ebdon J, Jones BV. Comparative (meta)genomic analysis and ecological profiling of human gut-specific bacteriophage ϕB124-14. PLoS One 2012; 7:e35053; PMID:22558115; http://dx.doi.org/10.1371/journal.pone.0035053
25. Smith DP, Peay KG. Sequence depth, not PCR replication, improves ecological inference from next generation DNA sequencing. PLoS One 2014; 9:e90234; PMID:24587293; http://dx.doi.org/10.1371/journal.pone.0090234
26. Brum JR, Ignacio-Espinoza JC, Roux S, Doulcier G, Acinas SG, Alberti A, Chaffron S, Cruaud C, de Vargas C, Gasol JM, et al. Ocean plankton. Patterns and ecological drivers of ocean viral communities. Science 2015; 348:1261498; PMID:25999515; http://dx.doi.org/10.1126/science.1261498
27. Breitbart M, Rohwer F. Here a virus, there a virus, everywhere the same virus? Trends Microbiol 2005; 13:278-84; PMID:15936660; http://dx.doi.org/10.1016/j.tim.2005.04.003
28. Ignacio-Espinoza JC, Solonenko SA, Sullivan MB. The global virome:not as big as we thought? Curr Opin Virol 2013; 3:566-71; PMID:23896279; http://dx.doi.org/10.1016/j.coviro.2013.07.004
29. Abeles SR, Ly M, Santiago-Rodriguez TM, Pride DT. Effects of Long Term Antibiotic Therapy on Human Oral and Fecal Viromes. PLoS One 2015; 10:e0134941; PMID:26309137; http://dx.doi.org/10.1371/journal.pone.0134941
30. Quesada-Gómez C, López-Ureña D, Acuña-Amador L, Villalobos-Zúñiga M, Du T, Freire R, Guzmán-Verri C, del Mar Gamboa-Coronado M, Lawley TD, Moreno E, et al. Emergence of an outbreak-associated Clostridium difficile variant with increased virulence. J Clin Microbiol 2015; 53:1216-26; PMID:25653402; http://dx.doi.org/10.1128/JCM.03058-14
31. Yadav H, Jain S, Nagpal R, Marotta F. Increased fecal viral content associated with obesity in mice. World J Diabetes 2016; 7:316-20; PMID:27555892; http://dx.doi.org/10.4239/wjd.v7.i15.316
32. Barr JJ, Auro R, Furlan M, Whiteson KL, Erb ML, Pogliano J, Stotland A, Wolkowicz R, Cutting AS, Doran KS, et al. Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc Natl Acad Sci U S A 2013; 110:10771-6; PMID:23690590; http://dx.doi.org/10.1073/pnas.1305923110
33. Hall RJ, Draper JL, Nielsen FG, Dutilh BE. Beyond research:a primer for considerations on using viral metagenomics in the field and clinic. Front Microbiol 2015; 6:224; PMID:25859244; http://dx.doi.org/10.3389/fmicb.2015.00224