Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection

Microbiome

Volumn 3, Issue 1, 2015, Pages

  Weingarden, Alexa ^a,e   González, Antonio ^b   Vázquez Baeza, Yoshiki ^c   Weiss, Sophie ^c   Humphry, Gregory ^b   Berg Lyons, Donna ^b   Knights, Dan ^d,e   Unno, Tatsuya ^e   Bobr, Aleh ^f   Kang, Johnthomas ^e,f   Khoruts, Alexander ^e,f   Knight, Rob ^b,g   Sadowsky, Michael J ^a,e  

^a UNIVERSITY OF MINNESOTA   (United States)

^b UNIVERSITY OF COLORADO   (United States)

^c UCB 450   (United States)

^d University of Minnesota   (United States)

^e Biotechnology Institute   (United States)

^f UNIVERSITY OF MINNESOTA MEDICAL SCHOOL   (United States)

^g HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Short and long term changes in microbiota following FMT

Indexed keywords

ANTIBIOTIC AGENT; RNA 16S;

ARTICLE; CLOSTRIDIUM DIFFICILE INFECTION; COLONOSCOPY; DONOR SELECTION; ENTEROBACTERIALES; FECAL MICROBIOTA TRANSPLANTATION; FECES ANALYSIS; FECES COMPOSITION; FECES MICROFLORA; HIGH THROUGHPUT SEQUENCING; HUMAN; MICROBIAL COMMUNITY; MICROBIAL POPULATION DYNAMICS; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; SEQUENCE ANALYSIS; TRANSPLANTATION;

BACTERIA (MICROORGANISMS); CLOSTRIDIUM DIFFICILE;

EID: 84931355745     PISSN: None     EISSN: 20492618     Source Type: Journal    
DOI: 10.1186/s40168-015-0070-0     Document Type: Article

References (32)

1. Khoruts A, Weingarden AR. Emergence of fecal microbiota transplantation as an approach to repair disrupted microbial gut ecology. Immunology letters 2014, 162:77-81. 10.1016/j.imlet.2014.07.016, 25106113.
2. Khoruts A, Dicksved J, Jansson JK, Sadowsky MJ. Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-associated diarrhea. J Clin Gastroenterol 2010, 44:354-60. 20048681.
3. Shahinas D, Silverman M, Sittler T, Chiu C, Kim P, Allen-Vercoe E, et al. Toward an understanding of changes in diversity associated with fecal microbiome transplantation based on 16S rRNA gene deep sequencing. mBio 2012, 3:e00338-12. 10.1128/mBio.00338-12, 23093385.
4. Hamilton MJ, Weingarden AR, Unno T, Khoruts A, Sadowsky MJ. High-throughput DNA sequence analysis reveals stable engraftment of gut microbiota following transplantation of previously frozen fecal bacteria. Gut Microbes 2013, 4:125-35. 10.4161/gmic.23571, 23333862.
5. van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med 2013, 368:407-15. 10.1056/NEJMoa1205037, 23323867.
6. Weingarden AR, Chen C, Bobr A, Yao D, Lu Y, Nelson VM, et al. Microbiota transplantation restores normal fecal bile acid composition in recurrent Clostridium difficile infection. Am J Physiol Gastrointest Liver Physiol 2014, 306:G310-9. 10.1152/ajpgi.00282.2013, 24284963.
7. Seekatz AM, Aas J, Gessert CE, Rubin TA, Saman DM, Bakken JS, et al. Recovery of the gut microbiome following fecal microbiota transplantation. mBio 2014, 5:e00893-00814. 10.1128/mBio.00893-14, 24939885.
8. Fuentes S, van Nood E, Tims S, Heikamp-de Jong I, ter Braak CJ, Keller JJ, et al. Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection. ISME J 2014, 8:1621-33. 10.1038/ismej.2014.13, 24577353.
9. Song Y, Garg S, Girotra M, Maddox C, von Rosenvinge EC, Dutta A, et al. Microbiota dynamics in patients treated with fecal microbiota transplantation for recurrent Clostridium difficile infection. PLoS One 2013, 8:e81330. 10.1371/journal.pone.0081330, 24303043.
10. Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A 2011, 108(Suppl 1):4554-61. 10.1073/pnas.1000087107, 20847294.
11. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 2014, 505:559-63. 10.1038/nature12820, 24336217.
12. Knights D, Ward TL, McKinlay CE, Miller H, Gonzalez A, McDonald D, et al. Rethinking "enterotypes". Cell Host Microbe 2014, 16:433-7. 10.1016/j.chom.2014.09.013, 25299329.
13. Backhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host-bacterial mutualism in the human intestine. Science 2005, 307:1915-20. 10.1126/science.1104816, 15790844.
14. Lupp C, Robertson ML, Wickham ME, Sekirov I, Champion OL, Gaynor EC, et al. Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae. Cell Host Microbe 2007, 2:119-29. 10.1016/j.chom.2007.06.010, 18005726.
15. Koren O, Goodrich JK, Cullender TC, Spor A, Laitinen K, Backhed HK, et al. Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell 2012, 150:470-80. 10.1016/j.cell.2012.07.008, 22863002.
16. Lozupone CA, Li M, Campbell TB, Flores SC, Linderman D, Gebert MJ, et al. Alterations in the gut microbiota associated with HIV-1 infection. Cell Host Microbe 2013, 14:329-39. 10.1016/j.chom.2013.08.006, 24034618.
17. Kawamoto S, Maruya M, Kato LM, Suda W, Atarashi K, Doi Y, et al. Foxp3(+) T cells regulate immunoglobulin a selection and facilitate diversification of bacterial species responsible for immune homeostasis. Immunity 2014, 41:152-65. 10.1016/j.immuni.2014.05.016, 25017466.
18. Hamilton MJ, Weingarden AR, Sadowsky MJ, Khoruts A. Standardized frozen preparation for transplantation of fecal microbiota for recurrent Clostridium difficile infection. Am J Gastroenterol 2012, 107:761-7. 10.1038/ajg.2011.482, 22290405.
19. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature 2007, 449:804-10. 10.1038/nature06244, 17943116.
20. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 2012, 6:1621-4. 10.1038/ismej.2012.8, 22402401.
21. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010, 7:335-6. 10.1038/nmeth.f.303, 20383131.
22. Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, et al. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods 2013, 10:57-9. 10.1038/nmeth.2276, 23202435.
23. McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 2012, 6:610-8. 10.1038/ismej.2011.139, 22134646.
24. Vazquez-Baeza Y, Pirrung M, Gonzalez A, Knight R. EMPeror: a tool for visualizing high-throughput microbial community data. GigaSci 2013, 2:16. 10.1186/2047-217X-2-16.
25. McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J, Wendel D, et al. The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. GigaSci 2012, 1:7. 10.1186/2047-217X-1-7.
26. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26:2460-1. 10.1093/bioinformatics/btq461, 20709691.
27. Lozupone CA, Stombaugh J, Gonzalez A, Ackermann G, Wendel D, Vazquez-Baeza Y, et al. Meta-analyses of studies of the human microbiota. Genome Res 2013, 23:1704-14. 10.1101/gr.151803.112, 23861384.
28. Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 2005, 71:8228-35. 10.1128/AEM.71.12.8228-8235.2005, 16332807.
29. Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman AL, et al. The long-term stability of the human gut microbiota. Science 2013, 341:1237439. 10.1126/science.1237439, 23828941.
30. Youngster I, Sauk J, Pindar C, Wilson RG, Kaplan JL, Smith MB, et al. Fecal microbiota transplant for relapsing Clostridium difficile infection using a frozen inoculum from unrelated donors: a randomized, open-label, controlled pilot study. Clin Infect Dis 2014, 58:1515-22. 10.1093/cid/ciu135, 24762631.
31. Kelly CR, Ihunnah C, Fischer M, Khoruts A, Surawicz C, Afzali A, et al. Fecal microbiota transplant for treatment of Clostridium difficile infection in immunocompromised patients. Am J Gastroenterol 2014, 109:1065-71. 10.1038/ajg.2014.133, 24890442.
32. Gevers D, Kugathasan S, Denson LA, Vazquez-Baeza Y, Van Treuren W, Ren B, et al. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe 2014, 15:382-92. 10.1016/j.chom.2014.02.005, 24629344.