Bacterial viability in faecal transplants: Which bacteria survive?

EBioMedicine

Volumn 41, Issue , 2019, Pages 509-516

  Papanicolas, Lito E ^a,b,c   Choo, Jocelyn M ^a,b   Wang, Yanan ^a,b   Leong, Lex E X ^a,b   Costello, Samuel P ^d   Gordon, David L ^e   Wesselingh, Steve L ^a,b   Rogers, Geraint B ^a,b  

^a SOUTH AUSTRALIAN HEALTH AND MEDICAL RESEARCH INSTITUTE   (Australia)

^b FLINDERS UNIVERSITY   (Australia)

^c ROYAL ADELAIDE HOSPITAL   (Australia)

^d UNIVERSITY OF ADELAIDE   (Australia)

^e FLINDERS UNIVERSITY   (Australia)

Author keywords

Bacterial viability; Fecal microbiota transplantation; Propidium monoazide; qPCR

Indexed keywords

RNA 16S; ACETIC ACID; BACTERIAL PROTEIN; BUTYRIC ACID DERIVATIVE; BUTYRYL-COA ACETOACETATE COA TRANSFERASE; COENZYME A TRANSFERASE; VOLATILE FATTY ACID;

ABNORMAL FECES COMPOSITION; ADULT; ALISTIPES; ANAEROBIC FERMENTATION; ANAEROSTIPES; ARTICLE; BACTERIAL COUNT; BACTERIAL MICROBIOME; BACTERIAL SURVIVAL; BACTERIAL VIABILITY; BACTEROIDES; BIFIDOBACTERIUM; CONTROLLED STUDY; DNA ISOLATION; ESCHERICHIA COLI; EUBACTERIUM HALLII; EUBACTERIUM RECTALE; EULONCHUS HALLI; FAECALIBACTERIUM; FAECALIBACTERIUM PRAUSNITZII; FATTY ACID ANALYSIS; FECAL MICROBIOTA TRANSPLANTATION; FECES ANALYSIS; FECES MICROFLORA; FEMALE; GENE SEQUENCE; HUMAN; HUMAN EXPERIMENT; INFLAMMATION; LACHNOSPIRACEAE; LIGHT EXPOSURE; MALE; MICROBIAL DIVERSITY; NONHUMAN; NORMAL HUMAN; OXYGEN SUPPLY; POPULATION ABUNDANCE; PREVOTELLA; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; SHIGELLA; SUBDOLIGRANULUM; SUBDOLIGRANULUM VARIABILE; YOUNG ADULT; BACTERIUM; BIOSYNTHESIS; CHEMISTRY; DNA SEQUENCE; FECES; FREEZING; GENETICS; INTESTINE FLORA; ISOLATION AND PURIFICATION; METABOLISM; MICROBIAL VIABILITY; MICROBIOLOGY;

ACETATES; BACTERIA; BACTERIAL PROTEINS; BUTYRATES; COENZYME A-TRANSFERASES; FATTY ACIDS, VOLATILE; FECAL MICROBIOTA TRANSPLANTATION; FECES; FREEZING; GASTROINTESTINAL MICROBIOME; HUMANS; MICROBIAL VIABILITY; REAL-TIME POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

EID: 85061630243     PISSN: None     EISSN: 23523964     Source Type: Journal    
DOI: 10.1016/j.ebiom.2019.02.023     Document Type: Article

References (36)

1. Fuentes, S., Rossen, N.G., van der Spek, M.J., et al. Microbial shifts and signatures of long-term remission in ulcerative colitis after faecal microbiota transplantation. ISME J 11:8 (2017), 1877–1889.
2. Frank, D.N., St Amand, A.L., Feldman, R.A., Boedeker, E.C., Harpaz, N., Pace, N.R., Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A 104:34 (2007), 13780–13785.
3. Kostic, A.D., Xavier, R.J., Gevers, D., The microbiome in inflammatory bowel disease: current status and the future ahead. Gastroenterology 146:6 (2014), 1489–1499.
4. Sokol, H., Pigneur, B., Watterlot, L., et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A 105:43 (2008), 16731–16736.
5. Wang, T., Cai, G., Qiu, Y., et al. Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers. ISME J 6:2 (2012), 320–329.
6. Qin, J., Li, Y., Cai, Z., et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490:7418 (2012), 55–60.
7. Remely, M., Aumueller, E., Merold, C., et al. Effects of short chain fatty acid producing bacteria on epigenetic regulation of FFAR3 in type 2 diabetes and obesity. Gene 537:1 (2014), 85–92.
8. Jiang, H., Ling, Z., Zhang, Y., et al. Altered fecal microbiota composition in patients with major depressive disorder. Brain Behav Immun 48 (2015), 186–194.
9. van Nood, E., Vrieze, A., Nieuwdorp, M., et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med 368:5 (2013), 407–415.
10. Cammarota, G., Masucci, L., Ianiro, G., et al. Randomised clinical trial: faecal microbiota transplantation by colonoscopy vs. vancomycin for the treatment of recurrent Clostridium difficile infection. Aliment Pharmacol Ther 41:9 (2015), 835–843.
11. Costello, S.P., Soo, W., Bryant, R.V., Jairath, V., Hart, A.L., Andrews, J.M., Systematic review with meta-analysis: faecal microbiota transplantation for the induction of remission for active ulcerative colitis. Aliment Pharmacol Ther 46:3 (2017), 213–224.
12. Costello, S.P., Tucker, E.C., La Brooy, J., Schoeman, M.N., Andrews, J.M., Establishing a fecal microbiota transplant service for the treatment of Clostridium difficile infection. Clin Infect Dis 62:7 (2016), 908–914.
13. Segal, J.P., Abbasi, F., Kanagasundaram, C., Hart, A., Does the internet promote the unregulated use of fecal microbiota transplantation: a potential public health issue?. Clin Exp Gastroenterol 11 (2018), 179–183.
14. Cammarota, G., Ianiro, G., Tilg, H., et al. European consensus conference on faecal microbiota transplantation in clinical practice. Gut 66:4 (2017), 569–580.
15. Trubiano, J.A., Cheng, A.C., Korman, T.M., et al. Australasian Society of Infectious Diseases updated guidelines for the management of Clostridium difficile infection in adults and children in Australia and New Zealand. Intern Med J 46:4 (2016), 479–493.
16. Mullish, B.H., Quraishi, M.N., Segal, J.P., et al. The use of faecal microbiota transplant as treatment for recurrent or refractory Clostridium difficile infection and other potential indications: joint British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS) guidelines. Gut 67:11 (2018), 1920–1941.
17. Lee, C.H., Steiner, T., Petrof, E.O., et al. Frozen vs Fresh fecal microbiota transplantation and clinical resolution of diarrhea in patients with recurrent Clostridium difficile infection: a randomized clinical trial. JAMA 315:2 (2016), 142–149.
18. Youngster, I., Russell, G.H., Pindar, C., Ziv-Baran, T., Sauk, J., Hohmann, E.L., Oral, capsulized, frozen fecal microbiota transplantation for relapsing Clostridium difficile infection. JAMA 312:17 (2014), 1772–1778.
19. Rigottier-Gois, L., Dysbiosis in inflammatory bowel diseases: the oxygen hypothesis. ISME J 7:7 (2013), 1256–1261.
20. Fouhy, F., Deane, J., Rea, M.C., et al. The effects of freezing on faecal microbiota as determined using MiSeq sequencing and culture-based investigations. PLoS One, 10(3), 2015, e0119355.
21. Chu, N.D., Smith, M.B., Perrotta, A.R., Kassam, Z., Alm, E.J., Profiling living bacteria informs preparation of fecal microbiota transplantations. PLoS One, 12(1), 2017, e0170922.
22. Nocker, A., Sossa-Fernandez, P., Burr, M.D., Camper, A.K., Use of propidium monoazide for live/dead distinction in microbial ecology. Appl Environ Microbiol 73:16 (2007), 5111–5117.
23. Papanicolas, L.E., Wang, Y., Choo, J.M., Gordon, D.L., Wesselingh, S.L., Rogers, G.B., Optimisation of a propidium monoazide based method to determine the viability of microbes in faecal slurries for transplantation. J Microbiol Methods 156 (2019), 40–45.
24. Australia New Zealand Clinical Trials Registry, Gastrointestinal eradication of multi-resistant gram negative bacteria by faecal microbiota transplantation (FMT). https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=371671&isReview=true, 2018. (Accessed 24 May 2018)
25. Choo, J.M., Leong, L.E., Rogers, G.B., Sample storage conditions significantly influence faecal microbiome profiles. Sci Rep, 5, 2015, 16350.
26. Wang, Y., Leong, L.E.X., Keating, R.L., et al. Opportunistic bacteria confer the ability to ferment prebiotic starch in the adult cystic fibrosis gut. Gut Microbes, 2018, 1–15.
27. Louis, P., Young, P., Holtrop, G., Flint, H.J., Diversity of human colonic butyrate-producing bacteria revealed by analysis of the butyryl-CoA:acetate CoA-transferase gene. Environ Microbiol 12:2 (2010), 304–314.
28. IDSA, Fecal Microbiota Transplant (FMT) protocol by enema for patients with recurrent Clostridium difficile infection. 2013.
29. Koh, A., De Vadder, F., Kovatcheva-Datchary, P., Backhed, F., From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites. Cell 165:6 (2016), 1332–1345.
30. McNabney, S.M., Henagan, T.M., Short chain fatty acids in the colon and peripheral tissues: a focus on butyrate, colon cancer, obesity and insulin resistance. Nutrients, 9(12), 2017.
31. Dominianni, C., Wu, J., Hayes, R.B., Ahn, J., Comparison of methods for fecal microbiome biospecimen collection. BMC Microbiol, 14, 2014, 103.
32. Flores, R., Shi, J., Yu, G., et al. Collection media and delayed freezing effects on microbial composition of human stool. Microbiome, 3, 2015, 33.
33. Tedjo, D.I., Jonkers, D.M., Savelkoul, P.H., et al. The effect of sampling and storage on the fecal microbiota composition in healthy and diseased subjects. PLoS One, 10(5), 2015, e0126685.
34. Helstad, A.G., Kimball, J.L., Maki, D.G., Recovery of anaerobic, facultative, and aerobic bacteria from clinical specimens in three anaerobic transport systems. J Clin Microbiol 5:6 (1977), 564–569.
35. Justesen, T., Jensen, A.M., Hoffmann, S., The survival of anaerobic bacteria at 4 degrees C and 22 degrees C on swabs in three transport systems. Statistical evaluation by application of a variance component model. Acta Pathol Microbiol Immunol Scand B 91:1 (1983), 17–22.
36. Hill, G.B., Effects of storage in an anaerobic transport system on bacteria in known polymicrobial mixtures and in clinical specimens. J Clin Microbiol 8:6 (1978), 680–688.