Preparation of a standardised faecal slurry for ex-vivo microbiota studies which reduces inter-individual donor bias

Journal of Microbiological Methods

Volumn 129, Issue , 2016, Pages 109-116

  O'Donnell, Michelle M ^a,b   Rea, Mary C ^a,b   O'Sullivan, Órla ^a,b   Flynn, Cal ^c   Jones, Beth ^c   McQuaid, Albert ^c   Shanahan, Fergus ^b   Ross, R Paul ^a,b,d  

^a TEAGASC FOOD RESEARCH CENTRE   (Ireland)

^b UNIVERSITY COLLEGE CORK   (Ireland)

^c Kerry Ingredients and Flavours   (United States)

^d UNIVERSITY COLLEGE CORK   (Ireland)

Author keywords

Cryo preservation; Fermentation; Microbiota; MiSeq; Standardisation

Indexed keywords

GLYCEROL; PHOSPHATE; BACTERIAL DNA;

ADULT; ANAEROBIC BACTERIUM; ARTICLE; BACTERIAL CELL; BACTERIAL COUNT; BATCH FERMENTATION; CELL VIABILITY; CENTRIFUGATION; CONTROLLED STUDY; CRYOPRESERVATION; EX VIVO STUDY; FECES; FECES ANALYSIS; FROZEN STANDARDISED INOCULUM; GENUS; HOMOGENISATION; HUMAN; INOCULATION; INTESTINE FLORA; INVESTIGATIVE PROCEDURES; MICROBIAL DIVERSITY; MICROBIOLOGICAL EXAMINATION; NEXT GENERATION SEQUENCING; NONHUMAN; NORMAL HUMAN; PELLETING; PHYLUM; POLYMERASE CHAIN REACTION; POOLING; POPULATION ABUNDANCE; PRIORITY JOURNAL; QUANTITATIVE POLYMERASE CHAIN REACTION; REPRODUCIBILITY; SAMPLING BIAS; STANDARDISED FECAL SLURRY; BIODIVERSITY; FERMENTATION; FREEZING; MICROBIOLOGY; MICROFLORA; PRESERVATION; PROCEDURES; REAL TIME POLYMERASE CHAIN REACTION; SPECIMEN HANDLING; STANDARD;

BIODIVERSITY; DNA, BACTERIAL; FECES; FERMENTATION; FREEZING; HUMANS; MICROBIOTA; PRESERVATION, BIOLOGICAL; REAL-TIME POLYMERASE CHAIN REACTION; REFERENCE STANDARDS; REPRODUCIBILITY OF RESULTS; SPECIMEN HANDLING;

EID: 84983541849     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2016.08.002     Document Type: Article

References (33)

1. Aguirre, M., Ramiro-Garcia, J., Koenen, M.E., Venema, K., To pool or not to pool? Impact of the use of individual and pooled fecal samples for in vitro fermentation studies. J. Microbiol. Methods 107 (2014), 1–7.
2. Barroso, E., Cueva, C., Peláez, C., Martínez-Cuesta, M.C., Requena, T., Development of human colonic microbiota in the computer-controlled dynamic SIMulator of the GastroIntestinal tract SIMGI. LWT-Food Sci. Technol. 61:2 (2015), 283–289.
3. Caporaso, J.G., Bittinger, K., Bushman, F.D., DeSantis, T.Z., Andersen, G.L., Knight, R., PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26:2 (2010), 266–267.
4. Collins, J., Auchtung, J.M., Schaefer, L., Eaton, K.A., Britton, R.A., Humanized microbiota mice as a model of recurrent Clostridium difficile disease. Microbiome 3:1 (2015), 1–15.
5. Core Team, R., R: A language and environment for statistical computing. 2012, R Foundation for Statistical Computing, Vienna, Austria 3-900051-07-0 http://www.R-project.org.
6. Dinan, T.G., Stilling, R.M., Stanton, C., Cryan, J.F., Collective unconscious: how gut microbes shape human behavior. J. Psychiatr. Res. 63 (2015), 1–9.
7. Edgar, R.C., Haas, B.J., Clemente, J.C., Quince, C., Knight, R., UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:16 (2011), 2194–2200.
8. Feria-Gervasio, D., Tottey, W., Gaci, N., Alric, M., Cardot, J.-M., Peyret, P., Martin, J.-F., Pujos, E., Sébédio, J.-L., Brugère, J.-F., Three-stage continuous culture system with a self-generated anaerobia to study the regionalized metabolism of the human gut microbiota. J. Microbiol. Methods 96 (2014), 111–118.
9. Fooks, L.J., Gibson, G.R., Mixed culture fermentation studies on the effects of synbiotics on the human intestinal pathogens Campylobacter jejuni and Escherichia coli. Anaerobe 9:5 (2003), 231–242.
10. Fouhy, F., Deane, J., Rea, M.C., O'Sullivan, Ó., Ross, R.P., O'Callaghan, G., Plant, B.J., Stanton, C., The effects of freezing on faecal microbiota as determined using MiSeq sequencing and culture-based investigations. PLoS One, 10(3), 2015, e0119355.
11. Gentleman, R.C., Carey, V.J., Bates, D.M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., Bioconductor: open software development for computational biology and bioinformatics. Genome Biol., 5(10), 2004, R80.
12. Guinane, C.M., Cotter, P.D., Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ. Ther. Adv. Gastroenterol. 6:4 (2013), 295–308.
13. Hamilton, M.J., Weingarden, A.R., Sadowsky, M.J., Khoruts, A., Standardized Frozen Preparation for Transplantation of Fecal Microbiota for Recurrent Clostridium difficile Infection. Am J Gastroenterol 107:5 (2012), 761–767.
14. Hamilton, M.J., Weingarden, A.R., Unno, T., Khoruts, A., Sadowsky, M.J., High-throughput DNA sequence analysis reveals stable engraftment of gut microbiota following transplantation of previously frozen fecal bacteria. Gut Microbes 4:2 (2013), 125–135.
15. Heberle, H., Meirelles, G.V., da Silva, F.R., Telles, G.P., Minghim, R., InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams. BMC Bioinformatics 16:1 (2015), 1–7.
16. Jones, M.L., Ganopolsky, J.G., Martoni, C.J., Labbé, A., Prakash, S., Emerging science of the human microbiome. Gut Microbes 5:4 (2014), 446–457.
17. Kelly, J.R., Kennedy, P.J., Cryan, J.F., Dinan, T.G., Clarke, G., Hyland, N.P., Breaking down the barriers: the gut microbiome, intestinal permeability and stress-related psychiatric disorders. Front. Cell. Neurosci., 9, 2015, 392.
18. Klindworth, A., Pruesse, E., Schweer, T., Peplies, J., Evaluation of general 16S ribosomal RNA gene PcR primers for classical and next generation sequencing based diversity studies. Nucleic Acids Res., 41(1), 2013, e1Je1.
19. Kuczynski, J., Stombaugh, J., WA, W., González, A., JG, C., Knight, R., Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr. Protoc. Microbiol., 2012 (1E. 5.1-1E. 5.20).
20. Lozupone, C., Knight, R., UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71:12 (2005), 8228–8235.
21. Minekus, M., Smeets-Peeters, M., Bernalier, A., Marol-Bonnin, S., Havenaar, R., Marteau, P., Alric, M., Fonty, G., A computer-controlled system to simulate conditions of the large intestine with peristaltic mixing, water absorption and absorption of fermentation products. Appl. Microbiol. Biotechnol. 53:1 (1999), 108–114.
22. Molly, K., Woestyne, M.V., Smet, I.D., Verstraete, W., Validation of the simulator of the human intestinal microbial ecosystem (SHIME) reactor using microorganism-associated activities. Microb. Ecol. Health Dis. 7:4 (1994), 191–200.
23. Payne, A.N., Zihler, A., Chassard, C., Lacroix, C., Advances and perspectives in in vitro human gut fermentation modeling. Trends Biotechnol. 30:1 (2012), 17–25.
24. Pruesse, E., Quast, C., Knittel, K., Fuchs, B.M., Ludwig, W., Peplies, J., Glöckner, F.O., SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35:21 (2007), 7188–7196.
25. Rajilić-Stojanović, M., Maathuis, A., Heilig, H.G., Venema, K., de Vos, W.M., Smidt, H., Evaluating the microbial diversity of an in vitro model of the human large intestine by phylogenetic microarray analysis. Microbiology 156:11 (2010), 3270–3281.
26. Rea, M.C., Dobson, A., O'Sullivan, O., Crispie, F., Fouhy, F., Cotter, P.D., Shanahan, F., Kiely, B., Hill, C., Ross, R.P., Effect of broad-and narrow-spectrum antimicrobials on Clostridium difficile and microbial diversity in a model of the distal colon. Proc. Natl. Acad. Sci. 108:Supplement 1 (2011), 4639–4644.
27. Respondek, F., Gerard, P., Bossis, M., Boschat, L., Bruneau, A., Rabot, S., Wagner, A., Martin, J.-C., Short-chain fructo-oligosaccharides modulate intestinal microbiota and metabolic parameters of humanized gnotobiotic diet induced obesity mice. PLoS One, 8(8), 2013, e71026.
28. Rodriguez-Colinas, B., Kolida, S., Baran, M., Ballesteros, A., Rastall, R., Plou, F., Analysis of fermentation selectivity of purified galacto-oligosaccharides by in vitro human faecal fermentation. Appl. Microbiol. Biotechnol. 97:13 (2013), 5743–5752.
29. Sarbini, S.R., Kolida, S., Naeye, T., Einerhand, A.W., Gibson, G.R., Rastall, R.A., The prebiotic effect of α-1,2 branched, low molecular weight dextran in the batch and continuous faecal fermentation system. J. Funct. Foods 5:4 (2013), 1938–1946.
30. Sinha, R., Abnet, C.C., White, O., Knight, R., Huttenhower, C., The microbiome quality control project: baseline study design and future directions. Genome Biol. 16:1 (2015), 1–6.
31. Swift, M.L., GraphPad prism, data analysis, and scientific graphing. J. Chem. Inf. Comput. Sci. 37:2 (1997), 411–412.
32. Turnbaugh, P.J., Ridaura, V.K., Faith, J.J., Rey, F.E., Knight, R., Gordon, J.I., The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci. Transl. Med. 1:6 (2009), 6ra14–16ra14.
33. Zhang, H., DiBaise, J.K., Zuccolo, A., Kudrna, D., Braidotti, M., Yu, Y., Parameswaran, P., Crowell, M.D., Wing, R., Rittmann, B.E., Human gut microbiota in obesity and after gastric bypass. Proc. Natl. Acad. Sci. 106:7 (2009), 2365–2370.