In vitro maintenance of a human proximal colon microbiota using the continuous fermentation system P-ECSIM

Applied Microbiology and Biotechnology

Volumn 91, Issue 5, 2011, Pages 1425-1433

  Feria Gervasio, David ^a   Denis, Sylvain ^a   Alric, Monique ^a   Brugère, Jean François ^a  

^a UNIVERSITÉ CLERMONT AUVERGNE   (France)

Author keywords

Gut microbiota; Human colon; In vitro digestive system

Indexed keywords

ANAEROBIC ATMOSPHERE; ANALYTICAL TECHNIQUES; BATCH CULTURE; CONTINUOUS CULTURE; CONTINUOUS FERMENTATION SYSTEMS; DIFFERENTIAL RESPONSE; DILUTION RATE; ENVIRONMENTAL CHANGE; ENVIRONMENTAL CONTROL SYSTEM; HUMAN COLON; HUMAN MICROBIOTA; IN VITRO DIGESTIVE SYSTEM; IN-VITRO; IN-VIVO; METABOLIC ACTIVITY; MICROBIOTAS; MOLECULAR FINGERPRINT; STEADY STATE; STORAGE TIME; SYSTEM SIMULATING; TECHNICAL DIFFICULTIES;

BATCH CELL CULTURE; DIGESTIVE SYSTEM; FERMENTATION; GLYCEROL; PHYSIOLOGY;

METABOLISM;

ABUNDANCE; COMPARATIVE STUDY; DILUTION; FERMENTATION; METABOLISM; MOLECULAR ANALYSIS; PHYSICOCHEMICAL PROPERTY;

ADULT; ARTICLE; ATMOSPHERE; BACTERIAL METABOLISM; BACTERIUM CULTURE; BACTEROIDES; BIFIDOBACTERIUM; CLOSTRIDIUM; COLON; FECES ANALYSIS; FEMALE; FERMENTATION; HUMAN; IN VITRO STUDY; INTESTINE FLORA; LACTOBACILLUS; NONHUMAN;

ADULT; BACTERIA; COLON; CULTURE TECHNIQUES; DIGESTION; FECES; FEMALE; FERMENTATION; GASES; HUMANS; METAGENOME; MODELS, BIOLOGICAL;

EID: 80052631492     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-011-3462-5     Document Type: Article

References (32)

1. C Allison C McFarlan GT MacFarlane 1989 Studies on mixed populations of human intestinal bacteria grown in single-stage and multistage continuous culture systems Appl Environ Microbiol 55 3 672 678 1:CAS:528:DyaL1MXhvV2jurg%3D (Pubitemid 19085123)
2. CA Bearne AK Mallett IR Rowland WE Brennan-Craddock 1990 Continuous culture of human faecal bacteria as an in vitro model for the colonic microflora Toxicol In Vitro 4 4-5 522 525 10.1016/0887-2333(90)90111-6 1:CAS:528:DyaK3MXhs1Slsr0%3D (Pubitemid 20364948)
3. H Beerens 1991 Detection of bifidobacteria by using propionic acid as a selective agent Appl Environ Microbiol 57 8 2418 2419 1:CAS:528: DyaK3MXlslyksr8%3D
4. JF Brugere A Mihajlovski M Missaoui P Peyret 2009 Tools for stools: the challenge of assessing human intestinal microbiota using molecular diagnostics Expert Rev Mol Diagn 9 4 353 365 10.1586/erm.09.16 1:CAS:528: DC%2BD1MXlvVWkt70%3D
5. M Cardinale L Brusetti P Quatrini S Borin AM Puglia A Rizzi E Zanardini C Sorlini C Corselli D Daffonchio 2004 Comparison of different primer sets for use in automated ribosomal intergenic spacer analysis of complex bacterial communities Appl Environ Microbiol 70 10 6147 6156 10.1128/AEM.70.10.6147-6156. 2004 1:CAS:528:DC%2BD2cXosl2hs7o%3D (Pubitemid 39471864)
6. MW Child A Kennedy AW Walker B Bahrami S Macfarlane GT Macfarlane 2006 Studies on the effect of system retention time on bacterial populations colonizing a three-stage continuous culture model of the human large gut using FISH techniques FEMS Microbiol Ecol 55 2 299 310 10.1111/j.1574-6941.2005.00016. x 1:CAS:528:DC%2BD28Xit1Snurw%3D
7. C Cinquin G Le Blay I Fliss C Lacroix 2004 Immobilization of infant fecal microbiota and utilization in an in vitro colonic fermentation model Microb Ecol 48 1 128 138 10.1007/s00248-003-2022-7 1:STN:280:DC%2BD2cvovVKnsA%3D%3D (Pubitemid 39160995)
8. MJ Claesson O O'Sullivan Q Wang J Nikkila JR Marchesi H Smidt WM de Vos RP Ross PW O'Toole 2009 Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine PLoS One 4 8 e6669 10.1371/journal.pone.0006669
9. JH Cummings EW Pomare WJ Branch CP Naylor GT Macfarlane 1987 Short chain fatty acids in human large intestine, portal, hepatic and venous blood Gut 28 10 1221 1227 10.1136/gut.28.10.1221 1:STN:280:DyaL1c%2Fls1CrsA%3D%3D (Pubitemid 17156038)
10. JH Cummings SA Bingham KW Heaton MA Eastwood 1992 Fecal weight, colon cancer risk, and dietary intake of nonstarch polysaccharides (dietary fiber) Gastroenterology 103 6 1783 1789 1:STN:280:DyaK3s%2Fotlymug%3D%3D
11. L Dethlefsen S Huse ML Sogin DA Relman 2008 The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing PLoS Biol 6 11 e280 10.1371/journal.pbio.0060280
12. PB Eckburg EM Bik CN Bernstein E Purdom L Dethlefsen M Sargent SR Gill KE Nelson DA Relman 2005 Diversity of the human intestinal microbial flora Science 308 5728 1635 1638 10.1126/science.1110591 (Pubitemid 40807514)
13. GR Gibson R Fuller 2000 Aspects of in vitro and in vivo research approaches directed toward identifying probiotics and prebiotics for human use J Nutr 130 2S Suppl 391S 395S 1:CAS:528:DC%2BD3cXhtVSlsLY%3D (Pubitemid 30073757)
14. GR Gibson JH Cummings GT Macfarlane 1988 Use of a three-stage continuous culture system to study the effect of mucin on dissimilatory sulfate reduction and methanogenesis by mixed populations of human gut bacteria Appl Environ Microbiol 54 11 2750 2755 1:CAS:528:DyaL1MXksVWn
15. MJ Hopkins R Sharp GT Macfarlane 2001 Age and disease related changes in intestinal bacterial populations assessed by cell culture, 16S rRNA abundance, and community cellular fatty acid profiles Gut 48 2 198 205 10.1136/gut.48.2.198 1:STN:280:DC%2BD3M7is1Wgtg%3D%3D (Pubitemid 32141843)
16. G Le Blay J Rytka A Zihler C Lacroix 2009 New in vitro colonic fermentation model for Salmonella infection in the child gut FEMS Microbiol Ecol 67 2 198 207 10.1111/j.1574-6941.2008.00625.x
17. GT Macfarlane S Macfarlane GR Gibson 1998 Validation of a three-stage compound continuous culture system for investigating the effect of retention time on the ecology and metabolism of bacteria in the human colon Microb Ecol 35 2 180 187 10.1007/s002489900072 1:CAS:528:DyaK1cXitFynsbk%3D (Pubitemid 28190244)
18. A Mihajlovski M Alric JF Brugere 2008 A putative new order of methanogenic Archaea inhabiting the human gut, as revealed by molecular analyses of the mcrA gene Res Microbiol 159 7-8 516 521 10.1016/j.resmic.2008.06.007 1:CAS:528:DC%2BD1cXhtFOltrvK
19. A Mihajlovski J Doré F Levenez M Alric J-F Brugère 2010 Molecular evaluation of the human gut methanogenic archaeal microbiota reveals an age-associated increase of the diversity Environ Microbiol Rep 2 272 280 10.1111/j.1758-2229.2009.00116.x 1:CAS:528:DC%2BC3cXms1anur4%3D
20. M Minekus M Smeets-Peeters A Bernalier S Marol-Bonnin R Havenaar P Marteau M Alric G Fonty JH Huis in't Veld 1999 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 1 108 114 10.1007/s002530051622 1:CAS:528:DC%2BD3cXkt1ejug%3D%3D (Pubitemid 30120182)
21. T Mitsuoka K Hayakawa 1973 The fecal flora in man. I. Composition of the fecal flora of various age groups Zentralbl Bakteriol Orig A 223 2 333 342 1:STN:280:DyaE3s3gtFyhuw%3D%3D
22. K Molly M Vande Woestyne W Verstraete 1993 Development of a 5-step multi-chamber reactor as a simulation of the human intestinal microbial ecosystem Appl Microbiol Biotechnol 39 2 254 258 10.1007/BF00228615 1:CAS:528:DyaK3sXks1Oisbc%3D (Pubitemid 23134616)
23. CJ Probert PM Emmett KW Heaton 1993 Intestinal transit time in the population calculated from self made observations of defecation J Epidemiol Community Health 47 4 331 333 10.1136/jech.47.4.331 1:STN:280: DyaK2c%2FksFCjsQ%3D%3D (Pubitemid 23256212)
24. J Qin R Li J Raes M Arumugam KS Burgdorf C Manichanh T Nielsen N Pons F Levenez T Yamada DR Mende J Li J Xu S Li D Li J Cao B Wang H Liang H Zheng Y Xie J Tap P Lepage M Bertalan JM Batto T Hansen D Le Paslier A Linneberg HB Nielsen E Pelletier P Renault T Sicheritz-Ponten K Turner H Zhu C Yu S Li M Jian Y Zhou Y Li X Zhang S Li N Qin H Yang J Wang S Brunak J Dore F Guarner K Kristiansen O Pedersen J Parkhill J Weissenbach P Bork SD Ehrlich J Wang 2010 A human gut microbial gene catalogue established by metagenomic sequencing Nature 464 7285 59 65 10.1038/nature08821 1:CAS:528:DC%2BC3cXislahsLc%3D
25. M Rajilić-Stojanović A Maathuis HG Heilig K Venema WM de Vos H Smidt 2010 Evaluating the microbial diversity of an in vitro model of the human large intestine by phylogenetic microarray analysis Microbiology 156 11 3270 3281 10.1099/mic.0.042044-0
26. CJ Rumney IR Rowland 1992 In vivo and in vitro models of the human colonic flora Crit Rev Food Sci Nutr 31 4 299 331 10.1080/10408399209527575 1:STN:280:DyaK383lsFynsg%3D%3D
27. J Tap S Mondot F Levenez E Pelletier C Caron JP Furet E Ugarte R Munoz-Tamayo DL Paslier R Nalin J Dore M Leclerc 2009 Towards the human intestinal microbiota phylogenetic core Environ Microbiol 11 10 2574 2584 10.1111/j.1462-2920.2009.01982.x
28. P Van den Abbeele C Grootaert M Marzorati S Possemiers W Verstraete P Gerard S Rabot A Bruneau S El Aidy M Derrien E Zoetendal M Kleerebezem H Smidt T Van de Wiele 2010 Microbial community development in a dynamic gut model is reproducible, colon region specific, and selective for Bacteroidetes and Clostridium cluster IX Appl Environ Microbiol 76 15 5237 5246 10.1128/AEM.00759-10
29. EJ Woodmansey 2007 Intestinal bacteria and ageing J Appl Microbiol 102 5 1178 1186 10.1111/j.1365-2672.2007.03400.x 1:CAS:528:DC%2BD2sXmslKgtbc%3D (Pubitemid 46633436)
30. Z Yu M Morrison 2004 Improved extraction of PCR-quality community DNA from digesta and fecal samples Biotechniques 36 5 808 812 1:CAS:528: DC%2BD2cXktV2nu7s%3D (Pubitemid 38620199)
31. H Zhang JK DiBaise A Zuccolo D Kudrna M Braidotti Y Yu P Parameswaran MD Crowell R Wing BE Rittmann R Krajmalnik-Brown 2009 Human gut microbiota in obesity and after gastric bypass Proc Natl Acad Sci U S A 106 7 2365 2370 10.1073/pnas.0812600106 1:CAS:528:DC%2BD1MXit12jtL4%3D
32. EG Zoetendal M Rajilic-Stojanovic WM de Vos 2008 High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota Gut 57 11 1605 1615 10.1136/gut.2007.133603 1:CAS:528:DC%2BD1cXhtl2gtr%2FI