To pool or not to pool? Impact of the use of individual and pooled fecal samples for in vitro fermentation studies

被引：101
作者：
Aguirre, Marisol [1 ,2 ,3 ]
Ramiro-Garcia, Javier [1 ,4 ]
Koenen, Marjorie E. [3 ]
Venema, Koen [1 ,3 ]
机构：
[1] Top Inst Food & Nutr, NL-6700 AA Wageningen, Netherlands
[2] Maastricht Univ, Sch Nutr Toxicol & Metab NUTRIM, Fac Hlth Med & Life Sci, Dept Human Biol, NL-6200 MD Maastricht, Netherlands
[3] Netherlands Org Appl Sci Res, TNO, NL-3700 AJ Zeist, Netherlands
[4] Wageningen Univ, Lab Microbiol Syst & Synthet Biol, NL-6703 HB Wageningen, Netherlands
来源：
JOURNAL OF MICROBIOLOGICAL METHODS | 2014年 / 107卷
关键词：
In vitro model; Fecal inoculum preparation; Pooling; Gut microbiota; Fermentation; HUMAN LARGE-INTESTINE; GUT MICROBIOTA; MODEL; BACTERIA; OLIGOSACCHARIDES; METABOLISM; PRODUCTS; PATTERNS; STARCH; CORE;
D O I：
10.1016/j.mimet.2014.08.022
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
This study investigated the stability and the activity of the microbiota from a single and a pool of donors in the TNO in vitro model of the colon (TIM-2 system). Our findings demonstrate the suitability of the preparation of a pool of fecal sample to be used for fermentation experiments. (C) 2014 Elsevier B.V. All rights reserved.
引用
收藏
页码：1 / 7
页数：7
相关论文
共 31 条
[1]   QIIME allows analysis of high-throughput community sequencing data [J].
Caporaso, J. Gregory ;
Kuczynski, Justin ;
Stombaugh, Jesse ;
Bittinger, Kyle ;
Bushman, Frederic D. ;
Costello, Elizabeth K. ;
Fierer, Noah ;
Pena, Antonio Gonzalez ;
Goodrich, Julia K. ;
Gordon, Jeffrey I. ;
Huttley, Gavin A. ;
Kelley, Scott T. ;
Knights, Dan ;
Koenig, Jeremy E. ;
Ley, Ruth E. ;
Lozupone, Catherine A. ;
McDonald, Daniel ;
Muegge, Brian D. ;
Pirrung, Meg ;
Reeder, Jens ;
Sevinsky, Joel R. ;
Tumbaugh, Peter J. ;
Walters, William A. ;
Widmann, Jeremy ;
Yatsunenko, Tanya ;
Zaneveld, Jesse ;
Knight, Rob .
NATURE METHODS, 2010, 7 (05) :335-336
[2]   Profiling human gut bacterial metabolism and its kinetics using [U-13C]glucose and NMR [J].
de Graaf, Albert A. ;
Maathuis, Annet ;
de Waard, Pieter ;
Deutz, Nicolaas E. P. ;
Dijkema, Cor ;
de Vos, Willem M. ;
Venema, Koen .
NMR IN BIOMEDICINE, 2010, 23 (01) :2-12
[3]   UCHIME improves sensitivity and speed of chimera detection [J].
Edgar, Robert C. ;
Haas, Brian J. ;
Clemente, Jose C. ;
Quince, Christopher ;
Knight, Rob .
BIOINFORMATICS, 2011, 27 (16) :2194-2200
[4]   Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data [J].
Hamady, Micah ;
Lozupone, Catherine ;
Knight, Rob .
ISME JOURNAL, 2010, 4 (01) :17-27
[5]   Ironing out the wrinkles in the rare biosphere through improved OTU clustering [J].
Huse, Susan M. ;
Welch, David Mark ;
Morrison, Hilary G. ;
Sogin, Mitchell L. .
ENVIRONMENTAL MICROBIOLOGY, 2010, 12 (07) :1889-1898
[6]   Linking phylogenetic identities of bacteria to starch fermentation in an in vitro model of the large intestine by RNA-based stable isotope probing [J].
Kovatcheva-Datchary, Petia ;
Egert, Markus ;
Maathuis, Annet ;
Rajilic-Stojanovic, Mirjana ;
de Graaf, Albert A. ;
Smidt, Hauke ;
de Vos, Willem M. ;
Venema, Koen .
ENVIRONMENTAL MICROBIOLOGY, 2009, 11 (04) :914-926
[7]   Species Composition of Bacteroidales Order Bacteria in the Feces of Healthy People of Various Ages [J].
Kulagina, Elena V. ;
Efimov, Boris A. ;
Maximov, Phillipp Y. ;
Kafarskaia, Lyudmila I. ;
Chaplin, Andrei V. ;
Shkoporov, Andrei N. .
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, 2012, 76 (01) :169-171
[8]   The Effect of the Undigested Fraction of Maize Products on the Activity and Composition of the Microbiota Determined in a Dynamic in Vitro Model of the Human Proximal Large Intestine [J].
Maathuis, Annet ;
Hoffman, Andrew ;
Evans, Annette ;
Sanders, Lisa ;
Venema, Koch .
JOURNAL OF THE AMERICAN COLLEGE OF NUTRITION, 2009, 28 (06) :657-666
[9]   Galacto-Oligosaccharides Have Prebiotic Activity in a Dynamic In Vitro Colon Model Using a 13C-Labeling Technique [J].
Maathuis, Annet J. H. ;
van den Heuvel, Ellen C. ;
Schoterman, Margriet H. C. ;
Venema, Koen .
JOURNAL OF NUTRITION, 2012, 142 (07) :1205-1212
[10]   Evaluation of microbial community reproducibility, stability and composition in a human distal gut chemostat model [J].
McDonald, Julie A. K. ;
Schroeter, Kathleen ;
Fuentes, Susana ;
Heikamp-deJong, Ineke ;
Khursigara, Cezar M. ;
de Vos, Willem M. ;
Allen-Vercoe, Emma .
JOURNAL OF MICROBIOLOGICAL METHODS, 2013, 95 (02) :167-174
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