The currently used commercial DNA-extraction methods give different results of clostridial and actinobacterial populations derived from human fecal samples
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Altschul, 1990, Basic local alignment search tool, J Mol Biol, 215, 403, 10.1016/S0022-2836(05)80360-2
Ariefdjohan, 2010, Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens, Nutr J, 9, 23, 10.1186/1475-2891-9-23
Armougom, 2009, Monitoring bacterial community of human gut microbiota reveals an increase in Lactobacillus in obese patients and methanogens in anorexic patients, PLoS ONE, 4, e7125, 10.1371/journal.pone.0007125
Balamurugan, 2010, Quantitative differences in intestinal Faecalibacterium prausnitzii in obese Indian children, Br J Nutr, 103, 335, 10.1017/S0007114509992182
Bullen, 1976, Bifidobacteria in the intestinal tract of infants: an in vivo study, J Med Microbiol, 9, 325, 10.1099/00222615-9-3-325
Cole, 2009, The Ribosomal Database Project: improved alignments and new tools for rRNA analysis, Nucleic Acids Res, 37, D141, 10.1093/nar/gkn879
Collado, 2008, Distinct composition of gut microbiota during pregnancy in overweight and normal-weight women, Am J Clin Nutr, 88, 894, 10.1093/ajcn/88.4.894
Collins, 1994, The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations, Int J Syst Bacteriol, 44, 812, 10.1099/00207713-44-4-812
Dridi, 2009, High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol, PLoS ONE, 4, e7063, 10.1371/journal.pone.0007063
Duncan, 2008, Proposal of a neotype strain (A1-86) for Eubacterium rectale. Request for an Opinion, Int J Syst Evol Microbiol, 58, 1735, 10.1099/ijs.0.2008/004580-0
Duncan, 2007, Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces, Appl Environ Microbiol, 73, 1073, 10.1128/AEM.02340-06
Duncan, 2008, Human colonic microbiota associated with diet, obesity and weight loss, Int J Obes, 32, 1720, 10.1038/ijo.2008.155
Eckburg, 2005, Microbiology: diversity of the human intestinal microbial flora, Science, 308, 1635, 10.1126/science.1110591
Fallani, 2010, Intestinal microbiota of 6-week-old infants across Europe: geographic influence beyond delivery mode, breast-feeding, and antibiotics, J Pediatr Gastroenterol Nutr, 51, 77, 10.1097/MPG.0b013e3181d1b11e
Favier, 2002, Molecular monitoring of succession of bacterial communities in human neonates, Appl Environ Microbiol, 68, 219, 10.1128/AEM.68.1.219-226.2002
Gill, 2006, Metagenomic analysis of the human distal gut microbiome, Science, 312, 1355, 10.1126/science.1124234
Harmsen, 2000a, Development of 16S rRNA-based probes for the Coriobacterium group and the Atopobium cluster and their application for enumeration of Coriobacteriaceae in human feces from volunteers of different age groups, Appl Environ Microbiol, 66, 4523, 10.1128/AEM.66.10.4523-4527.2000
Harmsen, 2000b, Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods, J Pediatr Gastroenterol Nutr, 30, 61, 10.1097/00005176-200001000-00019
Kageyama, 1999, Phylogenetic and phenotypic evidence for the transfer of Eubacterium aerofaciens to the genus Collinsella as Collinsella aerofaciens gen. nov., comb. nov, Int J Syst Bacteriol, 49, 557, 10.1099/00207713-49-2-557
Lauber, 2010, Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples, FEMS Microbiol Lett, 307, 80, 10.1111/j.1574-6968.2010.01965.x
Lay, 2005, Colonic microbiota signatures across five northern European countries, Appl Environ Microbiol, 71, 4153, 10.1128/AEM.71.7.4153-4155.2005
Ley, 2005, Obesity alters gut microbial ecology, P Natl Acad Sci USA, 102, 11070, 10.1073/pnas.0504978102
Ley, 2006, Microbial ecology: human gut microbes associated with obesity, Nature, 444, 1022, 10.1038/4441022a
Li, 2003, Evaluation of QIAamp® DNA Stool Mini Kit for ecological studies of gut microbiota, J Microbiol Methods, 54, 13, 10.1016/S0167-7012(02)00260-9
Magne, 2006, A longitudinal study of infant faecal microbiota during weaning, FEMS Microbiol Ecol, 58, 563, 10.1111/j.1574-6941.2006.00182.x
Mai, 2009, Associations between dietary habits and body mass index with gut microbiota composition and fecal water genotoxicity: an observational study in African American and Caucasian American volunteers, Nutr J, 8, 49, 10.1186/1475-2891-8-49
Matsuki, 2004, Use of 16S rRNA gene-targeted group-specific primers for real-time PCR analysis of predominant bacteria in human feces, Appl Environ Microbiol, 70, 7220, 10.1128/AEM.70.12.7220-7228.2004
Mättö, 2005, Composition and temporal stability of gastrointestinal microbiota in irritable bowel syndrome - A longitudinal study in IBS and control subjects, FEMS Immunol Med Microbiol, 43, 213, 10.1016/j.femsim.2004.08.009
Maukonen, 2006a, Desulfovibrionales-related bacteria in a paper mill environment as detected with molecular techniques and culture, J Ind Microbiol Biotechnol, 33, 45, 10.1007/s10295-005-0047-2
Maukonen, 2006b, PCR DGGE and RT-PCR DGGE show diversity and short-term temporal stability in the Clostridium coccoides-Eubacterium rectale group in the human intestinal microbiota, FEMS Microbiol Ecol, 58, 517, 10.1111/j.1574-6941.2006.00179.x
Maukonen, 2008, Intra-individual diversity and similarity of salivary and faecal microbiota, J Med Microbiol, 57, 1560, 10.1099/jmm.0.47352-0
McOrist, 2002, A comparison of five methods for extraction of bacterial DNA from human faecal samples, J Microbiol Methods, 50, 131, 10.1016/S0167-7012(02)00018-0
Molbak, 2006, Freezing at −80°C distorts the DNA composition of bacterial communities in intestinal samples, Curr Issues Intest Microbiol, 7, 29
Mueller, 2006, Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study, Appl Environ Microbiol, 72, 1027, 10.1128/AEM.72.2.1027-1033.2006
Nakamura, 2009, Molecular ecological analysis of fecal bacterial populations from term infants fed formula supplemented with selected blends of prebiotics, Appl Environ Microbiol, 75, 1121, 10.1128/AEM.02359-07
Ott, 2004, In vitro alterations of intestinal bacterial microbiota in fecal samples during storage, Diagn Microbiol Infect Dis, 50, 237, 10.1016/j.diagmicrobio.2004.08.012
Palmer, 2007, Development of the human infant intestinal microbiota, PLoS Biol, 5, 1556, 10.1371/journal.pbio.0050177
Roesch, 2009, Influence of fecal sample storage on bacterial community diversity, Open Microbiol J, 3, 40, 10.2174/1874285800903010040
Salonen, 2010, Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis, J Microbiol Methods, 81, 127, 10.1016/j.mimet.2010.02.007
Santacruz, 2009, Interplay between weight loss and gut microbiota composition in overweight adolescents, Obesity, 17, 1906, 10.1038/oby.2009.112
Santacruz, 2010, Gut microbiota composition is associated with body weight, weight gain and biochemical parameters in pregnant women, Br J Nutr, 104, 83, 10.1017/S0007114510000176
Schwiertz, 2010, Microbiota and SCFA in lean and overweight healthy subjects, Obesity, 18, 190, 10.1038/oby.2009.167
Stark, 1982, The microbial ecology of the large bowel of breast-fed and formula-fed infants during the first year of life, J Med Microbiol, 15, 189, 10.1099/00222615-15-2-189
Turnbaugh, 2006, An obesity-associated gut microbiome with increased capacity for energy harvest, Nature, 444, 1027, 10.1038/nature05414
Turnbaugh, 2009, A core gut microbiome in obese and lean twins, Nature, 457, 480, 10.1038/nature07540
Wang, 2007, Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy, Appl Environ Microbiol, 73, 5261, 10.1128/AEM.00062-07
Zhang, 2009, Human gut microbiota in obesity and after gastric bypass, P Natl Acad Sci USA, 106, 2365, 10.1073/pnas.0812600106