Armougom F, Raoult D (2008) Use of pyrosequencing and DNA barcodes to monitor variations in Firmicutes and Bacteroidetes communities in the gut microbiota of obese humans. BMC Genomics 9:576. doi:10.1186/1471-2164-9-576 ArticlePubMed CentralPubMed Google Scholar
Armougom F, Henry M, Vialettes B, Raccah D, Raoult D (2009) Monitoring bacterial community of human gut microbiota reveals an increase in Lactobacillus in obese patients and Methanogens in anorexic patients. PLoS One 4(9):e7125. doi:10.1371/journal.pone.0007125 ArticlePubMed CentralPubMed Google Scholar
Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Dore J, Antolin M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Merieux A, Melo Minardi R, M’Rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P (2011) Enterotypes of the human gut microbiome. Nature 473(7346):174–180. doi:10.1038/nature09944 ArticleCASPubMed CentralPubMed Google Scholar
Carroccio A, Iacono G, Cottone M, Di Prima L, Cartabellotta F, Cavataio F, Scalici C, Montalto G, Di Fede G, Rini G, Notarbartolo A, Averna MR (2003) Diagnostic accuracy of fecal calprotectin assay in distinguishing organic causes of chronic diarrhea from irritable bowel syndrome: a prospective study in adults and children. Clin Chem 49(6 Pt 1):861–867 ArticleCASPubMed Google Scholar
Chao A, Shen T-J (2003) Nonparametric estimation of Shannon’s index of diversity when there are unseen species in sample. Environ Ecol Stat 10(15):429–443 Article Google Scholar
Chiloiro M, Darconza G, Piccioli E, De Carne M, Clemente C, Riezzo G (2001) Gastric emptying and orocecal transit time in pregnancy. J Gastroenterol 36(8):538–543 ArticleCASPubMed Google Scholar
Cleusix V, Lacroix C, Vollenweider S, Le Blay G (2008) Glycerol induces reuterin production and decreases Escherichia coli population in an in vitro model of colonic fermentation with immobilized human feces. FEMS Microbiol Ecol 63(1):56–64. doi:10.1111/j.1574-6941.2007.00412.x ArticleCASPubMed Google Scholar
Cleusix V, Lacroix C, Dasen G, Leo M, Le Blay G (2010) Comparative study of a new quantitative real-time PCR targeting the xylulose-5-phosphate/fructose-6-phosphate phosphoketolase bifidobacterial gene (xfp) in faecal samples with two fluorescence in situ hybridization methods. J Appl Microbiol 108(1):181–193. doi:10.1111/j.1365-2672.2009.04408.x ArticleCASPubMed Google Scholar
Collado MC, Isolauri E, Laitinen K, Salminen S (2008) Distinct composition of gut microbiota during pregnancy in overweight and normal-weight women. Am J Clin Nutr 88(4):894–899 CASPubMed Google Scholar
Costa F, Mumolo MG, Bellini M, Romano MR, Ceccarelli L, Arpe P, Sterpi C, Marchi S, Maltinti G (2003) Role of faecal calprotectin as non-invasive marker of intestinal inflammation. Digestive and liver disease: official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver 35(9):642–647 ArticleCAS Google Scholar
De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G, Lionetti P (2010) Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci USA 107(33):14691–14696. doi:10.1073/pnas.1005963107 ArticlePubMed Google Scholar
Gueimonde M, Debor L, Tolkko S, Jokisalo E, Salminen S (2007) Quantitative assessment of faecal bifidobacterial populations by real-time PCR using lanthanide probes. J Appl Microbiol 102(4):1116–1122. doi:10.1111/j.1365-2672.2006.03145.x CASPubMed Google Scholar
Guilloteau P, Martin L, Eeckhaut V, Ducatelle R, Zabielski R, Van Immerseel F (2010) From the gut to the peripheral tissues: the multiple effects of butyrate. Nutr Res Rev 23(2):366–384. doi:10.1017/S0954422410000247 ArticleCASPubMed Google Scholar
Jost T, Lacroix C, Braegger C, Chassard C (2013) Assessment of bacterial diversity in breast milk using culture-dependent and culture-independent approaches. Br J Nutr. doi:10.1017/S0007114513000597 PubMed Google Scholar
Jost T, Lacroix C, Braegger CP, Rochat F, Chassard C (2013) Vertical mother–neonate transfer of maternal gut bacteria via breastfeeding. Environ Microbiol. doi:10.1111/1462-2920.12238 Google Scholar
Ke D, Picard FJ, Martineau F, Menard C, Roy PH, Ouellette M, Bergeron MG (1999) Development of a PCR assay for rapid detection of enterococci. J Clin Microbiol 37(11):3497–3503 CASPubMed CentralPubMed Google Scholar
Koren O, Goodrich JK, Cullender TC, Spor A, Laitinen K, Backhed HK, Gonzalez A, Werner JJ, Angenent LT, Knight R, Backhed F, Isolauri E, Salminen S, Ley RE (2012) Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell 150(3):470–480. doi:10.1016/j.cell.2012.07.008 ArticleCASPubMed CentralPubMed Google Scholar
Lawson M, Kern F Jr, Everson GT (1985) Gastrointestinal transit time in human pregnancy: prolongation in the second and third trimesters followed by postpartum normalization. Gastroenterology 89(5):996–999 CASPubMed Google Scholar
Lee ZM, Bussema C 3rd, Schmidt TM (2009) rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Res (Database issue) 37:D489–493. doi:10.1093/nar/gkn689 ArticleCAS Google Scholar
Martín R, Langa S, Reviriego C, Jiménez E, Marín ML, Olivares M, Boza J, Jiménez J, Fernández L, Xaus J, Rodríguez JM (2004) The commensal microflora of human milk: new perspectives for food bacteriotherapy and probiotics. Trends Food Sci Technol 15(3–4):121–127 Article Google Scholar
Nicholson JK, Holmes E, Kinross J, Burcelin R, Gibson G, Jia W, Pettersson S (2012) Host-gut microbiota metabolic interactions. Science 336(6086):1262–1267. doi:10.1126/science.1223813 ArticleCASPubMed Google Scholar
Payne AN, Chassard C, Zimmermann M, Muller P, Stinca S, Lacroix C (2011) The metabolic activity of gut microbiota in obese children is increased compared with normal-weight children and exhibits more exhaustive substrate utilization. Nutr Diabetes 1:e12. doi:10.1038/nutd.2011.8 ArticleCASPubMed CentralPubMed Google Scholar
Perez PF, Dore J, Leclerc M, Levenez F, Benyacoub J, Serrant P, Segura-Roggero I, Schiffrin EJ, Donnet-Hughes A (2007) Bacterial imprinting of the neonatal immune system: lessons from maternal cells? Pediatrics 119(3):e724–e732. doi:10.1542/peds.2006-1649 ArticlePubMed Google Scholar
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75(23):7537–7541. doi:10.1128/AEM.01541-09 ArticleCASPubMed CentralPubMed Google Scholar
Schwiertz A, Taras D, Schafer K, Beijer S, Bos NA, Donus C, Hardt PD (2010) Microbiota and SCFA in lean and overweight healthy subjects. Obesity (Silver Spring) 18(1):190–195. doi:10.1038/oby.2009.167 Article Google Scholar
Suau A, Bonnet R, Sutren M, Godon JJ, Gibson GR, Collins MD, Dore J (1999) Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl Environ Microbiol 65(11):4799–4807 CASPubMed CentralPubMed Google Scholar
van den Bogert B, de Vos WM, Zoetendal EG, Kleerebezem M (2011) Microarray analysis and barcoded pyrosequencing provide consistent microbial profiles depending on the source of human intestinal samples. Appl Environ Microbiol 77(6):2071–2080. doi:10.1128/AEM.02477-10 ArticlePubMed CentralPubMed Google Scholar
Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI (2012) Human gut microbiome viewed across age and geography. Nature 486(7402):222–227. doi:10.1038/nature11053 CASPubMed CentralPubMed Google Scholar