Abdo Z, Schüette UME, Bent SJ, Williams CJ, Forney LJ, Joyce P (2006) Statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes. Environ Microbiol 8:929–938
PubMed
Google Scholar
Ahlroos T, Tynkkynen S (2009) Quantitative strain-specific detection of Lactobacillus rhamnosus GG in human faecal samples by real-time PCR. J Appl Microbiol 106:506–514
CAS
PubMed
Google Scholar
Alakomi HL, Skytta E, Saarela M, Mattila-Sandholm T, Latva-Kala K, Helander IM (2000) Lactic acid permeabilizes gram-negative bacteria by disrupting the outer membrane. Appl Environ Microbiol 66:2001–2005
PubMed Central
CAS
PubMed
Google Scholar
Almeida MHB, Zoellner SS, Da Cruz AG, Moura MRL, Carvalho LMJ, Freitas MCJ, Sant’Ana AS (2008) Potentially probiotic açaí yogurt. Int J Dairy Technol 61:178–182
Google Scholar
Almeida CC, Lorena SLS, Pavan CR, Akasaka HMI, Mesquita MA (2012) Beneficial effects of long-term consumption of a probiotic combination of Lactobacillus casei Shirota and Bifidobacterium breve Yakult may persist after suspension of therapy in lactose-intolerant patients. Nutr Clin Pract 27:247–251
PubMed
Google Scholar
Al-Salami H, Butt G, Fawcett JP, Tucker IG, Golocorbin-Kon S, Mikov M (2008) Probiotic treatment reduces blood glucose levels and increases systemic absorption of gliclazide in diabetic rats. Eur J Drug Metab Pharmacokinet 33:101–106
CAS
PubMed
Google Scholar
Al-Saleh AA, Metwalli AAM, Abu-Tarboush HM (2006) Bile salts and acid tolerance and cholesterol removal from media by some lactic acid bacteria and bifidobacteria. J Saudi Soc Food Nutr 1:1–17
Google Scholar
Alvaro E, Andrieux C, Rochet V, Rigottier-Gois L, Lepercq P, Sutren M, Galan P, Duval Y, Juste C, Dore J (2007) Composition and metabolism of the intestinal microbiota in consumers and non-consumers of yogurt. Br J Nutr 97:126–133
CAS
PubMed
Google Scholar
Amit-Romach E, Uni Z, Reifen R (2010) Multistep mechanism of probiotic bacterium, the effect on innate immune system. Mol Nutr Food Res 54:277–284
CAS
PubMed
Google Scholar
Anderson RC, Cookson AL, McNabb WC, Park Z, McCann MJ, Kelly WJ, Roy NC (2010) Lactobacillus plantarum MB452 enhances the function of the intestinal barrier by increasing the expression levels of genes involved in tight junction formation. BMC Microbiol 10:1–11
Google Scholar
Ataie-Jafari A, Larijani B, Majd HA, Tahbaz F (2009) Cholesterol-lowering effect of probiotic yogurt in comparison with ordinary yogurt in mildly to moderately hypercholesterolemic subjects. Ann Nutr Metab 54:22–27
CAS
PubMed
Google Scholar
Bach J-F (2002) The effect of infections on susceptibility to autoimmune and allergic diseases. N Engl J Med 347:911–920
PubMed
Google Scholar
Barbara G, Stanghellini V, Brandi G, Cremon C, Di Nardo G, De Giorgio R, Corinaldesi R (2005) Interactions between commensal bacteria and gut sensorimotor function in health and disease. Am J Gastroenterol 100:2560–2568
CAS
PubMed
Google Scholar
Bermudez-Brito M, Plaza-Díaz J, Muñoz-Quezada S, Gómez-Llorent C, Gil A (2012) Probiotic mechanisms of action. Ann Nutr Metab 61:160–174
CAS
PubMed
Google Scholar
Bhardwaj A, Bhardwaj SV (2012) Role of probiotics in dental caries and periodontal disease. Arch Clin Exp Surg 1:45–49
Google Scholar
Bigliardi B, Galati F (2013) Innovation trends in food industry: the case of functional foods. Trends Food Sci Technol 31:118–129
CAS
Google Scholar
Björkstén B, Sepp E, Julge K, Voor T, Mikelsaar M (2001) Allergy development and the intestinal microflora during the first year of life. J Allergy Clin Immunol 108:516–520
PubMed
Google Scholar
Boerner BP, Sarvetnick NE (2011) Type 1 diabetes: role of intestinal microbiome in humans and mice. Ann N Y Acad Sci 1243:103–118
CAS
PubMed
Google Scholar
Borchers AT, Selmi C, Meyers FJ, Keen CL, Gershwin ME (2009) Probiotics and immunity. J Gastroenterol 44:26–46
PubMed
Google Scholar
Bravo JA, Forsythe P, Chew MV, Escaravage E, Savignac HM, Dinan TG, Bienenstock J, Cryan JF (2011) Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve. Proc Natl Acad Sci U S A 20:16050–16055
Google Scholar
Brown MV, Schwalbach MS, Hewson I, Fuhrman JA (2005) Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series. Environ Microbiol 7:1466–1479
CAS
PubMed
Google Scholar
Bull-Otterson L, Feng W, Kirpich I, Wang Y, Qin X, Liu Y, Gobejishvili L, Joshi-Barve S, Ayvaz T, Petrosino J, Kong M, Barker D, McClain C, Barve S (2013) Metagenomic analyses of alcohol induced pathogenic alterations in the intestinal microbiome and the effect of Lactobacillus rhamnosus GG treatment. PloS One 8, e53028
PubMed Central
CAS
PubMed
Google Scholar
Carroll IM, Chang YH, Park J, Sartor RB, Ringel Y (2010) Luminal and mucosal-associated intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome. Gut Pathog 2:1–9
Google Scholar
Christensen HR, Frokiaer H, Pestka JJ (2002) Lactobacilli differentially modulate expression of cytokines and maturation surface markers in murine dendritic cells. J Immunol 168:171–178
CAS
PubMed
Google Scholar
Collado MC, Gueimonde M, Hernández M, Sanz Y, Salminen S (2005) Adhesion of selected Bifidobacterium strains to human intestinal mucus and the role of adhesion in enteropathogen exclusion. J Food Prot 68:2672–2678
PubMed
Google Scholar
Collado MC, Calabuig M, Sanz Y (2007) Differences between the fecal microbiota of coeliac infants and healthy controls. Curr Issues Intest Microbiol 8:9–14
CAS
PubMed
Google Scholar
Collado MC, Isolauri E, Salminen S, Sanz Y (2009) The impact of probiotic on gut health. Curr Drug Metab 10:68–78
CAS
PubMed
Google Scholar
Da Cruz AG, Fonseca Faria JDA, Isay Saad SM, André Bolini HM, Sant’Ana AS, Cristianini M (2010) High pressure processing and pulsed electric fields: potential use in probiotic dairy foods processing. Trends Food Sci Technol 21:483–493
Google Scholar
De Keersmaecker SC, Verhoeven TL, Desair J, Marchal K, Vanderleyden J, Nagy I (2006) Strong antimicrobial activity of Lactobacillus rhamnosus GG against Salmonella typhimurium is due to accumulation of lactic acid. FEMS Microbiol Lett 259:89–96
PubMed
Google Scholar
De Sousa Moraes LF, Grzeskowiak LM, De Sales Teixeira TF, Gouveia Peluzio MDC (2014) Intestinal microbiota and probiotics in celiac disease. Clin Microbiol Rev 27:482–489
PubMed
Google Scholar
Del Campo R, Garriga M, Pérez-Aragón A, Guallarte P, Lamas A, Máiz L, Bayón C, Roy G, Cantón R, Zamora J, Baquero F, Suárez L (2014) Improvement of digestive health and reduction in proteobacterial populations in the gut microbiota of cystic fibrosis patients using a Lactobacillus reuteri probiotic preparation: a double blind prospective study. J Cyst Fibros 13:716–722
PubMed
Google Scholar
Delmont TO, Simonet P, Vogel TM (2012) Describing microbial communities and performing global comparisons in the ‘omic era. ISME J 6:1625–1628
PubMed Central
PubMed
Google Scholar
Dethlefsen L, Huse S, Sogin ML, Relman DA (2008) The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6:2383–2400
CAS
Google Scholar
Dolin BJ (2009) Effects of a proprietary Bacillus coagulans preparation on symptoms of diarrhea-predominant irritable bowel syndrome. Methods Find Exp Clin Pharmacol 31:655–659
CAS
PubMed
Google Scholar
Duc LH, Hong HA, Barbosa TM, Henriques AO, Cutting SM (2004) Characterization of Bacillus probiotics available for human use. Appl Environ Microbiol 70:2161–2171
PubMed Central
CAS
Google Scholar
Dunn WB, Bailey NJC, Johnson HE (2005) Measuring the metabolome: current analytical technologies. Analyst 130:606–625
CAS
PubMed
Google Scholar
Ebel B, Lemetais G, Beney L, Cachon R, Sokol H, Langella P, Gervais P (2014) Impact of probiotics on risk factors for cardiovascular diseases. A review. Crit Rev Food Sci Nutr 54:175–189
PubMed
Google Scholar
Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA (2005) Diversity of the human intestinal microbial flora. Science 308:1635–1638
PubMed Central
PubMed
Google Scholar
Engelbrektson A, Korzenik JR, Pittler A, Sanders ME, Klaenhammer TR, Leyer G, Kitts CL (2009) Probiotics to minimize the disruption of faecal microbiota in healthy subjects undergoing antibiotic therapy. J Med Microbiol 58:663–670
CAS
PubMed
Google Scholar
Espey MG (2013) Role of oxygen gradients in shaping redox relationships between the human intestine and its microbiota. Free Radic Biol Med 55:130–140
CAS
PubMed
Google Scholar
FAO/WHO (2002) Working group report on drafting guidelines for the evaluation of probiotics in food. Canada Food and Agriculture Organization of the United Nations (FAO) and the World Health Organization (WHO), Ontario. Available at: ftp://ftp.fao.org/es/esn/food/wgreport2.pdf. Accessed 30 Jul 2014
Feligini M, Panelli S, Sacchi R, Ghitti M, Capelli E (2015) Tracing the origin of raw milk from farm by using Automated Ribosomal Intergenic Spacer Analysis (ARISA) fingerprinting of microbiota. Food Control 50:51–56
CAS
Google Scholar
Ferguson RM, Merrifield DL, Harper GM, Rawling MD, Mustafa S, Picchietti S, Balcazar JL, Davies SJ (2010) The effect of Pediococcus acidilactici on the gut microbiota and immune status of on-growing red tilapia (Oreochromis niloticus). J Appl Microbiol 109:851–862
CAS
PubMed
Google Scholar
Filteau M, Matamoros S, Savard P, Roy D (2013) Molecular monitoring of fecal microbiota in healthy adults following probiotic yogurt intake. Pharma Nutr 1:123–129
CAS
Google Scholar
Finegold SM, Molitoris D, Song Y, Liu C, Vaisanen ML, Bolte E, McTeague M, Sandler R, Wexler H, Marlowe EM, Collins MD, Lawson PA, Summanen P, Baysallar M, Tomzynski TJ, Read E, Johnson E, Rolfe R, Nasir P, Shah H, Haake DA, Manning P, Kaul A (2002) Gastrointestinal microflora studies in late-onset autism. Clin Infect Dis 35:S6–S16
PubMed
Google Scholar
Fooks LJ, Gibson GR (2002) Probiotics as modulators of the gut flora. Br J Nutr 88:S39–S49
CAS
PubMed
Google Scholar
Fuentes S, Egert M, Jiménez-Valera M, Ramos-Cormenzana A, Ruiz-Bravo A, Smidt H, Monteoliva-Sanchez M (2008) Administration of Lactobacillus casei and Lactobacillus plantarum affects the diversity of murine intestinal lactobacilli, but not the overall bacterial community structure. Res Microbiol 159:237–243
CAS
PubMed
Google Scholar
García-Albiach R, Pozuelo de Felipe MJ, Ângulo S, Morosini MI, Bravo D, Baquero F, Del Campo R (2008) Molecular analysis of yogurt containing Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus in human intestinal microbiota. Am J Clin Nutr 87:91–96
PubMed
Google Scholar
Garrido D, Suau A, Pochart P, Cruchet S, Gotteland M (2005) Modulation of the fecal microbiota by the intake of a Lactobacillus johnsonii La1-containing product in human volunteers. FEMS Microbiol Lett 248:249–256
CAS
PubMed
Google Scholar
Gerritsen J, Smidt H, Rijkers GT, Vos WM (2011) Intestinal microbiota in human health and disease: the impact of probiotics. Genes Nutr 6:209–240
PubMed Central
PubMed
Google Scholar
Gibson GR, Roberfroid MB (1995) Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. J Nutr 125:1401–1412
CAS
PubMed
Google Scholar
Gilbert JA, Dupont CL (2011) Microbial metagenomics: beyond the genome. Ann Rev Mar Sci 3:347–371
PubMed
Google Scholar
Gómez-Llorente C, Muñoz S, Gil A (2010) Role of Toll-like receptors in the development of immunotolerance mediated by probiotics. Proc Nutr Soc 69:381–389
PubMed
Google Scholar
González-Rodríguez I, Sánchez B, Ruiz L, Turroni F, Ventura M, Ruas-Madiedo P, Gueimonde M, Margolles A (2012) Role of extracellular transaldolase from Bifidobacterium bifidum in mucin adhesion and aggregation. Appl Environ Microbiol 78:3992–3998
PubMed Central
PubMed
Google Scholar
Gosalbes MJ, Durbán A, Pignatelli M, Abellan JJ, Jiménez-Hernández N, Pérez-Cobas AE, Latorre A, Moya A (2011) Metatranscriptomic approach to analyze the functional human gut microbiota. PLoS ONE 6:e17447
PubMed Central
CAS
PubMed
Google Scholar
Guarner F, Malagelada JR (2003) Gut flora in health and disease. Lancet 361:512–519
PubMed
Google Scholar
Gueimonde M, Collado MC (2012) Metagenomics and probiotics. Clin Microbiol Infect 18:32–34
CAS
PubMed
Google Scholar
Guinane CM, Cotter PD (2013) Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ. Ther Adv Gastroenterol 6:295–308
Google Scholar
Hassan M, Kjos M, Nes IF, Diep DB, Lotfipour F (2012) Natural antimicrobial peptides from bacteria: characteristics and potential applications to fight against antibiotic resistance. J Appl Microbiol 113:723–736
CAS
PubMed
Google Scholar
He T, Priebe MG, Zhong Y, Huang C, Harmsen HJM, Raangs GC, Antoine JM, Welling GW, Vonk RJ (2008) Effects of yogurt and bifidobacteria supplementation on the colonic microbiota in lactose-intolerant subjects. J Appl Microbiol 104:595–604
CAS
PubMed
Google Scholar
Heller KJ (2001) Probiotic bacteria in fermented foods: product characteristics and starter organisms. Am J Clin Nutr 73:374S–379S
CAS
PubMed
Google Scholar
Heller MJ (2002) DNA microarray technology: devices, systems and applications. Annu Rev Biomed Eng 4:129–153
CAS
PubMed
Google Scholar
Herfel TM, Jacobi SK, Lin X, Jouni ZE, Chichlowski M, Stahl CH, Odle J (2013) Dietary supplementation of Bifidobacterium longum strain AH1206 increases its cecal abundance and elevates intestinal interleukin-10 expression in the neonatal piglet. Food Chem Toxicol 60:116–122
CAS
PubMed
Google Scholar
Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ, Pot B, Morelli L, Canani RB, Flint HJ, Salminen S, Calder PC, Sanders ME (2014) Expert consensus document: the International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepathol 11:506–514
Google Scholar
Hooda S, Boler BMV, Serao MCR, Brulc JM, Staeger MA, Boileau TW, Dowd SE, Fahey GC Jr, Swanson KS (2012) 454 Pyrosequencing reveals a shift in faecal microbiota of healthy adult men consuming polydextrose or soluble corn fiber. J Nutr 142:1259–1265
CAS
PubMed
Google Scholar
Hooper LV, Wong MH, Thelin A, Hansson L, Falk PG, Gordon JI (2001) Molecular analysis of commensal host-microbial relationships in the intestine. Science 291:881–884
CAS
PubMed
Google Scholar
Hooper LV, Stappenbeck TS, Hong CV, Gordon JI (2003) Angiogenins: a new class of microbicidal proteins involved in innate immunity. Nat Immunol 4:269–273
CAS
PubMed
Google Scholar
Hougee S, Vriesema AJ, Wijering SC, Knippels LM, Folkerts G, Nijkamp FP, Knol J, Garssen J (2010) Oral treatment with probiotics reduces allergic symptoms in ovalbumin-sensitized mice: a bacterial strain comparative study. Int Arch Allergy Immunol 151:107–117
CAS
PubMed
Google Scholar
Howarth GS, Wang H (2013) Role of endogenous microbiota, probiotics and their biological products in human health. Nutrients 5:58–81
PubMed Central
CAS
PubMed
Google Scholar
Huang Y, Wang J, Cheng Y, Zheng Y (2010) The hypocholesterolaemic effects of Lactobacillus acidophilus American Type Culture Collection 4356 in rats are mediated by the down-regulation of Niemann-Pick C1-Like 1. Br J Nutr 104:807–812
CAS
PubMed
Google Scholar
Hun L (2009) Bacillus coagulans significantly improved abdominal pain and bloating in patients with IBS. Postgrad Med 121:119–124
PubMed
Google Scholar
Im E, Choi YJ, Pothoulakis C, Rhee SH (2009) Bacillus polyfermenticus ameliorates colonic inflammation by promoting cytoprotective effects in colitic mice. J Nutr 139:1848–1854
PubMed Central
CAS
PubMed
Google Scholar
Jauhiainen T, Collin M, Narva M, Cheng ZJ, Poussa T, Vapaatalo H, Korpela R (2005) Effect of long-term intake of milk peptides and minerals on blood pressure and arterial function in spontaneously hypertensive rats. Milchwissenschaft 60:358–363
CAS
Google Scholar
Jensen GS, Benson KF, Carter SG, Endres JR (2010) GanedenBC30™ cell wall and metabolites: anti-inflammatory and immune modulating effects in vitro. BMC Immunol 11:1–15
Google Scholar
Joossens M, Huys G, Cnockaert M, De Preter V, Verbeke K, Rutgeerts P, Vandamme P, Vermeire S (2011) Dysbiosis of the faecal microbiota in patients with Crohn’s disease and their unaffected relatives. Gut 60:631–637
PubMed
Google Scholar
Kajander K, Myllyluoma E, Rajili´c –Stojanovi´c M, Kyronpalo S, Rasmussen M, Jarvenpaa S, Zoetendal EG, Vos WMD, Vapaatalo H, Korpela R (2008) Clinical trial: multispecies probiotic supplementation alleviates the symptoms of irritable bowel syndrome and stabilizes intestinal microbiota. Aliment Pharmacol Ther 27:48–57
CAS
PubMed
Google Scholar
Kerckhoffs AP, Samsom M, Van der Rest ME, De Vogel J, Knol J, Ben-Amor K, Akkermans LM (2009) Lower Bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients. World J Gastroenterol 15:2887–2892
PubMed Central
PubMed
Google Scholar
Kim YS, Ho SB (2010) Intestinal goblet cells and mucins in health and disease: recent insights and progress. Curr Gastroenterol Rep 12:319–330
PubMed Central
PubMed
Google Scholar
Kim Y, Lee D, Kim D, Cho J, Yang J, Chung M, Kim K, Ha N (2008) Inhibition of proliferation in colon cancer cell lines and harmful enzyme activity of colon bacteria by Bifidobacterium adolescentis SPM0212. Arch Pharm Res 31:468–473
CAS
PubMed
Google Scholar
Kimmel M, Keller D, Farmer S, Warrino DE (2010) A controlled clinical trial to evaluate the effect of GanedenBC30 on immunological markers. Methods Find Exp Clin Pharmacol 32:129–132
CAS
PubMed
Google Scholar
Kirjavainen PV, Apostolou E, Arvola T, Salminen SJ, Gibson GR, Isolauri E (2001) Characterizing the composition of intestinal microflora as a prospective treatment target in infant allergic disease. FEMS Immunol Med Microbiol 32:1–7
CAS
PubMed
Google Scholar
Kirjavainen PV, Salminen SJ, Isolauri E (2003) Probiotic bacteria in the management of atopic disease: underscoring the importance of viability. J Pediatr Gastroenterol Nutr 36:223–227
PubMed
Google Scholar
Kitts CL (2001) Terminal restriction fragment patterns: a tool for comparing microbial communities and assessing community dynamics. Curr Issues Intest Microbiol 2:17–25
CAS
PubMed
Google Scholar
Kostic AD, Xavier RJ, Gevers D (2014) The microbiome in inflammatory bowel disease: current status and the future ahead. Gastroenterology 146:1489–1499
CAS
PubMed
Google Scholar
Krasse P, Carlsson B, Dahl C, Paulsson A, Nilsson A, Sinkiewicz G (2005) Decreased gum bleeding and reduced gingivitis by the probiotic Lactobacillus reuteri. Swed Dent J 30:55–60
Google Scholar
Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, Takami H, Morita H, Sharma VK, Srivastava TP, Taylor TD, Noguchi H, Mori H, Ogura Y, Ehrlich DS, Itoh K, Takagi T, Sakaki Y, Hayashi T, Hattori M (2007) Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res 14:169–181
PubMed Central
CAS
PubMed
Google Scholar
Lahtinen SJ, Tammela L, Korpela J, Parhiala R, Ahokoski H, Mykkä nen H, Salminen SJ (2009) Probiotics modulate the Bifidobacterium microbiota of elderly nursing home residents. Age 31:59–66
PubMed Central
PubMed
Google Scholar
Langley SR, Dwyer J, Drozdov I, Yin X, Mayr M (2013) Proteomics: from single molecules to biological Pathways. Cardiovasc Res 97:612–622
PubMed Central
CAS
PubMed
Google Scholar
Lebeer S, Vanderleyden J, De Keersmaecker CJ (2010) Host interactions of probiotic bacterial surface molecules: comparison with commensals and pathogens. Nat Rev Microbiol 8:171–184
CAS
PubMed
Google Scholar
Lee NK, Park JS, Park E, Paik HD (2007) Adherence and anticarcinogenic effects of Bacillus polyfermenticus SCD in the large intestine. Lett Appl Microbiol 44:274–278
PubMed
Google Scholar
Lee J, Rheem S, Yun B, Ahn Y, Joung J, Lee SJ, Oh S, Chun T, Rheem I, Yea HS, Lim KS, Cha JM, Kim S (2013) Effects of probiotic yoghurt on symptoms and intestinal microbiota in patients with irritable bowel syndrome. Int J Dairy Technol 66:243–255
CAS
Google Scholar
Lee J-Y, Chu S-H, Jeon JY, Lee M-K, Park J-H, Lee D-C, Lee J-W, Kim N-K (2014) Effects of 12 weeks of probiotic supplementation on quality of life in colorectal cancer survivors: a double-blind, randomized, placebo-controlled trial. Dig Liver Dis 46:1126–1132
PubMed
Google Scholar
Lepage P, Leclerc MC, Joossens M, Mondot S, Blottière HM, Raes J, Ehrlich D, Dore J (2013) A metagenomic insight into our gut’s microbiome. Gut 62:146–158
PubMed
Google Scholar
Levy M, Thaiss CA, Elinav E (2014) The microbiota: a new player in the etiology of colorectal cancer. Curr Colorectal Cancer Rep 10:1–8
Google Scholar
Li F, Hullar MA, Lampe JW (2007) Optimization of terminal restriction fragment polymorphism (TRFLP) analysis of human gut microbiota. J Microbiol Methods 68:303–311
PubMed Central
CAS
PubMed
Google Scholar
Lutgendorff F, Akkermans LMA, Söderholm JD (2008) The role of microbiota and probiotics in stress-induced gastrointestinal damage. Curr Mol Med 8:282–298
CAS
PubMed
Google Scholar
Maathuis AJH, Keller D, Farmer S (2010) Survival and metabolic activity of the GanedenBC30 strain of Bacillus coagulans in a dynamic in vitro model of the stomach and small intestine. Benefic Microbes 1:31–36
CAS
Google Scholar
Maekawa T, Hajishengallis G (2014) Topical treatment with probiotic Lactobacillus brevis CD2 inhibits experimental periodontal inflammation and bone loss. J Periodontal Res 49:785–791
CAS
PubMed
Google Scholar
Makras L, Triantafyllou V, Fayol-Messaoudi D, Adriany T, Zoumpopoulou G, Tsakalidou E, Servin A, DeVuyst L (2006) Kinetic analysis of the antibacterial activity of probiotic lactobacilli towards Salmonella enterica serovar Typhimurium reveals a role for lactic acid and other inhibitory compounds. Res Microbiol 157:241–247
CAS
PubMed
Google Scholar
Malinen E, Krogius-Kurikka L, Lyra A, Nikkıla J, Jaaskelainen A, Rinttila T, Vilpponen-Salmela T, Von Wright AJ, Palva A (2010) Association of symptoms with gastrointestinal microbiota in irritable bowel syndrome. World J Gastroenterol 16:4532–4540
PubMed Central
CAS
PubMed
Google Scholar
Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E, Frangeul L, Nalin R, Jarrin C, Chardon P, Marteau P, Roca J, Dore J (2006) Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut 55:205–211
PubMed Central
CAS
PubMed
Google Scholar
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380
PubMed Central
CAS
PubMed
Google Scholar
Martinez RCR, Seney SL, Summers KL, Nomizo A, De Martinis ECP, Reid G (2009) Effect of Lactobacillus rhamnosus GR-1 and Lactobacillus reuteri RC-14 on the ability of Candida albicans to infect cells and induce inflammation. Microbiol Immunol 53:487–495
CAS
PubMed
Google Scholar
Martinez RCR, Cardarelli H, Borst W, Albrecht S, Schols H, Gutiérrez OP, Maathuis A, Franco BDGM, De Martinis ECP, Zoetendal E, Venema K, Saad SMI, Smidt H (2013) Effect of galactooligosaccharides and Bifidobacterium animalis Bb-12 on growth of Lactobacillus amylovorus DSM 16698, microbial community structure and metabolite production in an in vitro colonic model set up with human or pig microbiota. FEMS Microbiol Ecol 84:110–123
CAS
PubMed
Google Scholar
Marzotto M, Maffeis C, Paternoster T, Ferrario R, Rizzotti L, Pellegrino M, Dellaglio F, Torriani S (2006) Lactobacillus paracasei A survives gastrointestinal passage and affects the fecal microbiota of healthy infants. Res Microbiol 157:857–866
CAS
PubMed
Google Scholar
Mättö J, Maunuksela L, Kajander K, Palva A, Korpela R, Kassinen A, Saarela M (2005) Composition and temporal stability of gastrointestinal microbiota in irritable bowel syndrome—a longitudinal study in IBS and control subjects. FEMS Immunol Med Microbiol 43:213–222
PubMed
Google Scholar
Maukonen J, Satokari R, Matto J, So derlund H, Mattila-Sandholm T, Saarela M (2006) Prevalence and temporal stability of selected clostridial groups in irritable bowel syndrome in relation to predominant faecal bacteria. J Med Microbiol 55:625–633
CAS
PubMed
Google Scholar
McCartney AL (2002) Application of molecular biological methods for studying probiotics and the gut flora. Br J Nutr 88:S29–S37
CAS
PubMed
Google Scholar
Medici M, Vinderola CG, Perdigón G (2004) Gut mucosal immunomodulation by probiotic fresh cheese. Int Dairy J 14:611–618
Google Scholar
Messaoudi M, Violle N, Bisson J, Desor D, Javelot H, Rougeot C (2011) Beneficial psychological effects of a probiotic formulation (Lactobacillus helveticus R0052 and Bifidobacterium longum R0175) in healthy human volunteers. Gut Microbes 2:256–261
PubMed
Google Scholar
Miquel S, Martín R, Rossi O, Bermúdez-Humarán LG, Chatel JM, Sokol H, Thomas M, Wells JM, Langella P (2013) Faecalibacterium prausnitzii and human intestinal health. Curr Opin Microbiol 16:1–7
Google Scholar
Mirzaei H, Shahirfar H, Mobayen H (2012) Effect of consumption of fermented milk with Lactobacillus casei and Lactobacillus plantarum isolated from ligvan cheese against E. coli O157:H7 induced infections in BALB/C mice. Adv Biores 3:34–38
Google Scholar
Mohan R, Koebnick C, Schildt J, Schmidt S, Mueller M, Possner M, Radke M, Blaut M (2006) Effects of Bifidobacterium lactis Bb12 supplementation on intestinal microbiota of preterm infants: a double-blind, placebo-controlled, randomized study. J Clin Microbiol 44:4025–4031
PubMed Central
PubMed
Google Scholar
Montesi A, García-Albiach R, Pozuelo MJ, Pintado C, Goñi I, Rotger R (2005) Molecular and microbiological analysis of caecal microbiota in rats fed with diets supplemented either with prebiotics or probiotics. Int J Food Microbiol 98:281–289
CAS
PubMed
Google Scholar
Muyzer G (1999) DGGE / TGGE a method for identifying genes from natural ecosystems. Curr Opin Microbiol 2:317–322
CAS
PubMed
Google Scholar
Ng SC, Hart AL, Kamm MA, Stagg AJ, Knight SC (2009) Mechanisms of action of probiotics: recent advances. Inflamm Bowel Dis 15:300–310
CAS
PubMed
Google Scholar
Ng SC, Lam EFC, Lam TTY, Chan Y, Law W, Tse PCH, Kamm MA, Sung JJY, Chan FKL, Wu JCY (2013) Effect of probiotic bacteria on the intestinal microbiota in irritable bowel syndrome. J Gastroenterol Hepatol 28:1624–1631
PubMed
Google Scholar
Nielsen DS, Cho GS, Hanak A, Huch M, Franz CM, Arneborg N (2010) The effect of bacteriocin-producing Lactobacillus plantarum strains on the intracellular pH of sessile and planktonic Listeria monocytogenes single cells. Int J Food Microbiol 141:S53–S59
PubMed
Google Scholar
Nobaek S, Johansson M, Molin G, Ahrné S, Jeppsson B (2000) Alteration of intestinal microflora is associated with reduction in abdominal bloating and pain in patients with irritable bowel syndrome. Am J Gastroenterol 95:1231–1238
CAS
PubMed
Google Scholar
Nogueira JCR, Gonçalves MCR (2011) Probióticos - Revisão da Literatura. RBCS 15:487–492
Google Scholar
O’Mahony L, Mccarthy J, Kelly P, Hurley G, Luo F, Chen K, O’Sullivan GC, Kiely B, Collins JK, Shanahan F, Quigley EM (2005) Lactobacillus and Bifidobacterium in irritable bowel syndrome: symptom responses and relationship to cytokine profiles. Gastroenterology 128:541–551
PubMed
Google Scholar
O'Hara AM, Shanahan F (2006) The gut flora as a forgotten organ. EMBO Rep 7:688–693
PubMed Central
PubMed
Google Scholar
Ohland CL, Macnaughton WK (2010) Probiotic bacteria and intestinal epithelial barrier function. Am J Physiol Gastrointest Liver Physiol 298:G807–G819
CAS
PubMed
Google Scholar
Osborn AM, Moore ER, Timmis KN (2000) An evaluation of terminal restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. Environ Microbiol 2:39–50
CAS
PubMed
Google Scholar
Ouwehand AC, Bergsma N, Parhiala R, Lahtinen S, Gueimonde M, Finne-Soveri H, Strandberg T, Pitkälä K, Salminen S (2008) Bifidobacterium microbiota and parameters of immune function in elderly subjects. FEMS Immunol Med Microbiol 53:18–25
CAS
PubMed
Google Scholar
Paik H, Park J, Park E (2005) Effects of Bacillus polyfermenticus SCD on Lipid and antioxidant metabolisms in rats fed a high-fat and high-cholesterol diet. Biol Pharm Bull 28:1270–1274
CAS
PubMed
Google Scholar
Palomar MM, Galdeano CM, Perdigón G (2013) Influence of a probiotic Lactobacillus strain on the intestinal ecosystem in a stress model mouse. Brain Behav Immun 35:77–85
PubMed
Google Scholar
Paul J, Verma AK, Verma R (2007) Role of gut flora in inflammatory bowel disease: a state of art. In: Mendez-Vilas A (ed) Communicating current research and educational topics and trends in applied microbiology. Formatex, Madrid, pp 705–718
Google Scholar
Peterson DA, Frank DN, Pace NR, Gordon JI (2008) Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases. Cell Host Microbe 3:417–427
PubMed Central
CAS
PubMed
Google Scholar
Prakash S, Rodes L, Coussa-Charley M, Tomaro-Duchesneau C (2011) Gut microbiota: next frontier in understanding human health and development of biotherapeutics. Biologics 5:71–86
PubMed Central
PubMed
Google Scholar
Preidis GA, Saulnier DM, Blutt SE, Mistretta T, Riehle KP, Major AM, Venable SF, Finegold MJ, Petrosino JF, Conner ME, Versalovic J (2012) Probiotics stimulate enterocyte migration and microbial diversity in the neonatal mouse intestine. FASEB J26:1960–1969
Google Scholar
Rajilic-Stojanovic M (2013) Function of the microbiota. Best Pract Res Clin Gastroenterol 27:5–16
CAS
PubMed
Google Scholar
Rajilic-Stojanovic M, Smidt H, de Vos WM (2007) Diversity of the human gastrointestinal tract microbiota revisited. Environ Microbiol 9:2125–2136
PubMed
Google Scholar
Ramos MA, Weber B, Gonçalves JF, Santos GA, Rema P, Ozório ROA (2013) Dietary probiotic supplementation modulated gut microbiota and improved growth of juvenile rainbow trout (Oncorhynchus mykiss). Comp Biochem Physiol A 166:302–307
CAS
Google Scholar
Rampelli S, Candela M, Severgnini M, Biagi E, Turroni S, Roselli M, Carnevali P, Donini L, Brigidi P (2013) A probiotics-containing biscuit modulates the intestinal microbiota in the elderly. J Nutr Health Aging 17:166–172
CAS
PubMed
Google Scholar
Ranadheera RDCS, Baines SK, Adams MC (2010) Importance of food in probiotic efficacy. Food Res Int 43:1–7
CAS
Google Scholar
Rao AV, Bested AC, Beaulne TM, Katzman MA, Iorio C, Berardi JM, Logan AC (2009) A randomized, double-blind, placebo-controlled pilot study of a probiotic in emotional symptoms of chronic fatigue syndrome. Gut Pathog 1:1–6
Google Scholar
Rastogi G, Sani RK (2011) Molecular techniques to assess microbial community structure, function, and dynamics in the environment. In: Ahmad I, Ahmad F, Pichtel J (eds) Microbes and microbial technology: agricultural and environmental applications. Springer Science + Business Media LLC, New York, pp 29–57
Google Scholar
Rijkers GT, Bengmark S, Enck P, Haller D, Herz U, Kalliomaki M, Kudo S, Lenoir-Wijnkoop I, Mercenier A, Myllyluoma E, Rabot S, Rafter J, Szajewska H, Watzl B, Wells J, Wolvers D, Antoine JM (2010) Guidance for substantiating the evidence for beneficial effects of probiotics: current status and recommendations for future research. J Nutr 140:671S–676S
CAS
PubMed
Google Scholar
Roger LC, Costabile A, Holland DT, Hoyles L, McCartney AL (2010) Examination of faecal Bifidobacterium populations in breast- and formula-fed infants during the first 18 months of life. Microbiology 156:3329–3341
CAS
PubMed
Google Scholar
Rolfe RD (1991) Population dynamics of the intestinal tract. In: Blankenship LC (ed) Colonization control of human bacterial enteropathogens in poultry. Academic Press, San Diego, pp 59–75
Google Scholar
Russell WR, Duncan SH (2013) Advanced analytical methodologies to study the microbial metabolome of the human gut. Trends Analyt Chem 52:54–60
CAS
Google Scholar
Salminen S, Gueimonde M, Isolauri E (2005) Probiotics that modify disease risk. J Nutr 135:1294–1298
CAS
PubMed
Google Scholar
Sanders ME, Gibson G, Gill HS, Guarner F (2007) Probiotics: their potential to impact human health. CAST 36. Available at: http://www.cast-science.org/download.cfm?PublicationID=2930&File=f030d2d5777f5676ed033b112a7e65524518. Accessed 16 Oct 2014
Sartor RB (2006) Mechanisms of disease: pathogenesis of Crohn’s disease and ulcerative colitis. Nat Clin Pract Gastroenterol Hepatol 3:390–407
CAS
PubMed
Google Scholar
Satokari RM, Vaughan EE, Akkermans AD, Saarela M, de Vos WM (2001) Polymerase chain reaction and denaturing gradient gel electrophoresis monitoring of fecal Bifidobacterium populations in a prebiotic and probiotic feeding trial. Syst Appl Microbiol 24:227–231
CAS
PubMed
Google Scholar
Scanlan PD, Shanahan F, Clune Y, Collins JK, O’Sullivan GC, O’Riordan M, Holmes E, Wang Y, Marchesi JR (2008) Culture-independent analysis of the gut microbiota in colorectal cancer and polyposis. Environ Microbiol 10:789–798
CAS
PubMed
Google Scholar
Sekirov I, Russell SL, Antunes LCM, Finlay BB (2010) Gut microbiota in health and disease. Physiol Rev 90:859–904
CAS
PubMed
Google Scholar
Seppo L, Jauhiainen T, Poussa T, Korpela R (2003) A fermented milk high in bioactive peptides has a blood pressure-lowering effect in hypertensive subjects. Am J Clin Nutr 77:326–330
CAS
PubMed
Google Scholar
Shah NP (2007) Functional cultures and health benefits. Int Dairy J 17:1262–1277
Google Scholar
Sindhu SC, Khetarpaul N (2003) Effect of feeding probiotic fermented indigenous food mixture on serum cholesterol levels in mice. Nutr Res 23:1071–1080
CAS
Google Scholar
Smith CJ, Danilowicz BS, Clear AK, Costello FJ, Wilson B, Meijer WG (2005) T-Align, a web-based tool for comparison of multiple terminal restriction fragment length polymorphism profiles. FEMS Microbiol Ecol 54:375–380
CAS
PubMed
Google Scholar
Staliano CD, Martinez RCR, Saad SMI (2015) Beneficial microorganisms viability and sensory acceptance of a potentially synbiotic dairy-based tomato spread. LWT Food Sci Technol 62:682–688
CAS
Google Scholar
Su C, Lei L, Duan Y, Zhang K-Q, Yang J (2012) Culture-independent methods for studying environmental microorganisms: methods, application, and perspective. Appl Microbiol Biotechnol 93:993–1003
CAS
PubMed
Google Scholar
Sun Y-Z, Yang H-L, Ma R-L, Song K, Lin W-Y (2011) Molecular analysis of autochthonous microbiota along the digestive tract of juvenile grouper Epinephelus coioides following probiotic Bacillus pumilus administration. J Appl Microbiol 110:1093–1103
CAS
PubMed
Google Scholar
Suzuki S, Shimojo N, Tajiri Y, Kumemura M, Kohno Y (2007) Differences in the composition of intestinal Bifidobacterium species and the development of allergic diseases in infants in rural Japan. Clin Exp Allergy 37:506–511
CAS
PubMed
Google Scholar
Tabuchi M, Ozaki M, Tamura A, Yamada N, Ishida T, Hosoda M, Hosono A (2003) Antidiabetic effect of Lactobacillus GG in streptozotocin-induced diabetic rats. Biosci Biotechnol Biochem 67:1421–1424
CAS
PubMed
Google Scholar
Tachon S, Lee B, Marco ML (2014) Diet alters probiotic Lactobacillus persistence and function in the intestine. Environ Microbiol 16:2915–2926
CAS
PubMed
Google Scholar
Takeda S, Takeshita M, Kikuchi Y, Dashnyam B, Kawahara S, Yoshida H, Watanabe W, Muguruma M, Kurokawa M (2011) Efficacy of oral administration of heat-killed probiotics from Mongolian dairy products against influenza infection in mice: alleviation of influenza infection by its immunomodulatory activity through intestinal immunity. Int Immunopharmacol 11:1976–1983
CAS
PubMed
Google Scholar
Tannock GW, Munro K, Harmsen HJ, Welling GW, Smart J, Gopal PK (2000) Analysis of the fecal microflora of human subjects consuming a probiotic product containing Lactobacillus rhamnosus DR20. Appl Environ Microbiol 66:2578–2588
PubMed Central
CAS
PubMed
Google Scholar
Teughels W, Durukan A, Ozcelik O, Pauwels M, Quirynen M, Haytac MC (2013) Clinical and microbiological effects of Lactobacillus reuteri probiotics in the treatment of chronic periodontitis: a randomized placebo-controlled study. J Clin Periodontol 40:1025–1035
PubMed Central
PubMed
Google Scholar
Thirabunyanon M, Boonprasom P, Niamsup P (2009) Probiotic potential of lactic acid bacteria isolated from fermented dairy milks on antiproliferation of colon cancer cells. Biotechnol Lett 31:571–576
CAS
PubMed
Google Scholar
Tilg H, Moschen AR, Kaser A (2009) Obesity and the microbiota. Gastroenterology 136:1476–1483
PubMed
Google Scholar
Tsai Y-T, Cheng P-C, Pan T-M (2012) The immunomodulatory effects of lactic acid bacteria for improving immune functions and benefits. Appl Microbiol Biotechnol 96:853–862
CAS
PubMed
Google Scholar
Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:1027–1031
PubMed
Google Scholar
Valásková V, Baldrian P (2009) Denaturing gradient gel electrophoresis as a fingerprinting method for the analysis of soil microbial communities. Plant Soil Environ 55:413–423
Google Scholar
Vanhoutte T, De Preter V, De Brandt E, Verbeke K, Swings J, Huys G (2006) Molecular monitoring of the fecal microbiota of healthy human subjects during administration of lactulose and Saccharomyces boulardii. Appl Environ Microbiol 72:5990–5997
Veiga P, Gallini CA, Beal C, Michaud M, Delaney ML, DuBois A, Khlebnikov A, Vliegb JETV, Punit S, Glickman JN, Onderdonk A, Glimcher LH, Garrett WS (2010) Bifidobacterium animalis subsp. lactis fermented milk product reduces inflammation by altering a niche for colitogenic microbes. Proc Natl Acad Sci U S A 107:18132–18137
PubMed Central
CAS
PubMed
Google Scholar
Ventura M, Elli M, Reniero R, Zink R (2001) Molecular microbial analysis of Bifidobacterium isolates from different environments by the species-specific amplified ribosomal DNA restriction analysis (ARDRA). FEMS Microbiol Ecol 36:113–121
CAS
PubMed
Google Scholar
Verberkmoes NC, Russell AL, Shah M, Godzik A, Rosenquist M, Halfvarson J, Lefsrud MG, Apajalahti J, Tysk C, Hettich RL, Jansson JK (2009) Shotgun metaproteomics of the human distal gut microbiota. ISME J 3:179–189
CAS
PubMed
Google Scholar
Vergari F, Tibuzzi A, Basile G (2010) An overview of the functional food market: from marketing issues and commercial players to future demand from life in space. In: Giardi MT, Rea G, Berra B (eds) Bio-farms for nutraceuticals: functional food and safety control by biosensors. Landes Bioscience and Springer Science + Business Media, Austin, pp 308–327
Google Scholar
VidyaLaxme B, Rovetto A, Grau R, Agrawal R (2012) Synergistic effects of probiotic Leuconostoc mesenteroides and Bacillus subtilis in malted ragi (Eleucine corocana) food for antagonistic activity against V. cholerae and other beneficial properties. J Food Sci Technol 51:3072–3082
Google Scholar
Wang MF, Lin HC, Wang YY, Hsu CH (2004) Treatment of perennial allergic rhinitis with lactic acid bacteria. Pediatr Allergy Immunol 15:152–158
PubMed
Google Scholar
Wang Y, Hoenig JD, Malin KJ, Qamar S, Petrof EO, Sun J, Antonopoulos DA, Chang EB, Claud EC (2009) 16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis. ISME J 3:944–954
PubMed Central
CAS
PubMed
Google Scholar
Wikoff WR, Anfora AT, Liu J, Schultz PG, Lesley SA, Peters EC, Siuzdak G (2009) Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc Natl Acad Sci U S A 106:3698–3703
PubMed Central
CAS
PubMed
Google Scholar
Wu X, Ma C, Han L, Nawaz M, Gao F, Zhang X, Yu P, Zhao C, Li L, Zhou A, Wang J, Moore JE, Millar BC, Xu J (2010) Molecular characterization of the faecal microbiota in patients with type II diabetes. Curr Microbiol 61:69–78
CAS
PubMed
Google Scholar
Yanine N, Araya I, Brignardello-Petersen R, Carrasco-Labra A, González A, Preciado A, Villanueva J, Sanz M, Martin C (2013) Effects of probiotics in periodontal diseases: a systematic review. Clin Oral Investig 17:1627–1634
PubMed
Google Scholar
Yeon S, You YS, Kwon H, Yang EH, Ryu J, Kang BH, Kang J (2010) Fermented milk of Lactobacillus helveticus IDCC3801 reduces beta-amyloid and attenuates memory deficit. J Funct Foods 2:143–152
CAS
Google Scholar
Young VB, Schmidt TM (2004) Antibiotic-associated diarrhea accompanied by large-scale alterations in the composition of the fecal microbiota. J Clin Microbiol 42:1203–1206
PubMed Central
PubMed
Google Scholar
Zhang J, Wang L, Guo Z, Sun Z, Gesudu Q, Kwok L, Menghebilige, Zhang H (2014) 454 pyrosequencing reveals changes in the faecal microbiota of adults consuming Lactobacillus casei Zhang. FEMS Microbiol Ecol 88:612–622
CAS
PubMed
Google Scholar
Zhong Y, Priebe MG, Vonk RJ, Huang C-Y, Antoine J-M, He T, Harmsen HJM, Welling GW (2004) The role of colonic microbiota in lactose intolerance. Dig Dis Sci 49:78–83
CAS
PubMed
Google Scholar
Zoetendal EG, Mackie RI (2005) Molecular methods in microbial ecology. In: Tannock GW (ed) Probiotics and prebiotics: scientific aspects. Caister Academic Press, Dunedin, pp 1–24
Google Scholar