[1] Albesharat, R., Ehrmann, M.A., Korakli, M., Yazaji, S., and Vogel, R.F. (2011). Phenotypic and genotypic analyses of lactic acid bacteria in local fermented food, breast milk and feces of mothers and their babies.
Syst Appl Microbiol 34, 148-155
10.1016/j.syapm.2010.12.001[2] Andrew, J.W. (2002). The gut-brain axis in childhood developmental disorders.
J Pediatr Gastroenterol Nutr 34, S14-17
10.1097/00005176-200205001-00004[3] Angelakis, E., Million, M., Henry, M., and Raoult, D. (2011). Rapid and accurate bacterial identification in probiotics and yoghurts by MALDI-TOF mass spectrometry.
J Food Sci 76, M568-572
10.1111/j.1750-3841.2011.02369.x[4] Anhalt, J.P., and Fenselau, C. (1975). Identification of bacteria using mass spectrometry.
Anal Chem 47, 219-225
10.1021/ac60352a007[5] Barbara, G., Brummer, R.J., and Delzenne, N. (2007). Investigating the crosstalk between the gut microbiota and the host: the gut-brain axis.
Consensus Report . Warsaw.
[6] Ben, X.M, and Li, J. (2008). Low level of galacto-oligosaccharide in infant formula stimulates growth of intestinal Bifidobacteria and Lactobacilli.
World J Gastroenterol 14, 6564-6568
10.3748/wjg.14.6564[7] Beraza, N., and Trautwein, C. (2008). The Gut-Brain-Liver Axis: A New Option to Treat Obesity and Diabetes
? Hepatology 48, 1011-1013 .
10.1002/hep.22478[8] Bercik, P., Collins, S.M., and Verdu, E.F. (2012). Microbes and the gutbrain axis.
Neurogastroenterol Motil 224, 405-413
10.1111/j.1365-2982.2012.01906.x[9] Bercik, P., Denou, E., Collins, J., Jackson, W., Lu, J., Jury, J., Deng, Y., Blennerhassett, P., Macri, J., McCoy, K.D.,
. (2011). The Intestinal Microbiota Affect Central Levels of Brain-Derived Neurotropic Factor and Behavior in Mice
. Gastroenterology 141, 599-609
10.1053/j.gastro.2011.04.052[10] Bishop, R. (2010). Applications of fluorescence in situ hybridization(FISH) in detecting genetic aberrations of medical significance.
Biosci Horizons 3, 95-85
[11] Blaut, M., Collins, M.D., Welling, G.W., Doré, J., van, L.J., and de Vos, W. (2004). Molecular methods for the analysis of gut microbiota
. Microbial Ecology Health Disease 16, 71-85
10.1080/08910600410032367[12] Bocci, V. (1992). The neglected organ: bacterial fiora has a crucial immunostimulatory role.
Perspect Biol Med 35, 251-260
[13] Brian, W. P., Elizabeth, N., Elin, O., Emrah, K., Frode, N., Simon, T.H., Calvin, P., Mete, C., Christoph, D.R., Brian, J.B.,
. (2013). Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice
. Cell Metab 17, 141-152
10.1016/j.cmet.2012.12.007[14] Burcelin, R., Serino, M., Chabo, C., Blasco-Baque, V., and Amar, J. (2011). Gut microbiota and diabetes: from pathogenesis to therapeutic perspective.
Acta Diabetol 4, 257-273
10.1007/s00592-011-0333-6[15] Cattell, M., Lai, S., Cerny, R., and Medeiros, D.M. (2011). A new mechanistic scenario for the origin and evolution of vertebrate cartilage.
PLoS ONE 6, e22474.
10.1371/journal.pone.0022474[16] Cecilia, J., and Sonja, L. (2010). Long-term impacts of antibiotic exposure on the human intestinal microbiota.
Microbiology 156, 113216-3223
[17] Chong, B.E., Wall, D.B., Lubman, D.M., and Flynn, S.J. (1997). Rapid profiling of E. coli proteins up to 500 kDa from whole cell lysates using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.
Rapid Commun Mass Spectrom 11, 1900-1908
10.1002/(SICI)1097-0231(199711)11:17<1900::AID-RCM95>3.0.CO;2-K[18] Claesson, M.J., O’ Sullivan, O., Wang, Q., Nikkil?, J., Marchesi, J.R., Smidt, H., De Vos, W.M., Ross R .P.,and O’Toole, P.W. (2009). Comparative analysis of Pyrosequencing and a phylogenetic mi-croarray for exploring microbial community structures in the human distal intestine.
PLoS One 4, e6669.
10.1371/journal.pone.0006669[19] Claesson, M.J., Wang, Q., O’Sullivan, O., Greene-Diniz, R., Cole, J.R., Ross, R.P., and O’Toole, P.W. (2010). Comparison of two nextgeneration sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene re-gions.
Nucleic Acids Res 38, e200.
10.1093/nar/gkq873[20] Claydon, M.A., Davey, S.N., Edwards, J.V., and Gordon, D.B. (1996). The rapid identification of intact microorganisms using mass spec-trometry.
Nat Biotechnol 14, 1584-1586 .
10.1038/nbt1196-1584[21] Collado, M.C., Isolauri, E., Laitinen, K., and Salminen, S. (2008). Dis-tinct composition of gut microbiota during pregnancy in overweight and normal-weight women.
Am J Clin Nutr 88, 894-899
[22] Collins, S.M., Surette, M., and Bercik, P. (2012). The interplay between the intestinal microbiota and the brain
. Nat Rev Microbiol 10, 735-742 .
10.1038/nrmicro2876[23] Cryan, J.F., and Dinan, T.G. (2012). Mind-altering microorganisms: the impact of the gut microbiota on brain and behavior.
Nat Rev Neuro-sci 13, 701-712
10.1038/nrn3346[24] Cryan, J.F., and O’Mahony, S.M., (2011). The microbiome-gut-brain axis: from bowel to behavior.
Neurogastroenterol Motil 23, 187-192 .
10.1111/j.1365-2982.2010.01664.x[25] Desbonnet, L., Garrett, L., Clarke, G., Bienenstock, J., and Dinan, T.G. (2008). The probiotic Bifidobacteria infantis: An assessment of potential antidepressant properties in the rat
. J Psychiatr Res 43, 164-174
10.1016/j.jpsychires.2008.03.009[26] Dethlefsen, L., Sue, H., Mitchell, L.S., and Relman, D.A. (2008). The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing.
PLoS Biol 6, e280.
10.1371/journal.pbio.0060280[27] Dumont, M.G., Neufeld, J.D., and Murrell, J.C. (2006). Isotopes as tools for microbial ecologists.
Curr Opin Biotech 17, 57-58
10.1016/j.copbio.2006.01.004[28] Eckburg, P.B., Elisabeth, M.B., Charles, N.B., Elizabeth, P., Dethlefsen, L., Sargent, M., Gill, R.S., Nelson, K.E., and Relman, D.A. (2005). Diversity of the human intestinal microbial flora
. Science 308, 1635-1638
10.1126/science.1110591[29] Zhang, S. M., Tian, F., Huang,Q. F., Zhao, Y.F., Guo, X.K. and Zhang, F. Q. (2011). Bacterial diversity of subgingival plaque in 6 healthy Chinese individuals
. Exp Ther Med 2, 1023-1029
[30] Finegold, S.M., Molitoris, D., Song, Y., Liu, C., Vaisanen, M.L., Bolte, E., McTeague, M., Sandler, R., Wexler, H., Marlowe, E.M.,
. (2002). Gastrointestinal microfiora studies in late-onset autism.
Clin Infect Dis 35, S6-16 .
10.1086/341914[31] Fredrik, B., Ruth, E.L., Justin, L.S., Daniel, A.P., and Jeffrey, I.G. (2005). Host-bacterial mutualism in the human intestine.
Science 307, 1915-1920
10.1126/science.1104816[32] Gill, S.R., Pop, M., DeBoy, R.T., Eckburg, P.B., Turnbaugh, P.J., Sam-uel, B.S., Gordon, J.I, Relman, D.A., Fraser-Liggett, C.M., and Ka-ren, E. (2006). Nelson metagenomic analysis of the human distal gut microbiome.
Science 312, 1355-1359
10.1126/science.1124234[33] Greenblum, S., Turnbaugh, P.J., and Borenstein, E. (2012). Metagen-omic systems biology of the human gut microbiome reveals topological shifts associated with obesity and infiammatory bowel disease
. Proc Natl Acad Sci U S A 109, 594-599
10.1073/pnas.1116053109[34] Greiner, T., Bfickhed, F. (2011). Effects of the gut microbiota on obesity and glucose homeostasis.
Trends Endocrinol Metab 22, 117-123
10.1016/j.tem.2011.01.002[35] Hamady, M., Walker, J.J., Harris, J.K., Gold, N.J., and Knight, R. (2008). Error correcting barcoded primers for pyrosequencing hundreds of samples in multiplex.
Nat Methods 5, 235-237
10.1038/nmeth.1184[36] He, Z., Gentry, T.J., Schadt, C.W., Wu, L., Liebich, J., Chong, S.C., Huang, Z., Wu, W., Gu, B., Jardine, P.,
. (2007). GeoChip: a comprehensive microarray for investigating biogeochemical, eco-logical and environmental processes.
ISME J 1, 67-77
10.1038/ismej.2007.2[37] Heijtz, R.D., Wang, S., Anuar, F., Qian, Y., Bj?rkholm, B., Samuelsson, A., Hibberd, M.L., Forssberg, H., and Pettersson, S. (2011). Normal gut microbiota modulates brain development and behavior.
Proc Natl Acad Sci U S A 108, 3047-3052
10.1073/pnas.1010529108[38] Hernandez-Sanabria, E., Guan, L.L., Laksiri, A., Li, M., Mujibi, D.F., Stothard, P., Moore, S.S., and Leon-Quintero, M.C. (2010). Cor-relation of particular bacterial PCR-denaturing gradient gel electro-phoresis patterns with bovine ruminal fermentation parameters and feed efficiency traits.
App Envior Biol 76, 6338-6350
10.1128/AEM.01052-10[39] Holland, R.D., Wilkes, J.G., Rafii, F., Sutherland, J.B., Persons, C.C., Voorhees, K.J., and Lay J .O. Jr. (1996). Rapid identification of intact whole bacteria based on spectral patterns using matrix-assisted laser desorption/ionization with time-of-flight mass spectrometry.
Rapid Commun Mass Spectrom 10, 1227-1232
10.1002/(SICI)1097-0231(19960731)10:10<1227::AID-RCM659>3.0.CO;2-6[40] Hopkins, M.J., and Sharp, R. (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, 198-205
10.1136/gut.48.2.198[41] Huang, W.E., Stoecker, K., Griffiths, R., Newbold, L., Daims, H., White-ley, A.S., and Wagner, M. (2007). Raman-fish: Combining stable-isotope Raman spectroscopy and fiuorescence in situ hybridization for the single cell analysis of identity and function.
Environ Microbiol 9, 1878-1889
10.1111/j.1462-2920.2007.01352.x[42] Jock, S., and Geider, K. (2004). Molecular differentiation of Erwinia amylovora strains from North America and of two Asian pear patho-gens by analyses of PFGE patterns and hrpN genes.
Environ Mi-crobiol 6, 480-490
10.1111/j.1462-2920.2004.00583.x[43] Kim, P.I., Erickson, B.D., and Cerniglia, C.E. (2005). A membrane-array method to detect specific human intestinal bacteria in fecal samples using reverse transcriptase-PCR and chemiluminescence.
J Microbiol Biotechnol 15, 310-320
[44] Krishnamurthy, T., and Ross, P.L. (1996). Rapid identification of bacte-ria by direct matrix-assisted laser desorption/ionization mass spec-trometric analysis of whole cells.
Rapid Commun Mass Spectrom 10, 1992-1996
10.1002/(SICI)1097-0231(199612)10:15<1992::AID-RCM789>3.0.CO;2-V[45] Kurz, C.M., Moosdijk, S.V., Thielecke, H., and Velten, T. (2011). To-wards a cellular multi-parameter analysis platform: fluorescence in situ hybridization (FISH) on microhole-array chips.
Conf Proc IEEE Eng Med Biol Soc , 8408-8411
[46] Kuypers, M.M.M., and J?rgensen, B.B. (2007). The future of single-cell environmental microbiology.
Environ Microbiol 9, 6-7
10.1111/j.1462-2920.2006.01222_5.x[47] Lagier, J.C., Million, M., Hugon, P., Armougom, F., and Raoult, D. (2012). Human Gut Microbiota: Repertoire and Variations.
Front Cell Infect Microbiol 2, 136.
10.3389/fcimb.2012.00136[48] Lewis, S., and Cochrane, S. (2007). Alteration of sulfate and hydrogen metabolism in the human colon by changing intestinal transit rate.
Am J Gastroenterol 102, 624-633
10.1111/j.1572-0241.2006.01020.x[49] Lotta, N., Reetta, S., and Janne, N. (2013). Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease.
BMC Mi-crobiology 13, 12.
10.1186/1471-2180-13-12[50] Loy, A., Lehner, A., and Lee, N. (2002). Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment.
Appl Environ Mi-crobiol 68, 5064-5081
10.1128/AEM.68.10.5064-5081.2002[51] Manco, M. (2012). Gut microbiota and developmental programming of the brain: from evidence in behavioral endophenotypes to novel perspective in obesity.
Front Cell Inf Microbio 2, 109.
10.3389/fcimb.2012.00109[52] Migrenne, S., Marsollier, N., Cruciani-Guglielmacci, C., Magnan, C. (2006). Importance of the gut-brain axis in the control of glucose Homeostasis.
Curr Opin Pharmacol 6, 592-597 .
10.1016/j.coph.2006.08.004[53] Musso, G., Gambino, M., and Cassader, M. (2010). Obesity, diabetes, and gut microbiota.
Diabetes Care 33, 2277-2284
10.2337/dc10-0556[54] Neufeld, K.M., Kang, N., Bienenstock, J., and Foster, J.A. (2011). Re-duced anxiety-like behavior and central neurochemical change in germ-free mice.
Neurogastroenterol Motil 23, 255-264
10.1111/j.1365-2982.2010.01620.x[55] Nordlie, R.C., and Foster, J.D. (1999). Regulation of glucose produc-tion by the liver.
Annu Rev Nutr 19, 379-406
10.1146/annurev.nutr.19.1.379[56] Paliy, O., Kenche, H., Abernathy, F., and Michail, S. (2009). High-throughput quantitative analysis of the human intestinal microbiota with a phylogenetic microarray.
Appl Environ Microbiol 75, 3572-3579 .
10.1128/AEM.02764-08[57] Palmer, C., Bik, E.M., and DiGiulio, D.B. (2007). Development of the human infant intestinal microbiota.
PLoS Biol 5, e177.
10.1371/journal.pbio.0050177[58] Palmer, C., Bik, E.M., and Eisen, M.B. (2006). Rapid quantitative profil-ing of complex microbial populations.
Nucleic Acids Res 34, e5.
10.1093/nar/gnj007[59] Peterson, D.A., Frank, D.N., Pace, N.R., and Gordon, J.I. (2008). Metagenomic approaches for defining the pathogenesis of inflam-matory bowel diseases.
Cell Host Microbe 3, 417-427
10.1016/j.chom.2008.05.001[60] Rakoff, N.S., Paglino, J., Eslami, V.F., Edberg, S., and Medzhitov, R. (2004). Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis.
Cell 118, 229-241
10.1016/j.cell.2004.07.002[61] Sam, A.H., Troke, R.C., Tan, T.M., and Bewick, G.A. (2012). The role of the gut/brain axis in modulating food intake.
Neuropharmacology 63, 46-56 .
10.1016/j.neuropharm.2011.10.008[62] Savage, D.C. (1977). Microbial ecology of the gastrointestinal tract.
Annu Rev Microbiol 31, 107-133
10.1146/annurev.mi.31.100177.000543[63] Shanahan, F. (2002). The host-microbe interface within the gut.
Best Pract Res Clin Gastroenterol 16, 915-931 .
10.1053/bega.2002.0342[64] Sintchenko, V., Iredell, J.R., and Gilbert, G.L. (2007). Pathogen profil-ing for disease management and surveillance.
Nat Rev Microbiol 5, 464-470
10.1038/nrmicro1656[65] Sogin, L.M., Morrison, H.G., Huber, J.A., Welch, D.M., Huse, S.M., Neal, P.R., Arrieta, J.M., and Herndl, J.G. (2006). Microbial diversity in the deep sea and the underexplored “rare biosphere”.
Proc NatAcad Sci U S A 103, 12115-12120
10.1073/pnas.0605127103[66] Stappenbeck, T.S., Hooper, L.V., and Gordon, J.I. (2001). Commensal host-bacterial relationships in the gut.
Science 292, 1115-1118 .
10.1126/science.1058709[67] Stappenbeck, T.S., Hooper, L.V., and Gordon, J.I. (2002). Develop-mental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells.
Proc Natl Acad Sci U S A 99, 15451-15455
10.1073/pnas.202604299[68] Sudo, N., Chida, Y., Aiba, Y., Sonoda, J., Oyama, N., Yu, X.N., Kubo, C., and Koga, Y. (2004). Postnatal microbial colonization programs the hypothalamic-pituitary-adrenal system for stress response in mice.
J Physiol 558, 263-275 .
10.1113/jphysiol.2004.063388[69] Turnbaugh, P.J., Hamady, M., Yatsunenko, T., Cantarel, B.L., Duncan, A., Ley, R.E., Sogin, M.L., Jones, W.J., Roe, B.A., Affourtit, J.P.,
. (2008). A core gut microbiome in obese and lean twins.
Nature 457, 480-484
10.1038/nature07540[70] Turnbull, A.V., and Rivier, C.L. (1999). Regulation of the hypothalamic-pituitary-adrenal axis by cytokines: actions and mechanisms of ac-tion.
Physiol rev 79, 1-71 .
[71] Walker, J.R., Ediger, J.P., Graff, L.A., Greenfeld, J.M., Clara, I., Lix, L., Rawsthorne, P., Miller, N., Rogala, L., McPhail, C.M., and Bern-stein, C.N. (2008). The Manitoba IBD cohort study: a population-based study of the prevalence of lifetime and 12-month anxiety and mood disorders.
Am J Gastroenterol 103, 1989-1997
10.1111/j.1572-0241.2008.01980.x[72] Wang, P.Y., Caspi, L., Lam, C.K., Chari, M., Li, X., Light, P.E., Gutier-rez-Juarez, R., Ang, M., Schwartz, G.J., and Lam, T.K. (2008). Up-per intestinal lipids trigger a gut-brain-liver axis to regulate glucose production.
Nature 452, 1012-1016
10.1038/nature06852[73] Welker, M. (2012). MALDI-TOF MS for identification of microorgan-isms: a new era in clinical microbiological research and diagnosis. In: Hays, J.P., van Leeuwen, W.B. (Eds.),
The Role of New Tech-nologies in Medical Microbiological Research and Diagnosis, Ben-tham Science Publishers, Bussum .
[74] Whitehead, W.E., Palsson, O., and Jones, K.R. (2002). Systematic re-view of the comorbidity of irritable bowel syndrome with other disor-ders: what are the causes and implications.
Gastroenterology 122, 1140-1156
10.1053/gast.2002.32392[75] Wook, H.S., Kim, I.S., Lee, J.S., and Chung, K.S. (2011). Culture-Based and Denaturing Gradient Gel Electrophoresis Analysis of the Bacterial Community Structure from the Intestinal Tracts of Earth-worms (Eisenia fetida).
J Microbiol Biotechnol 21, 885-892
10.4014/jmb.1009.09041[76] Wu, L., Thompson, D.K., Liu, X., Fields, M.W., Bagwell, C.E., Tiedje, J.M., and Zhou, J. (2004). Development and evaluation of microar-ray-based whole genome hybridization for detection of microorgan-isms within the context of environmental applications.
Environ Sci Technol 38, 6775-6782
10.1021/es049508i[77] Zhang, H., DiBaise, J.K, Zuccolo, A., Kudrna, D., Braidotti, M., Yu, Y., Parameswaran, P., Crowell, M.D., Wing, R., and Rittmann, B.E. (2009). Human gut microbiota in obesity and after gastric bypass.
Proc Natl Acad Sci U S A 106, 2365-2370
10.1073/pnas.0812600106[78] Zimmer, C. (2010). How microbes defend and define us.
New York Times . 17 July.
[79] Simrén, M., Barbara, G., Flint, H.J., Spiegel, B.M., Spiller, R.C., Vanner, S., Verdu, E.F., Whorwell, P. J., and Zoetendal, E. G. (2013). Intestinal microbiota in functional bowel disorders: a Rome founda-tion report.
Gut 62, 159-176
10.1136/gutjnl-2012-302167[80] Sekirov, I., Russell, S. L., Antunes, L. C. M., and Brett Finlay, B. (2010). Gut Microbiota in Health and Disease.
Physiol Rev 90, 859-904
10.1152/physrev.00045.2009