Omics for the study of probiotic microorganisms

Food Research International

Volumn 54, Issue 1, 2013, Pages 1061-1071

  Sánchez, Borja ^a   Ruiz, Lorena ^a   Gueimonde, Miguel ^a   Margolles, Abelardo ^a  

^a DEPARTMENT OF MICROBIOLOGY AND BIOCHEMISTRY OF DAIRY PRODUCTS   (Spain)

Author keywords

Bifidobacterium; Genomics; Lactobacillus; Metagenomics; Proteomics; Transcriptomics

Indexed keywords

BIFIDOBACTERIUM; GENOMICS; LACTOBACILLUS; METAGENOMICS; PROTEOMICS; TRANSCRIPTOMICS;

MICROBIOLOGY; MOLECULAR BIOLOGY;

BACTERIA;

BACTERIA (MICROORGANISMS); BIFIDOBACTERIUM; LACTOBACILLUS;

EID: 84886242828     PISSN: 09639969     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.foodres.2013.01.029     Document Type: Review

References (128)

1. Aebersold R., Mann M. Mass spectrometry-based proteomics. Nature 2003, 422:198-207.
2. Aires J., Anglade P., Baraige F., Zagorec M., Champomier-Verges M.C., Butel M.J. Proteomic comparison of the cytosolic proteins of three Bifidobacterium longum human isolates and B. longum NCC2705. BMC Microbiology 2010, 10:29.
3. Alcantara C., Zuniga M. Proteomic and transcriptomic analysis of the response to bile stress of Lactobacillus casei BL23. Microbiology-SGM 2012, 158:1206-1218.
4. Andersen J.M., Barrangou R., Abou Hachem M., Lahtinen S., Goh Y.J., Svensson B., et al. Transcriptional and functional analysis of galactooligosaccharide uptake by lacS in Lactobacillus acidophilus. Proceedings of the National Academy of Sciences of the United States of America 2011, 108:17785-17790.
5. Arumugam M., Raes J., Pelletier E., Le Paslier D., Yamada T., Mende D.R., et al. Enterotypes of the human gut microbiome. Nature 2011, 473:174-180.
6. Azcarate-Peril M.A., Altermann E., Goh Y.J., Tallon R., Sanoxky-Dawes R.B., Pfeiler E.A., et al. Analysis of the genome sequence of Lactobacillus gasseri ATCC 33323 reveals the molecular basis of an autochthonous intestinal organism. Applied and Environmental Microbiology 2008, 74:4610-4625.
7. Barrangou R., Azcarate-Peril M.A., Duong T., Conners S.B., Kelly R.M., Klaenhammer T.R. Global analysis of carbohydrate utilization by Lactobacillus acidophilus using cDNA microarrays. Proceedings of the National Academy of Sciences of the United States of America 2006, 103:3816-3821.
8. Beck H.C., Madsen S.M., Glenting J., Petersen J., Israelsen H., Norrelykke M.R., et al. Proteomic analysis of cell surface-associated proteins from probiotic Lactobacillus plantarum. FEMS Microbiology Letters 2009, 297:61-66.
9. Benndorf D., Vogt C., Jehmlich N., Schmidt Y., Thomas H., Woffendin G., et al. Improving protein extraction and separation methods for investigating the metaproteome of anaerobic benzene communities within sediments. Biodegradation 2009, 20:737-750.
10. Berni Canani R., Cucchiara S., Cuomo R., Pace F., Papale F. Saccharomyces boulardii: A summary of the evidence for gastroenterology clinical practice in adults and children. European Review for Medical and Pharmacological Sciences 2011, 15:809-822.
11. Bottacini F., Medini D., Pavesi A., Turroni F., Foroni E., Riley D., et al. Comparative genomics of the genus Bifidobacterium. Microbiology-SGM 2010, 156:3243-3254.
12. Bron P.A., Wels M., Bongers R.S., van Bokhorst-van de Veen H., Wiersma A., Overmars L., et al. Transcriptomes reveal genetic signatures underlying physiological variations imposed by different fermentation conditions in Lactobacillus plantarum. PLoS One 2012, 7:e38720.
13. Burns P., Sánchez B., Vinderola G., Ruas-Madiedo P., Ruiz L., Margolles A., et al. Inside the adaptation process of Lactobacillus delbrueckii subsp. lactis to bile. International Journal of Food Microbiology 2010, 142:132-141.
14. Candela M., Bergmann S., Vici M., Vitali B., Turroni S., Eikmanns B.J., et al. Binding of human plasminogen to Bifidobacterium. Journal of Bacteriology 2007, 189:5929-5936.
15. Candela M., Biagi E., Maccaferri S., Turroni S., Brigidi P. Intestinal microbiota is a plastic factor responding to environmental changes. Trends in Microbiology 2012, 20:385-391.
16. Chen S.N., Rillig M.C., Wang W. Improving soil protein extraction for metaproteome analysis and glomalin-related soil protein detection. Proteomics 2009, 9:4970-4973.
17. Cho I., Yamanishi S., Cox L., Methé B.A., Zavadil J., Li K., et al. Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature 2012, 488:621-626.
18. Chourey K., Jansson J., VerBerkmoes N., Shah M., Chavarria K.L., Tom L.M., et al. Direct cellular lysis/protein extraction protocol for soil metaproteomics. Journal of Proteome Research 2010, 9:6615-6622.
19. Coute Y., Hernandez C., Appel R.D., Sanchez J.C., Margolles A. Labeling of Bifidobacterium longum cells with C-13-substituted leucine for quantitative proteomic analyses. Applied and Environmental Microbiology 2007, 73:5653-5656.
20. Cutting S.M. Bacillus probiotics. Food Microbiology 2011, 28:214-220.
21. De Dea Lindner J., Canchaya C., Zhang Z., Neviani E., Fitzgerald G.F., van Sinderen D., et al. Exploiting Bifidobacterium genomes: The molecular basis of stress response. International Journal of Food Microbiology 2007, 120:13-24.
22. Del Chierico F., Vernocchi P., Bonizzi L., Carsetti R., Castellazzi A.M., Dallapiccola B., et al. Early-life gut microbiota under physiological and pathological conditions: The central role of combined meta-omics-based approaches. Journal of Proteomics 2012, 75:4580-4587.
23. Denou E., Pridmore R.D., Berger B., Panoff J.M., Arigoni F., Brussow H. Identification of genes associated with the long-gut-persistence phenotype of the probiotic Lactobacillus johnsonii strain NCC533 using a combination of genomics and transcriptome analysis. Journal of Bacteriology 2008, 190:3161-3168.
24. Di Cagno R., De Angelis M., Calasso M., Gobbetti M. Proteomics of the bacterial cross-talk by quorum sensing. Journal of Proteomics 2011, 74:19-34.
25. Diplock A.T., Aggett P.J., Ashwell M., Bornet F., Fern E.B., Roberfroid M.B. Scientific concepts of functional foods in Europe consensus document. The British Journal of Nutrition 1999, 81:S1-S27.
26. FAO/WHO Probiotics in food. FAO food and nutrition paper no. 85 2006.
27. Fleischmann R.D., Adams M.D., White O., Clayton R.A., Kirkness E.F., Kerlavage A.R., et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995, 269:496-512.
28. Foroni E., Serafini F., Amidani D., Turroni F., He F., Bottacini F., et al. Genetic analysis and morphological identification of pilus-like structures in members of the genus Bifidobacterium. Microbial Cell Factories 2011, 10:S16.
29. Fukuda S., Toh H., Hase K., Oshima K., Nakanishi Y., Yoshimura K., et al. Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature 2011, 469:543-547.
30. García-Mazcorro J.F., Lanerie D.J., Dowd S.E., Paddock C.G., Grützner N., Steiner J.M., et al. Effect of a multi-species synbiotic formulation on fecal bacterial microbiota of healthy cats and dogs as evaluated by pyrosequencing. FEMS Microbiology Ecology 2011, 78:542-554.
31. Gilad O., Jacobsen S., Stuer-Lauridsen B., Pedersen M.B., Garrigues C., Svensson B. Combined transcriptome and proteome analysis of Bifidobacterium animalis subsp. lactis BB-12 grown on xylo-oligosaccharides and a model of their utilization. Applied and Environmental Microbiology 2010, 76:7285-7291.
32. González R., Klaassens E.S., Malinen E., de Vos W.M., Vaughan E.E. Differential transcriptional response of Bifidobacterium longum to human milk, formula milk, and galactooligosaccharide. Applied and Environmental Microbiology 2008, 74:4686-4694.
33. Gorg A., Boguth G., Obermaier C., Weiss W. Two-dimensional electrophoresis of proteins in an immobilized pH4-12 gradient. Electrophoresis 1998, 19:1516-1519.
34. Granato D., Branco G.F., Cruz A.G., Faria J.D.F., Shah N.P. Probiotic dairy products as functional foods. Comprehensive Reviews in Food Science and Food Safety 2010, 9:455-470.
35. Grozdanov L., Raasch C., Schulze J., Sonnenborn U., Gottschalk G., Hacker J., et al. Analysis of the genome structure of the nonpathogenic probiotic Escherichia coli strain Nissle 1917. Journal of Bacteriology 2004, 186:5432-5441.
36. Guandalini S. Probiotics for prevention and treatment of diarrhea. Journal of Clinical Gastroenterology 2011, 45:S149-S153.
37. Guarner F., Perdigon G., Corthier G., Salminen S., Koletzko B., Morelli L. Should yoghurt cultures be considered probiotic?. The British Journal of Nutrition 2005, 93:783-786.
38. Gueimonde M., Collado M.C. Metagenomics and probiotics. Clinical Microbiology and Infection Supplement 2012, 4:32-34.
39. Gueimonde M., Garrigues C., van Sinderen D., de los Reyes-Gavilán C.G., Margolles A. Bile-inducible efflux transporter from Bifidobacterium longum NCC2705, conferring bile resistance. Applied and Environmental Microbiology 2009, 75:3153-3160.
40. Hamon E., Horvatovich P., Izquierdo E., Bringel F., Marchioni E., Aoude-Werner D., et al. Comparative proteomic analysis of Lactobacillus plantarum for the identification of key proteins in bile tolerance. BMC Microbiology 2011, 11:63.
41. Hooper L.V., Macpherson A.J. Immune adaptations that maintain homeostasis with the intestinal microbiota. Nature Reviews. Immunology 2010, 10:159-169.
42. Human Microbiome Project Consortium Structure, function and diversity of the healthy human microbiome. Nature 2012, 486:207-214.
43. Ishikawa E., Shima T., Sudam K., Shirasawa Y., Sato T., Umesaki Y. Comparison of Bifidobacterium breve strain Yakult transcriptomes in germ-free mice with those in fecal cultures. Journal of Bioscience and Bioengineering 2011, 112:451-457.
44. Izquierdo E., Horvatovich P., Marchioni E., Aoude-Werner D., Sanz Y., Ennahar S. 2-DE and MS analysis of key proteins in the adhesion of Lactobacillus plantarum, a first step toward early selection of probiotics based on bacterial biomarkers. Electrophoresis 2009, 30:949-956.
45. Kankainen M., Paulin L., Tynkkynen S., von Ossowsky I., Reunanen J., Partanen P., et al. Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human-mucus binding protein. Proceedings of the National Academy of Sciences of the United States of America 2009, 106:17193-17198.
46. Kant R., Blom J., Palva A., Siezen R.J., de Vos W.M. Comparative genomics of Lactobacillus. Microbial Biotechnology 2010, 4:323-332.
47. Kelly P., Maguire P.B., Bennett M., Fitzgerald D.J., Edwards R.J., Thiede B., et al. Correlation of probiotic Lactobacillus salivarius growth phase with its cell wall-associated proteome. FEMS Microbiology Letters 2005, 252:153-159.
48. Klaassens E.S., Ben-Amor K., Vriesema A., Vaughan E.E., de Vos W.M. The fecal bifidobacterial transcriptome of adults. A microarray approach. Gut Microbes 2011, 2:217-226.
49. Klaassens E.S., Boesten R.J., Haarman M., Knol J., Schuren F.H., Vaughan E.E., et al. Mixed-species genomic microarray analysis of fecal samples reveals differential transcriptional responses of bifidobacteria in breast-fed and formula-fed infants. Applied and Environmental Microbiology 2009, 75:2668-2676.
50. Kleerebezem M., Boekhorst J., van Kranenburg R., Molenaar D., Kuipers O.P., Leer R., et al. Complete genome sequence of Lactobacillus plantarum WCFS1. Proceedings of the National Academy of Sciences of the United States of America 2003, 100:1990-1995.
51. Kolmeder C.A., de Been M., Nikkila J., Ritamo I., Matto J., Valmu L., et al. Comparative metaproteomics and diversity analysis of human intestinal microbiota testifies for its temporal stability and expression of core functions. PLoS One 2012, 7:e29913.
52. Koponen J., Laakso K., Koskenniemi K., Kankainen M., Savijoki K., Nyman T.A., et al. Effect of acid stress on protein expression and phosphorylation in Lactobacillus rhamnosus GG. Journal of Proteomics 2012, 75:1357-1374.
53. Koskenniemi K., Koponen J., Kankainen M., Savijoki K., Tynkkynen S., de Vos W.M., et al. Proteome analysis of Lactobacillus rhamnosus GG using 2-D DIGE and mass spectrometry shows differential protein production in laboratory and industrial-type growth media. Journal of Proteome Research 2009, 8:4993-5007.
54. Koskenniemi K., Laakso K., Koponen J., Kankainen M., Greco D., Auvinen P., et al. Proteomics and transcriptomics characterization of bile stress response in probiotic Lactobacillus rhamnosus GG. Molecular & Cellular Proteomics 2011, 10. (M110.002741).
55. Laakso K., Koskenniemi K., Koponen J., Kankainen M., Surakka A., Salusjarvi T., et al. Growth phase-associated changes in the proteome and transcriptome of Lactobacillus rhamnosus GG in industrial-type whey medium. Microbial Biotechnology 2011, 4:746-766.
56. Lamberti C., Mangiapane E., Pessione A., Mazzoli R., Giunta C., Pessione E. Proteomic characterization of a selenium-metabolizing probiotic Lactobacillus reuteri Lb2 BM for nutraceutical applications. Proteomics 2011, 11:2212-2221.
57. Lee K., Lee H.G., Choi Y.J. Proteomic analysis of the effect of bile salts on the intestinal and probiotic bacterium Lactobacillus reuteri. Journal of Biotechnology 2008, 137:14-19.
58. Lee K., Lee H.G., Pi K., Choi Y.J. Effect of low pH on protein expression by the probiotic bacterium Lactobacillus reuteri. Proteomics 2008, 8:1624-1630.
59. Leimena M.M., Wels M., Bongers R.S., Smid E.J., Zoetendal E.G., Kleerebezem M. Comparative analysis of Lactobacillus plantarum WCFS1 transcriptomes by using DNA microarray and next-generation sequencing technologies. Applied and Environmental Microbiology 2012, 78:4141-4148.
60. Li X.X., LeBlanc J., Elashoff D., Borneman J., Goodglick L., Braun J. Detecting disease-related biological neighborhoods by human mucosal interface metaproteome analysis. Clinical Immunology 2010, 135:S75.
61. Lippolis R., Gnoni A., Abbrescia A., Panelli D., Maiorano S., Paternoster M.S., et al. Comparative proteomic analysis of four Bacillus clausii strains: Proteomic expression signature distinguishes protein profile of the strains. Journal of Proteomics 2011, 74:2846-2855.
62. Liu D.W., Wang S.A., Xu B., Guo Y.H., Zhao J.L., Liu W., et al. Proteomics analysis of Bifidobacterium longum NCC2705 growing on glucose, fructose, mannose, xylose, ribose, and galactose. Proteomics 2011, 11:2628-2638.
63. LoCascio R.G., Desai P., Sela D.A., Weimer B., Mills D.A. Broad conservation of milk utilization genes in Bifidobacterium longum subsp. infantis as revealed by comparative genomic hybridization. Applied and Environmental Microbiology 2010, 76:7373-7381.
64. Lukjancenko O., Ussery D.W., Wassenaar T.M. Comparative genomics of Bifidobacterium, Lactobacillus and related probiotic genera. Microbial Ecology 2012, 63:651-673.
65. Maccaferri S., Candela M., Turroni S., Centanni M., Severgnini M., Consolandi C., et al. IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation. Gut Microbes 2012, 3:406-413.
66. Majumder A., Sultan A., Jersie-Christensen R.R., Ejby M., Schmidt B.G., Lahtinen S.J., et al. Proteome reference map of Lactobacillus acidophilus NCFM and quantitative proteomics towards understanding the prebiotic action of lactitol. Proteomics 2011, 11:3470-3481.
67. Mangiapane E., Lamberti C., Galano E., Pessione A., Giunta C., Amoresano A., et al. Physiological changes induced by selenium in a probiotic Lactobacillus reuteri strain: A proteomic study. The FEBS Journal 2011, 278:S432.
68. Marco M.L., de Vires M.C., Wels M., Molenaar D., Mangell P., Ahrne S., et al. Convergence in probiotic Lactobacillus gut-adaptive responses in humans and mice. The ISME Journal 2010, 4:1481-1484.
69. Marco M.L., Peters T.H.F., Bongers R.S., Molenaar D., van Hemert S., Sonnenburg J.L., et al. Lifestyle of Lactobacillus plantarum in the mouse cecum. Environmental Microbiology 2009, 11:2747-2757.
70. Margolles A., de los Reyes-Gavilán C.G. Purification and functional characterization of a novel alpha-L-arabinofuranosidase from Bifidobacterium longum B667. Applied and Environmental Microbiology 2003, 69:5096-5103.
71. +-ATPase activity in Bifidobacterium with special reference to acid tolerance. International Journal of Food Microbiology 2004, 93:109-113.
72. McNulty N.P., Yatsunenko T., Hsiao A., Faith J.J., Muegge B.D., Goodman A.L., et al. The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Science Translational Medicine 2011, 3:106ra106.
73. Meijerink M., van Hemert S., Taverne N., Wels M., de Vos P., Bron P.A., et al. Identification of genetic loci in Lactobacillus plantarum that modulate the immune response of dendritic cells using comparative genome hybridization. PLoS One 2010, 5:e10632.
74. Michail S., Kenche H. Gut microbiota is not modified by randomized, double-blind, placebo-controlled trial of VSL#3 in diarrhea-predominant irritable bowel syndrome. Probiotics and Antimicrobial Proteins 2011, 3:1-7.
75. O'Connell-Motherway M., Zomer A., Leahy S.C., Reunanen J., Bottacini F., Claesson M.J., et al. Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (tad) pili as an essential and conserved host-colonization factor. Proceedings of the National Academy of Sciences of the United States of America 2011, 108:11217-11222.
76. O'Connell Motherway M., Kinsella M., Fitzgerald G.F., van Sinderen D. Transcriptional and functional characterization of genetic elements involved in galacto-oligosaccharide utilization by Bifidobacterium breve UCC2003. Microbial Biotechnology 2012, 10.1111/1751-7915.12011.
77. Olszak T., An D., Zeissig S., Vera M.P., Richter J., Franke A., et al. Microbial exposure during early life has persistent effects on natural killer T cell function. Science 2012, 336:489-493.
78. Riboulet-Bisson E., Sturme M.H., Jeffery I.B., O'Donnell M.M., Neville B.A., Forde B.M., et al. Effect of Lactobacillus salivarius bacteriocin Abp118 on the mouse and pig intestinal microbiota. PLoS One 2012, 7:e31113.
79. Roberfroid M., Gibson G.R., Hoyles L., McCartney A.L., Rastall R., Rowland I., et al. Prebiotic effects: Metabolic and health benefits. The British Journal of Nutrition 2010, 104(S2):1-63.
80. Rooijers K., Kolmeder C., Juste C., Dore J., de Been M., Boeren S., et al. An iterative workflow for mining the human intestinal metaproteome. BMC Genomics 2011, 12:6.
81. Round J.L., Mazmanian S.K. The gut microbiota shapes intestinal immune responses during health and disease. Nature Reviews. Immunology 2009, 9:313-323.
82. Ruiz L., Álvarez-Martín P., Mayo B., de los Reyes-Gavilán C.G., Gueimonde M., Margolles A. Controlled gene expression in bifidobacteria by use of a bile-responsive element. Applied and Environmental Microbiology 2012, 6:307-318.
83. Ruiz L., Coute Y., Sánchez B., de los Reyes-Gavilán C.G., Sanchez J.C., Margolles A. The cell-envelope proteome of Bifidobacterium longum in an in vitro bile environment. Microbiology-SGM 2009, 155:957-967.
84. Ruiz L., Gueimonde M., Ruas-Madiedo P., Ribbera A., de Los Reyes-Gavilán C.G., Ventura M., et al. Molecular clues to understand the aerotolerance phenotype of Bifidobacterium animalis subsp. lactis. Applied and Environmental Microbiology 2012, 78:644-650.
85. Ruiz L., O'Connell-Motherway M., Zomer A., de los Reyes-Gavilán C.G., Margolles A., van Sinderen D. A bile-inducible membrane protein mediates bifidobacteria bile resistance. Microbial Biotechnology 2012, 5:523-535.
86. Ruiz L., Sánchez B., de los Reyes-Gavilán C.G., Gueimonde M., Margolles A. Coculture of Bifidobacterium longum and Bifidobacterium breve alters their protein expression profiles and enzymatic activities. International Journal of Food Microbiology 2009, 133:148-153.
87. Ruiz L., Zomer A., O'Connell-Motherway M., van Sinderen D., Margolles A. Discovering novel bile protection systems in Bifidobacterium breve UCC2003 through functional genomics. Applied and Environmental Microbiology 2012, 78:1123-1131.
88. Ruiz-Moyano S., Tao N.N., Underwood M.A., Mills D.A. Rapid discrimination of Bifidobacterium animalis subspecies by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Food Microbiology 2012, 30:432-437.
89. Sánchez B., Champomier-Verges M.C., Anglade P., Baraige F., de los Reyes-Gavilán C.G., Margolles A., et al. Proteomic analysis of global changes in protein expression during bile salt exposure of Bifidobacterium longum NCIMB 8809. Journal of Bacteriology 2005, 187:5799-5808.
90. Sánchez B., Champomier-Verges M.C., Anglade P., Baraige F., de los Reyes-Gavilán C.G., Margolles A., et al. A preliminary analysis of Bifidobacterium longum exported proteins by two-dimensional electrophoresis. Journal of Molecular Microbiology and Biotechnology 2008, 14:74-79.
91. Sánchez B., Champomier-Verges M.C., Collado M.D., Anglade P., Baraige F., Sanz Y., et al. Low-pH adaptation and the acid tolerance response of Bifidobactetium longum biotype longum. Applied and Environmental Microbiology 2007, 73:6450-6459.
92. Sánchez B., Champomier-Verges M.C., Stuer-Lauridsen B., Ruas-Madiedo P., Anglade P., Baraige F., et al. Adaptation and response of Bifidobacterium animalis subsp. lactis to bile: A proteomic and physiological approach. Applied and Environmental Microbiology 2007, 73:6757-6767.
93. Sánchez B., de los Reyes-Gavilán C.G., Margolles A. The F1F0-ATPase of Bifidobacterium animalis is involved in bile tolerance. Environmental Microbiology 2006, 8:1825-1833.
94. Sánchez B., de los Reyes-Gavilán C.G., Margolles A., Gueimonde M. Probiotic fermented milks: Present and future. International Journal of Dairy Technology 2009, 62:472-483.
95. Sánchez B., Ruiz L., de los Reyes-Gavilán C.G., Margolles A. Proteomics of stress response in Bifidobacterium. Frontiers in Bioscience 2008, 13:6905-6919.
96. Sarmiento-Rubiano L.A., Berger B., Moine D., Zúñiga M., Pérez-Martínez G., Yebra M.J. Characterization of a novel Lactobacillus species closely related to Lactobacillus johnsonii using a combination of molecular and comparative genomics methods. BMC Genomics 2010, 11:504.
97. Savijoki K., Lietzen N., Kankainen M., Alatossava T., Koskenniemi K., Varmanen P., et al. Comparative proteome cataloging of Lactobacillus rhamnosus strains GG and Lc705. Journal of Proteome Research 2011, 10:3460-3473.
98. Savijoki K., Suokko A., Palva A., Valmu L., Kalkkinen N., Varmanen P. Effect of heat-shock and bile salts on protein synthesis of Bifidobacterium longum revealed by [35S]methionine labelling and two-dimensional gel electrophoresis. FEMS Microbiology Letters 2005, 248:207-215.
99. Schell M.A., Karmirantzou M., Snel B., Vilanova D., Berger B., Pessi G., et al. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proceedings of the National Academy of Sciences of the United States of America 2002, 99:14422-14427.
100. Sekirov I., Russell S.L., Antunes L.C., Finlay B.B. Gut microbiota in health and disease. Physiological Reviews 2010, 90:859-904.
101. Sela D.A., Chapman J., Adeuya A., Kim J.H., Chen F., Whitehead T.R., et al. The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome. Proceedings of the National Academy of Sciences of the United States of America 2008, 105:18964-18969.
102. Siciliano R.A., Cacace G., Mazzeo M.F., Morelli L., Elli M., Rossi M., et al. Proteomic investigation of the aggregation phenomenon in Lactobacillus crispatus. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 2008, 1784:335-342.
103. Siezen R.J., Tzeneva V.A., Castioni A., Wels M., Phan H.T., Rademaker J.L., et al. Phenotypic and genomic diversity of Lactobacillus plantarum strains isolated from various environmental niches. Environmental Microbiology 2010, 12:758-773.
104. Siggins A., Gunnigle E., Abram F. Exploring mixed microbial community functioning: Recent advances in metaproteomics. FEMS Microbiology Ecology 2012, 80:265-280.
105. Stappenbeck T.S., Hooper L.V., Gordon J.I. Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. Proceedings of the National Academy of Sciences of the United States of America 2002, 99:15451-15455.
106. Troost F.J., van Baarlen P., Lindsey P., Kodde A., de Vos W.M., Kleerebezem M., et al. Identification of the transcriptional response of human intestinal mucosa to Lactobacillus plantarum WCFS1 in vivo. BMC Genomics 2008, 9:374.
107. Turnbaugh P.J., Hamady M., Yatsunenko T., Cantarel B.L., Duncan A., Ley R.E., et al. A core gut microbiome in obese and lean twins. Nature 2009, 457:480-484.
108. Turroni F., Bottacini F., Foroni E., Mulder I., Kim J.H., Zomer A., et al. Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging. Proceedings of the National Academy of Sciences of the United States of America 2010, 107:19514-19519.
109. Turroni F., Foroni E., Montanini B., Viappiani A., Strati F., Duranti S., et al. Global genome transcription profiling of Bifidobacterium bifidum PRL2010 under in vitro conditions and identification of reference genes for quantitative Real-Time PCR. Applied and Environmental Microbiology 2011, 77:8578-8587.
110. Turroni F., Foroni E., Serafini F., Viappiani A., Montanini B., Bottacini F., et al. Ability of Bifidobacterium breve to grow on different types of milk: Exploring the metabolism of milk through genome analysis. Applied and Environmental Microbiology 2011, 77:7408-7417.
111. Turroni F., van Sinderen D., Ventura M. Genomics and ecological overview of the genus Bifidobacterium. International Journal of Food Microbiology 2011, 149:37-44.
112. Van Baarlen P., Troost F., van der Meer C., Hooiveld G., Boekschoten M., Brummer R.J.M., et al. Human mucosal in vivo transcriptome responses to three lactobacilli indicate how probiotics may modulate human cellular pathways. Proceedings of the National Academy of Sciences of the United States of America 2011, 108:4562-4569.
113. van Baarlen P., Troost F.J., van Hemert S., van der Meer C., de Vos W.M., de Groot P.J., et al. Differential NF-kappaB pathways induction by Lactobacillus plantarum in the duodenum of healthy humans correlating with immune tolerance. Proceedings of the National Academy of Sciences of the United States of America 2009, 106:2371-2376.
114. Van de Guchte M., Penaud S., Grimaldi C., Barbe V., Bryson K., Nicolas P., et al. The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution. Proceedings of the National Academy of Sciences of the United States of America 2006, 103:9274-9279.
115. Ventura M., Canchaya C., van Sinderen D., Fitzgerald G.F., Zink R. Bifidobacterium lactis DSM 10140: Identification of the atp (atpBEFHAGDC) operon and analysis of its genetic structure, characteristics, and phylogeny. Applied and Environmental Microbiology 2004, 70:3110-3121.
116. Ventura M., O'Flaherty S., Claesson M.J., Turroni F., Klaenhammer T.R., van Sinderen D., et al. Genome-scale analysis of health-promoting bacteria: Probiogenomics. Nature Reviews. Microbiology 2009, 7:61-71.
117. Ventura M., Turroni F., Zomer A., Foroni E., Giubellini V., Bottacini F., et al. The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity. PLoS Genetics 2009, 5:e1000785.
118. Vitali B., Turroni S., Dal Piaz F., Candela M., Wasinger V., Brigidi P. Genetic and proteomic characterization of rifaximin resistance in Bifidobacterium infantis BI07. Research in Microbiology 2007, 158:355-362.
119. Vitali B., Wasinger V., Brigidi P., Guilhaus M. A proteomic view of Bifidobacterium infantis generated by multi-dimensional chromatography coupled with tandem mass spectrometry. Proteomics 2005, 5:1859-1867.
120. Whitehead K., Versalovic J., Roos S., Britton R.A. Genomic and genetic characterization of the bile stress response of probiotic Lactobacillus reuteri ATCC 55730. Applied and Environmental Microbiology 2008, 74:1812-1819.
121. Wu G.D., Chen J., Hoffmann C., Bittinger K., Chen Y.Y., Keilbaugh S.A., et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 2011, 334:105-108.
122. Wu C.D., Zhang J., Chen W., Wang M., Du G.C., Chen J. A combined physiological and proteomic approach to reveal lactic-acid-induced alterations in Lactobacillus casei Zhang and its mutant with enhanced lactic acid tolerance. Applied Microbiology and Biotechnology 2012, 93:707-722.
123. Wu R.N., Zhang W.Y., Sun T.S., Wu J.R., Yue X.Q., Meng H., et al. Proteomic analysis of responses of a new probiotic bacterium Lactobacillus casei Zhang to low acid stress. International Journal of Food Microbiology 2011, 147:181-187.
124. Xiao M., Xu P., Zhao J.Y., Wang Z., Zuo F.L., Zhang J.W., et al. Oxidative stress-related responses of Bifidobacterium longum subsp. longum BBMN68 at the proteomic level after exposure to oxygen. Microbiology-SGM 2011, 157:1573-1588.
125. Yuan J., Wang B., Sun Z.K., Bo X., Yuan X., He X., et al. Analysis of host-inducing proteome changes in Bifidobacterium longum NCC2705 grown in vivo. Journal of Proteome Research 2008, 7:375-385.
126. Zhang W., Li F., Nie L. Integrating multiple 'omics' analysis for microbial biology: Application and methodologies. Microbiology-SGM 2010, 156:287-301.
127. Zhu L., Hu W., Liu D.T., Tian W.H., Yu G., Liu X.K., et al. A reference proteomic database of Lactobacillus plantarum CMCC-P0002. PLoS One 2011, 6:e25596.
128. Zomer A., Fernandez M., Kearney B., Fitzgerald G.F., Ventura M., van Sinderen D. An interactive regulatory network controls stress response in Bifidobacterium breve UCC2003. Journal of Bacteriology 2009, 191:7039-7049.