Functional genomics of lactic acid bacteria: From food to health

Microbial Cell Factories

Volumn 13, Issue , 2014, Pages

  Douillard, Franҫois P ^a   de Vos, Willem M ^a,b  

^a UNIVERSITY OF HELSINKI   (Finland)

^b WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

adaptation; applied genomics; evolution; Genome comparison; pili; respiration

Indexed keywords

CATABOLITE CONTROL PROTEIN A; CIS ACTING ELEMENT; PROBIOTIC AGENT;

ADAPTATION; AMINO ACID METABOLISM; AMINO ACID TRANSPORT; ARTICLE; CHEESE; FERMENTATION; FERMENTED PRODUCT; FUNCTIONAL GENOMICS; GASTROINTESTINAL TRACT; GENE EXPRESSION; GENE SEQUENCE; GENOME ANALYSIS; HEALTH STATUS; HORIZONTAL GENE TRANSFER; INDUCED MUTATION; LACTIC ACID BACTERIUM; LACTOBACILLUS; LACTOBACILLUS CASEI; LACTOBACILLUS PLANTARUM; LACTOCOCCUS LACTIS; LEUCONOSTOC; MICROARRAY ANALYSIS; MOUTH CAVITY; NONHUMAN; QUORUM SENSING; REGULATORY MECHANISM; STREPTOCOCCUS THERMOPHILUS; TRANSGENIC ORGANISM; BACTERIAL GENOME; CLASSIFICATION; EVOLUTION; FOOD CONTROL; GENETICS; GROWTH, DEVELOPMENT AND AGING; HUMAN; LACTOBACILLACEAE; MICROBIOLOGY; MOUTH MUCOSA; PHYLOGENY;

BIOLOGICAL EVOLUTION; FOOD MICROBIOLOGY; GASTROINTESTINAL TRACT; GENE TRANSFER, HORIZONTAL; GENOME, BACTERIAL; HUMANS; LACTOBACILLACEAE; MOUTH MUCOSA; PHYLOGENY;

EID: 84906841405     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/1475-2859-13-S1-S8     Document Type: Article

References (221)

1. Tannock GW. Normal microflora: an introduction to microbes inhabiting the human body. 1995, Springer.
2. Vaughan EE, Heilig HGHJ, Ben-Amor K, de Vos WM. Diversity, vitality and activities of intestinal lactic acid bacteria and bifidobacteria assessed by molecular approaches. FEMS Microbiol Rev 2005, 29:477-490. 10.1016/j.fmrre.2005.04.009, 16125009.
3. Zoetendal EG, Rajilic´-Stojanovic´ M, de Vos WM. High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut 2008, 57:1605-1615. 10.1136/gut.2007.133603, 18941009.
4. Human Microbiome Project C. Structure, function and diversity of the healthy human microbiome. Nature 2012, 486:207-214. 10.1038/nature11234, 3564958, 22699609.
5. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010, 464:59-65. 10.1038/nature08821, 3779803, 20203603.
6. Sekelja M, Rud I, Knutsen SH, Denstadli V, Westereng B, Naes T, Rudi K. Abrupt temporal fluctuations in the chicken fecal microbiota are explained by its gastrointestinal origin. Appl Environ Microbiol 2012, 78:2941-2948. 10.1128/AEM.05391-11, 3318845, 22307311.
7. Frese SA, MacKenzie DA, Peterson DA, Schmaltz R, Fangman T, Zhou Y, Zhang C, Benson AK, Cody LA, Mulholland F, et al. Molecular characterization of host-specific biofilm formation in a vertebrate gut symbiont. PLoS Genet 2013, 9:e1004057. 10.1371/journal.pgen.1004057, 3873254, 24385934.
8. Saxelin M, Tynkkynen S, Mattila-Sandholm T, de Vos WM. Probiotic and other functional microbes: from markets to mechanisms. Curr Opin Biotechnol 2005, 16:204-211. 10.1016/j.copbio.2005.02.003, 15831388.
9. Petschow B, Dore J, Hibberd P, Dinan T, Reid G, Blaser M, Cani PD, Degnan FH, Foster J, Gibson G, et al. Probiotics, prebiotics, and the host microbiome: the science of translation. Ann N Y Acad Sci 2013, 1306:1-17. 10.1111/nyas.12303, 24266656.
10. Tannock GW. A special fondness for lactobacilli. Appl Environ Microbiol 2004, 70:3189-3194. 10.1128/AEM.70.6.3189-3194.2004, 427720, 15184111.
11. Douglas LM. The bacillus of long life. 1911, London: TC & EC Jack.
12. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, et A. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995, 269:496-512. 10.1126/science.7542800, 7542800.
13. Bolotin A, Wincker P, Mauger S, Jaillon O, Malarme K, Weissenbach J, Ehrlich SD, Sorokin A. The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403. Genome Res 2001, 11:731-753. 10.1101/gr.GR-1697R, 311110, 11337471.
14. Kleerebezem M, Boekhorst J, van Kranenburg R, Molenaar D, Kuipers OP, Leer R, Tarchini R, Peters SA, Sandbrink HM, Fiers MWEJ, et al. Complete genome sequence of Lactobacillus plantarum WCFS1. Proc Natl Acad Sci USA 2003, 100:1990-1995. 10.1073/pnas.0337704100, 149946, 12566566.
15. Johnson BR, Klaenhammer TR. Impact of genomics on the field of probiotic research: historical perspectives to modern paradigms. Antonie Van Leeuwenhoek 2014,
16. de Vos WM. Systems solutions by lactic acid bacteria: from paradigms to practice. Microb Cell Fact 2011, 10(Suppl 1):S2. 10.1186/1475-2859-10-S1-S2, 3231926, 21995776.
17. Linares DM, Kok J, Poolman B. Genome sequences of Lactococcus lactis MG1363 (revised) and NZ9000 and comparative physiological studies. J Bacteriol 2010, 192:5806-5812. 10.1128/JB.00533-10, 2953693, 20639323.
18. de Ruyter PG, Kuipers OP, de Vos WM. Controlled gene expression systems for Lactococcus lactis with the food-grade inducer nisin. Appl Environ Microbiol 1996, 62:3662-3667. 168174, 8837421.
19. Makarova K, Slesarev A, Wolf Y, Sorokin A, Mirkin B, Koonin E, Pavlov A, Pavlova N, Karamychev V, Polouchine N, et al. Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci USA 2006, 103:15611-15616. 10.1073/pnas.0607117103, 1622870, 17030793.
20. de Vos WM, Vos P, de Haard H, Boerrigter I. Cloning and expression of the Lactococcus lactis subsp. cremoris SK11 gene encoding an extracellular serine proteinase. Gene 1989, 85:169-176. 10.1016/0378-1119(89)90477-0, 2515994.
21. Ainsworth S, Zomer A, de Jager V, Bottacini F, van Hijum SA, Mahony J, van Sinderen D. Complete genome of Lactococcus lactis subsp. cremoris UC509.9, host for a model lactococcal P335 bacteriophage. Genome Announc 2013, 1. 3569286, 23405300.
22. Kelly WJ, Altermann E, Lambie SC, Leahy SC. Interaction between the genomes of Lactococcus lactis and phages of the P335 species. Front Microbiol 2013, 4:257. 3757294, 24009606.
23. Siezen RJ, Bayjanov J, Renckens B, Wels M, van Hijum SAFT, Molenaar D, van Hylckama Vlieg JET. Complete genome sequence of Lactococcus lactis subsp. lactis KF147, a plant-associated lactic acid bacterium. J Bacteriol 2010, 192:2649-2650. 10.1128/JB.00276-10, 2863553, 20348266.
24. Settanni L, Moschetti G. Non-starter lactic acid bacteria used to improve cheese quality and provide health benefits. Food Microbiol 2010, 27:691-697. 10.1016/j.fm.2010.05.023, 20630311.
25. Papanikolaou Z, Hatzikamari M, Georgakopoulos P, Yiangou M, Litopoulou-Tzanetaki E, Tzanetakis N. Selection of dominant NSLAB from a mature traditional cheese according to their technological properties and in vitro intestinal challenges. J Food Sci 2012, 77:M298-306. 10.1111/j.1750-3841.2012.02685.x, 23163947.
26. Broadbent JR, Hughes JE, Welker DL, Tompkins TA, Steele JL. Complete genome sequence for Lactobacillus helveticus CNRZ 32, an industrial cheese starter and cheese flavor adjunct. Genome Announc 2013, 1. 3751602, 23969047.
27. Luesink EJ, van Herpen REMA, Grossiord BP, Kuipers OP, de Vos WM. Transcriptional activation of the glycolytic las operon and catabolite repression of the gal operon in Lactococcus lactis are mediated by the catabolite control protein CcpA. Mol Microbiol 1998, 30:789-798. 10.1046/j.1365-2958.1998.01111.x, 10094627.
28. Zomer AL, Buist G, Larsen R, Kok J, Kuipers OP. Time-resolved determination of the CcpA regulon of Lactococcus lactis subsp. cremoris MG1363. J Bacteriol 2007, 189:1366-1381. 10.1128/JB.01013-06, 1797362, 17028270.
29. Loll B, Saenger W, Biesiadka J. Structure of full-length transcription regulator CcpA in the apo form. Biochim Biophys Acta 2007, 1774:732-736. 10.1016/j.bbapap.2007.03.020, 17500051.
30. Aleksandrzak-Piekarczyk T, Polak J, Jezierska B, Renault P, Bardowski J. Genetic characterization of the CcpA-dependent, cellobiose-specific PTS system comprising CelB, PtcB and PtcA that transports lactose in Lactococcus lactis IL1403. Int J Food Microbiol 2011, 145:186-194. 10.1016/j.ijfoodmicro.2010.12.011, 21262549.
31. Barrangou R, Azcarate-Peril MA, Duong T, Conners SB, Kelly RM, Klaenhammer TR. Global analysis of carbohydrate utilization by Lactobacillus acidophilus using cDNA microarrays. Proc Natl Acad Sci USA 2006, 103:3816-3821. 10.1073/pnas.0511287103, 1533782, 16505367.
32. Andersen JM, Barrangou R, Hachem MA, Lahtinen SJ, Goh YJ, Svensson B, Klaenhammer TR. Transcriptional analysis of prebiotic uptake and catabolism by Lactobacillus acidophilus NCFM. PLoS One 2012, 7:e44409. 10.1371/journal.pone.0044409, 3446993, 23028535.
33. McLeod A, Snipen L, Naterstad K, Axelsson L. Global transcriptome response in Lactobacillus sakei during growth on ribose. BMC Microbiol 2011, 11:145. 10.1186/1471-2180-11-145, 3146418, 21702908.
34. Mazzeo MF, Cacace G, Peluso A, Zotta T, Muscariello L, Vastano V, Parente E, Siciliano RA. Effect of inactivation of ccpA and aerobic growth in Lactobacillus plantarum: A proteomic perspective. J Proteomics 2012, 75:4050-4061. 10.1016/j.jprot.2012.05.019, 22634038.
35. Muscariello L, Marino C, Capri U, Vastano V, Marasco R, Sacco M. CcpA and three newly identified proteins are involved in biofilm development in Lactobacillus plantarum. J Basic Microbiol 2013, 53:62-71. 10.1002/jobm.201100456, 22585750.
36. van den Bogaard PTC, Kleerebezem M, Kuipers OP, de Vos WM. Control of lactose transport, beta-galactosidase activity, and glycolysis by CcpA in Streptococcus thermophilus: evidence for carbon catabolite repression by a non-phosphoenolpyruvate-dependent phosphotransferase system sugar. J Bacteriol 2000, 182:5982-5989. 10.1128/JB.182.21.5982-5989.2000, 94730, 11029416.
37. Gao P, Pinkston KL, Bourgogne A, Cruz MR, Garsin DA, Murray BE, Harvey BR. Library screen identifies Enterococcus faecalis CcpA, the catabolite control protein A, as an effector of Ace, a collagen adhesion protein linked to virulence. J Bacteriol 2013, 195:4761-4768. 10.1128/JB.00706-13, 3807442, 23974022.
38. Carvalho AL, Turner DL, Fonseca LL, Solopova A, Catarino T, Kuipers OP, Voit EO, Neves AR, Santos H. Metabolic and transcriptional analysis of acid stress in Lactococcus lactis, with a focus on the kinetics of lactic acid pools. PLoS One 2013, 8:e68470. 10.1371/journal.pone.0068470, 3700934, 23844205.
39. de Jong A, Hansen ME, Kuipers OP, Kilstrup M, Kok J. The transcriptional and gene regulatory network of Lactococcus lactis MG1363 during growth in milk. PLoS ONE 2013, 8:e53085. 10.1371/journal.pone.0053085, 3547956, 23349698.
40. Groot Kormelink T, Koenders E, Hagemeijer Y, Overmars L, Siezen RJ, de Vos WM, Francke C. Comparative genome analysis of central nitrogen metabolism and its control by GlnR in the class Bacilli. BMC Genomics 2012, 13:191. 10.1186/1471-2164-13-191, 3412718, 22607086.
41. Larsen R, Kloosterman TG, Kok J, Kuipers OP. GlnR-mediated regulation of nitrogen metabolism in Lactococcus lactis. J Bacteriol 2006, 188:4978-4982. 10.1128/JB.00025-06, 1483007, 16788206.
42. den Hengst CD, van Hijum SAFT, Geurts JMW, Nauta A, Kok J, Kuipers OP. The Lactococcus lactis CodY regulon: identification of a conserved cis-regulatory element. J Biol Chem 2005, 280:34332-34342. 10.1074/jbc.M502349200, 16040604.
43. Guedon E, Sperandio B, Pons N, Ehrlich SD, Renault P. Overall control of nitrogen metabolism in Lactococcus lactis by CodY, and possible models for CodY regulation in Firmicutes. Microbiology 2005, 151:3895-3909. 10.1099/mic.0.28186-0, 16339935.
44. Marugg JD, van Kranenburg R, Laverman P, Rutten GA, de Vos WM. Identical transcriptional control of the divergently transcribed prtP and prtM genes that are required for proteinase production in Lactococcus lactis SK11. J Bacteriol 1996, 178:1525-1531. 177834, 8626277.
45. Dressaire C, Redon E, Gitton C, Loubiere P, Monnet V, Cocaign-Bousquet M. Investigation of the adaptation of Lactococcus lactis to isoleucine starvation integrating dynamic transcriptome and proteome information. Microb Cell Fact 2011, 10(Suppl 1):S18. 10.1186/1475-2859-10-S1-S18, 3236307, 21995707.
46. Liu F, Du L, Du P, Huo G. Possible promoter regions within the proteolytic system in Streptococcus thermophilus and their interaction with the CodY homolog. FEMS Microbiol Lett 2009, 297:164-172. 10.1111/j.1574-6968.2009.01672.x, 19552712.
47. Hendriksen WT, Bootsma HJ, Estevao S, Hoogenboezem T, de Jong A, de Groot R, Kuipers OP, Hermans PWM. CodY of Streptococcus pneumoniae: link between nutritional gene regulation and colonization. J Bacteriol 2008, 190:590-601. 10.1128/JB.00917-07, 2223708, 18024519.
48. McDowell EJ, Callegari EA, Malke H, Chaussee MS. CodY-mediated regulation of Streptococcus pyogenes exoproteins. BMC Microbiol 2012, 12:114. 10.1186/1471-2180-12-114, 3438106, 22721528.
49. Branco dos Santos F, de Vos WM, Teusink B. Towards metagenome-scale models for industrial applications - the case of Lactic Acid Bacteria. Curr Opin Biotechnol 2013, 24:200-206. 10.1016/j.copbio.2012.11.003, 23200025.
50. Bachmann H, de Wilt L, Kleerebezem M, van Hylckama Vlieg JE. Time-resolved genetic responses of Lactococcus lactis to a dairy environment. Environ Microbiol 2010, 12:1260-1270. 10.1111/j.1462-2920.2010.02168.x, 20192965.
51. Cretenet M, Laroute V, Ulve V, Jeanson S, Nouaille S, Even S, Piot M, Girbal L, Le Loir Y, Loubiere P, et al. Dynamic analysis of the Lactococcus lactis transcriptome in cheeses made from milk concentrated by ultrafiltration reveals multiple strategies of adaptation to stresses. Appl Environ Microbiol 2011, 77:247-257. 10.1128/AEM.01174-10, 3019719, 21075879.
52. Le Boucher C, Courant F, Jeanson S, Chereau S, Maillard MB, Royer AL, Thierry A, Dervilly-Pinel G, Le Bizec B, Lortal S. First mass spectrometry metabolic fingerprinting of bacterial metabolism in a model cheese. Food Chem 2013, 141:1032-1040. 10.1016/j.foodchem.2013.03.094, 23790883.
53. Taibi A, Dabour N, Lamoureux M, Roy D, LaPointe G. Comparative transcriptome analysis of Lactococcus lactis subsp. cremoris strains under conditions simulating Cheddar cheese manufacture. Int J Food Microbiol 2011, 146:263-275. 10.1016/j.ijfoodmicro.2011.02.034, 21435733.
54. Erkus O, de Jager VCL, Spus M, van Alen-Boerrigter IJ, van Rijswijck IMH, Hazelwood L, Janssen PWM, van Hijum SAFT, Kleerebezem M, Smid EJ. Multifactorial diversity sustains microbial community stability. ISME J 2013, 7:2126-2136. 10.1038/ismej.2013.108, 23823494.
55. Johansen P, Vindelov J, Arneborg N, Brockmann E. Development of quantitative PCR and metagenomics-based approaches for strain quantification of a defined mixed-strain starter culture. Syst Appl Microbiol 2014, 37:186-193. 10.1016/j.syapm.2013.12.006, 24582508.
56. Aguado-Urda M, Gibello A, Blanco Mdel M, Ferna´ndez-Garayza´bal JF, Lo´pez-Alonso V, Lo´pez-Campos GH. Global transcriptome analysis of Lactococcus garvieae strains in response to temperature. PLoS One 2013, 8:e79692. 10.1371/journal.pone.0079692, 3817100, 24223997.
57. Brooijmans R, Smit B, Santos F, van Riel J, de Vos WM, Hugenholtz J. Heme and menaquinone induced electron transport in lactic acid bacteria. Microb Cell Fact 2009, 8:28. 10.1186/1475-2859-8-28, 2696406, 19480672.
58. Ja¨a¨skela¨inen E, Johansson P, Kostiainen O, Nieminen T, Schmidt G, Somervuo P, Mohsina M, Vanninen P, Auvinen P, Bjo¨rkroth J. Significance of heme-based respiration in meat spoilage caused by Leuconostoc gasicomitatum. Appl Environ Microbiol 2013, 79:1078-1085. 10.1128/AEM.02943-12, 3568588, 23204416.
59. Pedersen MB, Gaudu P, Lechardeur D, Petit MA, Gruss A. Aerobic respiration metabolism in lactic acid bacteria and uses in biotechnology. Annu Rev Food Sci Technol 2012, 3:37-58. 10.1146/annurev-food-022811-101255, 22385163.
60. Zhai Z, Douillard FP, An H, Wang G, Guo X, Luo Y, Hao Y. Proteomic characterization of the acid tolerance response in Lactobacillus delbrueckii subsp. bulgaricus CAUH1 and functional identification of a novel acid stress-related transcriptional regulator Ldb0677. Environ Microbiol 2013, 16:1524-1537.
61. Wunsche A, Hammer E, Bartholomae M, Volker U, Burkovski A, Seidel G, Hillen W. CcpA forms complexes with CodY and RpoA in Bacillus subtilis. FEBS J 2012, 279:2201-2214. 10.1111/j.1742-4658.2012.08604.x, 22512862.
62. Levdikov VM, Blagova E, Joseph P, Sonenshein AL, Wilkinson AJ. The structure of CodY, a GTP- and isoleucine-responsive regulator of stationary phase and virulence in gram-positive bacteria. J Biol Chem 2006, 281:11366-11373. 10.1074/jbc.M513015200, 16488888.
63. Geiger T, Wolz C. Intersection of the stringent response and the CodY regulon in low GC Gram-positive bacteria. Int J Med Microbiol 2014, 304:150-155. 10.1016/j.ijmm.2013.11.013, 24462007.
64. Wolz C, Geiger T, Goerke C. The synthesis and function of the alarmone (p)ppGpp in firmicutes. Int J Med Microbiol 2010, 300:142-147. 10.1016/j.ijmm.2009.08.017, 19783475.
65. Winstedt L, Frankenberg L, Hederstedt L, von Wachenfeldt C. Enterococcus faecalis V583 contains a cytochrome bd-type respiratory oxidase. J Bacteriol 2000, 182:3863-3866. 10.1128/JB.182.13.3863-3866.2000, 94564, 10851008.
66. Portela CAF, Smart KF, Tumanov S, Cook GM, Villas-Boas SG. The global metabolic response of Enterococcus faecalis to oxygen. J Bacteriol 2014,
67. Brooijmans RJW, Poolman B, Schuurman-Wolters GK, de Vos WM, Hugenholtz J. Generation of a membrane potential by Lactococcus lactis through aerobic electron transport. J Bacteriol 2007, 189:5203-5209. 10.1128/JB.00361-07, 1951855, 17496098.
68. Oxaran V, Ledue-Clier F, Dieye Y, Herry JM, Pechoux C, Meylheuc T, Briandet R, Juillard V, Piard JC. Pilus biogenesis in Lactococcus lactis: molecular characterization and role in aggregation and biofilm formation. PLoS One 2012, 7:e50989. 10.1371/journal.pone.0050989, 3516528, 23236417.
69. Kankainen M, Paulin L, Tynkkynen S, von Ossowski I, Reunanen J, Partanen P, Satokari R, Vesterlund S, Hendrickx APA, Lebeer S, et al. Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein. Proc Natl Acad Sci USA 2009, 106:17193-17198. 10.1073/pnas.0908876106, 2746127, 19805152.
70. Segers ME, Lebeer S. Lactobacillus rhamnosus GG - host interactions. Microb Cell Fact 2014,
71. Meyrand M, Guillot A, Goin M, Furlan S, Armalyte J, Kulakauskas S, Cortes-Perez NG, Thomas G, Chat S, Pechoux C, et al. Surface proteome analysis of a natural isolate of Lactococcus lactis reveals the presence of pili able to bind human intestinal epithelial cells. Mol Cell Proteomics 2013, 12:3935-3947. 10.1074/mcp.M113.029066, 24002364.
72. Vaughan EE, de Vries MC, Zoetendal EG, Ben-Amor K, Akkermans ADL, de Vos WM. The intestinal LABs. Antonie Van Leeuwenhoek 2002, 82:341-352. 10.1023/A:1020672724450, 12369201.
73. Walter J. Ecological role of lactobacilli in the gastrointestinal tract: implications for fundamental and biomedical research. Appl Environ Microbiol 2008, 74:4985-4996. 10.1128/AEM.00753-08, 2519286, 18539818.
74. Bello FD, Walter J, Hammes WP, Hertel C. Increased complexity of the species composition of lactic acid bacteria in human feces revealed by alternative incubation condition. Microb Ecol 2003, 45:455-463. 10.1007/s00248-003-2001-z, 12704557.
75. Heilig HGHJ, Zoetendal EG, Vaughan EE, Marteau P, Akkermans ADL, de Vos WM. Molecular diversity of Lactobacillus spp. and other lactic acid bacteria in the human intestine as determined by specific amplification of 16S ribosomal DNA. Appl Environ Microbiol 2002, 68:114-123. 10.1128/AEM.68.1.114-123.2002, 126540, 11772617.
76. Ahrne S, Nobaek S, Jeppsson B, Adlerberth I, Wold AE, Molin G. The normal Lactobacillus flora of healthy human rectal and oral mucosa. J Appl Microbiol 1998, 85:88-94. 10.1046/j.1365-2672.1998.00480.x, 9721659.
77. Molin G, Jeppsson B, Johansson ML, Ahrne´ S, Nobaek S, Stahl M, Bengmark S. Numerical taxonomy of Lactobacillus spp. associated with healthy and diseased mucosa of the human intestines. J Appl Bacteriol 1993, 74:314-323. 10.1111/j.1365-2672.1993.tb03031.x, 8468264.
78. Klijn N, Weerkamp AH, de Vos WM. Genetic marking of Lactococcus lactis shows its survival in the human gastrointestinal tract. Appl Environ Microbiol 1995, 61:2771-2774. 167550, 7618890.
79. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 2014, 505:559-563.
80. Douillard FP, Ribbera A, Kant R, Pietila TE, Jarvinen HM, Messing M, Randazzo CL, Paulin L, Laine P, Ritari J, et al. Comparative genomic and functional analysis of 100 Lactobacillus rhamnosus strains and their comparison with strain GG. PLoS Genet 2013, 9:e1003683. 10.1371/journal.pgen.1003683, 3744422, 23966868.
81. Macklaim J, Fernandes A, Di Bella J, Hammond J-A, Reid G, Gloor G. Comparative meta-RNA-seq of the vaginal microbiota and differential expression by Lactobacillus iners in health and dysbiosis. Microbiome 2013, 1:12. 10.1186/2049-2618-1-12, 3971606, 24450540.
82. de Vos WM, de Vos EAJ. Role of the intestinal microbiome in health and disease: from correlation to causation. Nutr Rev 2012, 70(Suppl 1):S45-56.
83. Karlsson FH, Tremaroli V, Nookaew I, Bergstrom G, Behre CJ, Fagerberg B, Nielsen J, Backhed F. Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature 2013, 498:99-103. 10.1038/nature12198, 23719380.
84. de Vos WM, Nieuwdorp M. Genomics: a gut prediction. Nature 2013, 498:48-49. 10.1038/nature12251, 23719383.
85. Beni´tez-Pa´ez A, Belda-Ferre P, Simo´n-Soro A, Mira A. Microbiota diversity and gene expression dynamics in human oral biofilms. BMC Genomics 2014, 15:311. 10.1186/1471-2164-15-311, 24767457.
86. Hojo K, Mizoguchi C, Taketomo N, Ohshima T, Gomi K, Arai T, Maeda N. Distribution of salivary Lactobacillus and Bifidobacterium species in periodontal health and disease. Biosci Biotechnol Biochem 2007, 71:152-157. 10.1271/bbb.60420, 17213656.
87. Strahinic I, Busarcevic M, Pavlica D, Milasin J, Golic N, Topisirovic L. Molecular and biochemical characterizations of human oral lactobacilli as putative probiotic candidates. Oral Microbiol Immunol 2007, 22:111-117. 10.1111/j.1399-302X.2007.00331.x, 17311634.
88. Jagtap P, McGowan T, Bandhakavi S, Tu ZJ, Seymour S, Griffin TJ, Rudney JD. Deep metaproteomic analysis of human salivary supernatant. Proteomics 2012, 12:992-1001. 10.1002/pmic.201100503, 3517020, 22522805.
89. Ahola AJ, Yli-Knuuttila H, Suomalainen T, Poussa T, Ahlstrom A, Meurman JH, Korpela R. Short-term consumption of probiotic-containing cheese and its effect on dental caries risk factors. Arch Oral Biol 2002, 47:799-804. 10.1016/S0003-9969(02)00112-7, 12446187.
90. Nadkarni MA, Chen Z, Wilkins MR, Hunter N. Comparative genome analysis of Lactobacillus rhamnosus clinical isolates from initial stages of dental pulp infection: identification of a new exopolysaccharide cluster. PLoS ONE 2014, 9:e90643. 10.1371/journal.pone.0090643, 3954586, 24632842.
91. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010, 464:59-65. 10.1038/nature08821, 3779803, 20203603.
92. Louis P, Scott KP, Duncan SH, Flint HJ. Understanding the effects of diet on bacterial metabolism in the large intestine. J Appl Microbiol 2007, 102:1197-1208. 10.1111/j.1365-2672.2007.03322.x, 17448155.
93. Harmsen HJM, Raangs GC, He T, Degener JE, Welling GW. Extensive set of 16S rRNA-based probes for detection of bacteria in human feces. Appl Environ Microbiol 2002, 68:2982-2990. 10.1128/AEM.68.6.2982-2990.2002, 123985, 12039758.
94. Booijink CCGM, El-Aidy S, Rajilic´-Stojanovic´ M, Heilig HGHJ, Troost FJ, Smidt H, Kleerebezem M, De Vos WM, Zoetendal EG. High temporal and inter-individual variation detected in the human ileal microbiota. Environ Microbiol 2010, 12:3213-3227. 10.1111/j.1462-2920.2010.02294.x, 20626454.
95. Zoetendal EG, Raes J, van den Bogert B, Arumugam M, Booijink CCGM, Troost FJ, Bork P, Wels M, de Vos WM, Kleerebezem M. The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. ISME J 2012, 6:1415-1426. 10.1038/ismej.2011.212, 3379644, 22258098.
96. van den Bogert B, Erkus O, Boekhorst J, de Goffau M, Smid EJ, Zoetendal EG, Kleerebezem M. Diversity of human small intestinal Streptococcus and Veillonella populations. FEMS Microbiol Ecol 2013, 85:376-388. 10.1111/1574-6941.12127, 23614882.
97. Bernardeau M, Guguen M, Vernoux JP. Beneficial lactobacilli in food and feed: long-term use, biodiversity and proposals for specific and realistic safety assessments. FEMS Microbiol Rev 2006, 30:487-513. 10.1111/j.1574-6976.2006.00020.x, 16774584.
98. Vesa T, Pochart P, Marteau P. Pharmacokinetics of Lactobacillus plantarum NCIMB 8826, Lactobacillus fermentum KLD, and Lactococcus lactis MG 1363 in the human gastrointestinal tract. Aliment Pharmacol Ther 2000, 14:823-828. 10.1046/j.1365-2036.2000.00763.x, 10848668.
99. Lahti L, Salonen A, Kekkonen RA, Salojarvi J, Jalanka-Tuovinen J, Palva A, Oresic M, de Vos WM. Associations between the human intestinal microbiota, Lactobacillus rhamnosus GG and serum lipids indicated by integrated analysis of high-throughput profiling data. PeerJ 2013, 26. 3628737, 23638368.
100. Selle K, Klaenhammer TR. Genomic and phenotypic evidence for probiotic influences of Lactobacillus gasseri on human health. FEMS Microbiol Rev 2013, 37:915-935.
101. Denou E, Pridmore RD, Berger B, Panoff JM, 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. J Bacteriol 2008, 190:3161-3168. 10.1128/JB.01637-07, 2347406, 18223069.
102. Toh H, Oshima K, Nakano A, Takahata M, Murakami M, Takaki T, Nishiyama H, Igimi S, Hattori M, Morita H. Genomic Adaptation of the Lactobacillus casei Group. PLoS ONE 2013, 8:e75073. 10.1371/journal.pone.0075073, 3792948, 24116025.
103. Cai H, Rodri´guez BT, Zhang W, Broadbent JR, Steele JL. Genotypic and phenotypic characterization of Lactobacillus casei strains isolated from different ecological niches suggests frequent recombination and niche specificity. Microbiol 2007, 153:2655-2665. 10.1099/mic.0.2007/006452-0, 17660430.
104. Raftis EJ, Salvetti E, Torriani S, Felis GE, O'Toole PW. Genomic diversity of Lactobacillus salivarius. Appl Environ Microbiol 2011, 77:954-965. 10.1128/AEM.01687-10, 3028724, 21131523.
105. Corr SC, Li Y, Riedel CU, O'Toole PW, Hill C, Gahan CG. Bacteriocin production as a mechanism for the antiinfective activity of Lactobacillus salivarius UCC118. Proc Natl Acad Sci USA 2007, 104:7617-7621. 10.1073/pnas.0700440104, 1863472, 17456596.
106. Claesson MJ, Li Y, Leahy S, Canchaya C, van Pijkeren JP, Cerdeño-Ta´rraga AM, Parkhill J, Flynn S, O'Sullivan GC, Collins JK, et al. Multireplicon genome architecture of Lactobacillus salivarius. Proc Natl Acad Sci USA 2006, 103:6718-6723. 10.1073/pnas.0511060103, 1436024, 16617113.
107. Naito S, Hayashidani H, Kaneko K, Ogawa M, Benno Y. Development of intestinal lactobacilli in normal piglets. J Appl Bacteriol 1995, 79:230-236. 10.1111/j.1365-2672.1995.tb00940.x, 7592119.
108. Molin G, Johansson ML, Sta˚hl M, Ahrne´ S, Andersson R, Jeppsson B, Bengmark S. Systematics of the Lactobacillus population on rat intestinal mucosa with special reference to Lactobacillus reuteri. Antonie Van Leeuwenhoek 1992, 61:175-183. 10.1007/BF00584224, 1325752.
109. Frese SA, Benson AK, Tannock GW, Loach DM, Kim J, Zhang M, Oh PL, Heng NCK, Patil PB, Juge N, et al. The Evolution of host specialization in the vertebrate gut symbiont Lactobacillus reuteri. PLoS Genet 2011, 7:e1001314. 10.1371/journal.pgen.1001314, 3040671, 21379339.
110. Moran NA, Plague GR. Genomic changes following host restriction in bacteria. Curr Opin Genet Dev 2004, 14:627-633. 10.1016/j.gde.2004.09.003, 15531157.
111. Forde BM, Neville BA, O'Donnell MM, Riboulet-Bisson E, Claesson MJ, Coghlan A, Ross RP, O'Toole PW. Genome sequences and comparative genomics of two Lactobacillus ruminis strains from the bovine and human intestinal tracts. Microb Cell Fact 2011, 10(Suppl 1):S13. 10.1186/1475-2859-10-S1-S13, 3231920, 21995554.
112. Altermann E, Russell WM, Azcarate-Peril MA, Barrangou R, Buck BL, McAuliffe O, Souther N, Dobson A, Duong T, Callanan M, et al. Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM. Proc Natl Acad Sci USA 2005, 102:3906-3912. 10.1073/pnas.0409188102, 554803, 15671160.
113. Callanan M, Kaleta P, O'Callaghan J, O'Sullivan O, Jordan K, McAuliffe O, Sangrador-Vegas A, Slattery L, Fitzgerald GF, Beresford T, Ross RP. Genome sequence of Lactobacillus helveticus, an organism distinguished by selective gene loss and insertion sequence element expansion. J Bacteriol 2008, 190:727-735. 10.1128/JB.01295-07, 2223680, 17993529.
114. Douillard FP, Ribbera A, Ja¨rvinen HM, Kant R, Pietila¨ TE, Randazzo C, Paulin L, Laine PK, Caggia C, von Ossowski I, et al. Comparative genomic and functional analysis of Lactobacillus casei and Lactobacillus rhamnosus strains marketed as probiotics. Appl Environ Microbiol 2013, 79:1923-1933. 10.1128/AEM.03467-12, 3592221, 23315726.
115. van Pijkeren JP, Canchaya C, Ryan KA, Li Y, Claesson MJ, Sheil B, Steidler L, O'Mahony L, Fitzgerald GF, van Sinderen D, O'Toole PW. Comparative and functional analysis of sortase-dependent proteins in the predicted secretome of Lactobacillus salivarius UCC118. Appl Environ Microbiol 2006, 72:4143-4153. 10.1128/AEM.03023-05, 1489637, 16751526.
116. Call EK, Klaenhammer TR. Relevance and application of sortase and sortase-dependent proteins in lactic acid bacteria. Front Microbiol 2013, 4:73. 3619620, 23579319.
117. Neville BA, Forde BM, Claesson MJ, Darby T, Coghlan A, Nally K, Ross RP, O'Toole PW. Characterization of pro-inflammatory flagellin proteins produced by Lactobacillus ruminis and related motile lactobacilli. PLoS ONE 2012, 7:e40592. 10.1371/journal.pone.0040592, 3393694, 22808200.
118. Azcarate-Peril MA, Altermann E, Goh YJ, Tallon R, Sanozky-Dawes RB, Pfeiler EA, O'Flaherty S, Buck BL, Dobson A, Duong T, et al. Analysis of the genome sequence of Lactobacillus gasseri ATCC 33323 reveals the molecular basis of an autochthonous intestinal organism. Appl Environ Microbiol 2008, 74:4610-4625. 10.1128/AEM.00054-08, 2519322, 18539810.
119. Yanagihara S, Hirota T, Yamamoto N. Transcriptional response of Lactobacillus acidophilus L-92 after attachment to epithelial Caco-2 cells. J Biosci Bioeng 2012, 114:582-585. 10.1016/j.jbiosc.2012.07.001, 22841868.
120. Ashida N, Yanagihara S, Shinoda T, Yamamoto N. Characterization of adhesive molecule with affinity to Caco-2 cells in Lactobacillus acidophilus by proteome analysis. J Biosci Bioeng 2011, 112:333-337. 10.1016/j.jbiosc.2011.06.001, 21763196.
121. Konstantinov SR, Smidt H, de Vos WM, Bruijns SCM, Singh SK, Valence F, Molle D, Lortal S, Altermann E, Klaenhammer TR, van Kooyk Y. S layer protein A of Lactobacillus acidophilus NCFM regulates immature dendritic cell and T cell functions. Proc Natl Acad Sci USA 2008, 105:19474-19479. 10.1073/pnas.0810305105, 2592362, 19047644.
122. Johnson B, Selle K, O'Flaherty S, Goh YJ, Klaenhammer T. Identification of extracellular surface-layer associated proteins in Lactobacillus acidophilus NCFM. Microbiology 2013, 159:2269-2282. 10.1099/mic.0.070755-0, 3836491, 24002751.
123. Koskenniemi K, Laakso K, Koponen J, Kankainen M, Greco D, Auvinen P, Savijoki K, Nyman TA, Surakka A, Salusja¨rvi T, et al. Proteomics and transcriptomics characterization of bile stress response in probiotic Lactobacillus rhamnosus GG. Mol Cell Prot 2011, 10. 3033674, 21078892.
124. Koponen J, Laakso K, Koskenniemi K, Kankainen M, Savijoki K, Nyman TA, de Vos WM, Tynkkynen S, Kalkkinen N, Varmanen P. Effect of acid stress on protein expression and phosphorylation in Lactobacillus rhamnosus GG. J Proteomics 2012, 75:1357-1374. 10.1016/j.jprot.2011.11.009, 22119544.
125. Alca´ntara C, Zu´ñiga M. Proteomic and transcriptomic analysis of the response to bile stress of Lactobacillus casei BL23. Microbiology 2012, 158:1206-1218. 10.1099/mic.0.055657-0, 22322960.
126. Goh YJ, Klaenhammer TR. A functional glycogen biosynthesis pathway in Lactobacillus acidophilus: expression and analysis of the glg operon. Mol Microbiol 2013, 89:1187-1200. 10.1111/mmi.12338, 23879596.
127. Bron PA, Grangette C, Mercenier A, de Vos WM, Kleerebezem M. Identification of Lactobacillus plantarum genes that are induced in the gastrointestinal tract of mice. J Bacteriol 2004, 186:5721-5729. 10.1128/JB.186.17.5721-5729.2004, 516819, 15317777.
128. Troost FJ, van Baarlen P, Lindsey P, Kodde A, de Vos WM, Kleerebezem M, Brummer RJ. Identification of the transcriptional response of human intestinal mucosa to Lactobacillus plantarum WCFS1 in vivo. BMC Genomics 2008, 9:374. 10.1186/1471-2164-9-374, 2519092, 18681965.
129. van Baarlen P, Troost FJ, van Hemert S, van der Meer C, de Vos WM, de Groot PJ, Hooiveld GJEJ, Brummer RJ, Kleerebezem M. Differential NF-kappaB pathways induction by Lactobacillus plantarum in the duodenum of healthy humans correlating with immune tolerance. Proc Natl Acad Sci USA 2009, 106:2371-2376. 10.1073/pnas.0809919106, 2650163, 19190178.
130. Marco ML, Peters THF, Bongers RS, Molenaar D, Van Hemert S, Sonnenburg JL, Gordon JI, Kleerebezem M. Lifestyle of Lactobacillus plantarum in the mouse caecum. Environ Microbiol 2009, 11:2747-2757. 10.1111/j.1462-2920.2009.02001.x, 2978903, 19638173.
131. Marco ML, de Vries MC, Wels M, Molenaar D, Mangell P, Ahrne S, de Vos WM, Vaughan EE, Kleerebezem M. Convergence in probiotic Lactobacillus gut-adaptive responses in humans and mice. ISME J 2010, 4:1481-1484. 10.1038/ismej.2010.61, 20505752.
132. Revero´n I, de las Rivas B, Muñoz R, Lo´pez de Felipe F. Genome-wide transcriptomic responses of a human isolate of Lactobacillus plantarum exposed to p-coumaric acid stress. Molecular Nutrition & Food Research 2012, 56:1848-1859. 10.1002/mnfr.201200384, 23065750.
133. Bron PA, Marco M, Hoffer SM, Van Mullekom E, de Vos WM, Kleerebezem M. Genetic characterization of the bile salt response in Lactobacillus plantarum and analysis of responsive promoters in vitro and in situ in the gastrointestinal tract. J Bacteriol 2004, 186:7829-7835. 10.1128/JB.186.23.7829-7835.2004, 529069, 15547253.
134. Hamon E, Horvatovich P, Izquierdo E, Bringel F, Marchioni E, Aoude-Werner D, Ennahar S. Comparative proteomic analysis of Lactobacillus plantarum for the identification of key proteins in bile tolerance. BMC Microbiol 2011, 11:63. 10.1186/1471-2180-11-63, 3073879, 21447177.
135. van Bokhorst-van de VH, Smelt MJ, Wels M, van Hijum SAFT, de Vos P, Kleerebezem M, Bron PA. Genotypic adaptations associated with prolonged persistence of Lactobacillus plantarum in the murine digestive tract. Biotechnol J 2013, 8:895-904. 10.1002/biot.201200259, 24066356.
136. Kim JF, Jeong H, Lee JS, Choi SH, Ha M, Hur CG, Kim JS, Lee S, Park HS, Park YH, Oh TK. Complete genome sequence of Leuconostoc citreum KM20. J Bacteriol 2008, 190:3093-3094. 10.1128/JB.01862-07, 2293239, 18281406.
137. Lee K, Pi K. Effect of transient acid stress on the proteome of intestinal probiotic Lactobacillus reuteri. Biochemistry (Mosc) 2010, 75:460-465. 10.1134/S0006297910040097, 20618135.
138. Denou E, Berger B, Barretto C, Panoff JM, Arigoni F, Brussow H. Gene expression of commensal Lactobacillus johnsonii strain NCC533 during in vitro growth and in the murine gut. J Bacteriol 2007, 189:8109-8119. 10.1128/JB.00991-07, 2168692, 17827285.
139. Pendharkar S, Magopane T, Larsson PG, de Bruyn G, Gray GE, Hammarstrom L, Marcotte H. Identification and characterisation of vaginal lactobacilli from South African women. BMC Infect Dis 2013, 13:43. 10.1186/1471-2334-13-43, 3600991, 23351177.
140. Marti´nez-Peña MD, Castro-Escarpulli G, Aguilera-Arreola MG. Lactobacillus species isolated from vaginal secretions of healthy and bacterial vaginosis-intermediate Mexican women: a prospective study. BMC Infect Dis 2013, 13:189. 10.1186/1471-2334-13-189, 3655868, 23617246.
141. Zhou X, Hansmann MA, Davis CC, Suzuki H, Brown CJ, Schutte U, Pierson JD, Forney LJ. The vaginal bacterial communities of Japanese women resemble those of women in other racial groups. FEMS Immunol Med Microbiol 2010, 58:169-181. 10.1111/j.1574-695X.2009.00618.x, 2868947, 19912342.
142. Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SSK, McCulle SL, Karlebach S, Gorle R, Russell J, Tacket CO, et al. Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci USA 2011, 108(Suppl 1):4680-4687. 3063603, 20534435.
143. Zhou X, Brown CJ, Abdo Z, Davis CC, Hansmann MA, Joyce P, Foster JA, Forney LJ. Differences in the composition of vaginal microbial communities found in healthy Caucasian and black women. ISME J 2007, 1:121-133. 10.1038/ismej.2007.12, 18043622.
144. Drell T, Lillsaar T, Tummeleht L, Simm J, Aaspõllu A, Vain E, Saarma I, Salumets A, Donders GGG, Metsis M. Characterization of the vaginal micro- and mycobiome in asymptomatic reproductive-age Estonian women. PLoS One 2013, 8:e54379. 10.1371/journal.pone.0054379, 3553157, 23372716.
145. Motevaseli E, Shirzad M, Raoofian R, Hasheminasab SM, Hatami M, Dianatpour M, Modarressi MH. Differences in vaginal lactobacilli composition of Iranian healthy and bacterial vaginosis infected women: a comparative analysis of their cytotoxic effects with commercial vaginal probiotics. Iran Red Crescent Med J 2013, 15:199-206. 10.5812/ircmj.3533, 3745747, 23983998.
146. Antonio MA, Hawes SE, Hillier SL. The identification of vaginal Lactobacillus species and the demographic and microbiologic characteristics of women colonized by these species. J Infect Dis 1999, 180:1950-1956. 10.1086/315109, 10558952.
147. Shipitsyna E, Roos A, Datcu R, Halle´n A, Fredlund H, Jensen JS, Engstrand L, Unemo M. Composition of the vaginal microbiota in women of reproductive age--sensitive and specific molecular diagnosis of bacterial vaginosis is possible?. PLoS One 2013, 8:e60670. 10.1371/journal.pone.0060670, 3621988, 23585843.
148. O'Hanlon DE, Moench TR, Cone RA. Vaginal pH and microbicidal lactic acid when lactobacilli dominate the microbiota. PLoS One 2013, 8:e80074. 10.1371/journal.pone.0080074, 3819307, 24223212.
149. Vera Pingitore E, Hebert EM, Nader-Macias ME, Sesma F. Characterization of salivaricin CRL 1328, a two-peptide bacteriocin produced by Lactobacillus salivarius CRL 1328 isolated from the human vagina. Res Microbiol 2009, 160:401-408. 10.1016/j.resmic.2009.06.009, 19591924.
150. Kaewnopparat S, Dangmanee N, Kaewnopparat N, Srichana T, Chulasiri M, Settharaksa S. In vitro probiotic properties of Lactobacillus fermentum SK5 isolated from vagina of a healthy woman. Anaerobe 2013, 22:6-13.
151. Homayouni A, Bastani P, Ziyadi S, Mohammad-Alizadeh-Charandabi S, Ghalibaf M, Mortazavian AM, Mehrabany EV. Effects of probiotics on the recurrence of bacterial vaginosis: a review. J Low Genit Tract Dis 2014, 18:79-86. 10.1097/LGT.0b013e31829156ec, 24299970.
152. Mastromarino P, Vitali B, Mosca L. Bacterial vaginosis: a review on clinical trials with probiotics. New Microbiol 2013, 36:229-238.
153. Mendes-Soares H, Suzuki H, Hickey RJ, Forney LJ. Comparative functional genomics of Lactobacillus spp. reveals possible mechanisms for specialization of vaginal lactobacilli to their environment. J Bacteriol 2014, 196:1458-1470. 10.1128/JB.01439-13, 24488312.
154. Macklaim JM, Gloor GB, Anukam KC, Cribby S, Reid G. At the crossroads of vaginal health and disease, the genome sequence of Lactobacillus iners AB-1. Proc Natl Acad Sci USA 2011, 108(Suppl 1):4688-4695. 3063587, 21059957.
155. Murata K, Hoshina T, Saito M, Ohkusu K, Yamamura K, Tanoue Y, Ihara K, Hara T. Bacterial pericarditis caused by Lactobacillus iners in an infant. Diagn Microbiol Infect Dis 2012, 74:181-182. 10.1016/j.diagmicrobio.2012.06.008, 22818098.
156. Tanaka Y, Watanabe J, Mogi Y. Monitoring of the microbial communities involved in the soy sauce manufacturing process by PCR-denaturing gradient gel electrophoresis. Food Microbiol 2012, 31:100-106. 10.1016/j.fm.2012.02.005, 22475947.
157. McMillan A, Macklaim JM, Burton JP, Reid G. Adhesion of Lactobacillus iners AB-1 to human fibronectin: a key mediator for persistence in the vagina?. Reprod Sci 2013, 20:791-796. 10.1177/1933719112466306, 23202727.
158. Osset J, Bartolome´ RM, Garci´a E, Andreu A. Assessment of the capacity of Lactobacillus to inhibit the growth of uropathogens and block their adhesion to vaginal epithelial cells. J Infect Dis 2001, 183:485-491. 10.1086/318070, 11133381.
159. Saunders S, Bocking A, Challis J, Reid G. Effect of Lactobacillus challenge on Gardnerella vaginalis biofilms. Colloids Surf B Biointerfaces 2007, 55:138-142. 10.1016/j.colsurfb.2006.11.040, 17234391.
160. Rampersaud R, Planet PJ, Randis TM, Kulkarni R, Aguilar JL, Lehrer RI, Ratner AJ. Inerolysin, a cholesterol-dependent cytolysin produced by Lactobacillus iners. J Bacteriol 2011, 193:1034-1041. 10.1128/JB.00694-10, 3067590, 21169489.
161. Malik S, Petrova MI, Claes IJJ, Verhoeven TLA, Busschaert P, Vaneechoutte M, Lievens B, Lambrichts I, Siezen RJ, Balzarini J, et al. The highly autoaggregative and adhesive phenotype of the vaginal Lactobacillus plantarum strain CMPG5300 is sortase dependent. Appl Environ Microbiol 2013, 79:4576-4585. 10.1128/AEM.00926-13, 3719525, 23709503.
162. Bohbot JM, Cardot JM. Vaginal impact of the oral administration of total freeze-dried culture of LCR 35 in healthy women. Infect Dis Obstet Gynecol 2012, 2012:503648. 3373062, 22701297.
163. Parma M, Dindelli M, Caputo L, Redaelli A, Quaranta L, Candiani M. The role of vaginal Lactobacillus Rhamnosus (Normogin(R)) in preventing Bacterial Vaginosis in women with history of recurrences, undergoing surgical menopause: a prospective pilot study. Eur Rev Med Pharmacol Sci 2013, 17:1399-1403.
164. Colodner R, Edelstein H, Chazan B, Raz R. Vaginal colonization by orally administered Lactobacillus rhamnosus GG. Isr Med Assoc J 2003, 5:767-769.
165. EFSA BIOHAZ Panel (EFSAPO. Scientific Opinion on the maintenance of the list of QPS biological agents intentionally added to food and feed (2013 update). EFSA Journal 2013, 11:108.
166. Foulquie´ Moreno MR, Sarantinopoulos P, Tsakalidou E, De Vuyst L. The role and application of enterococci in food and health. Int J Food Microbiol 2006, 106:1-24. 10.1016/j.ijfoodmicro.2005.06.026, 16216368.
167. Lebreton F, Willems RJL, Gilmore MS. Enterococcus Diversity, Origins in Nature, and Gut Colonization. Enterococci: From commensals to leading causes of drug resistant infection 2014, Boston, Gilmore MS, Clewell DB, Ike Y, Shankar N.
168. Gilmore MS, Lebreton F, van Schaik W. Genomic transition of enterococci from gut commensals to leading causes of multidrug-resistant hospital infection in the antibiotic era. Curr Opin Microbiol 2013, 16:10-16. 10.1016/j.mib.2013.01.006, 3649759, 23395351.
169. Galloway-Peña J, Roh JH, Latorre M, Qin X, Murray BE. Genomic and SNP analyses demonstrate a distant separation of the hospital and community-associated clades of Enterococcus faecium. PLoS One 2012, 7:e30187. 10.1371/journal.pone.0030187, 3266884, 22291916.
170. Lukjancenko O, Ussery DW, Wassenaar TM. Comparative genomics of Bifidobacterium, Lactobacillus and related probiotic genera. Microb Ecol 2012, 63:651-673. 10.1007/s00248-011-9948-y, 3324989, 22031452.
171. Gouriet F, Million M, Henri M, Fournier PE, Raoult D. Lactobacillus rhamnosus bacteremia: an emerging clinical entity. Eur J Clin Microbiol Infect Dis 2012, 31:2469-2480. 10.1007/s10096-012-1599-5, 22544343.
172. Salminen MK, Tynkkynen S, Rautelin H, Saxelin M, Vaara M, Ruutu P, Sarna S, Valtonen V, Ja¨rvinen A. Lactobacillus bacteremia during a rapid increase in probiotic use of Lactobacillus rhamnosus GG in Finland. Clin Infect Dis 2002, 35:1155-1160. 10.1086/342912, 12410474.
173. Plumed-Ferrer C, Uusikyla K, Korhonen J, von Wright A. Characterization of Lactococcus lactis isolates from bovine mastitis. Vet Microbiol 2013, 167:592-599. 10.1016/j.vetmic.2013.09.011, 24080351.
174. Hadjisymeou S, Loizou P, Kothari P. Lactococcus lactis cremoris infection: not rare anymore?. BMJ Case Rep 2013, 2013.
175. Inoue M, Saito A, Kon H, Uchida H, Koyama S, Haryu S, Sasaki T, Nishijima M. Subdural empyema due to Lactococcus lactis cremoris: case report. Neurol Med Chir (Tokyo) 2014, 54:341-317. 10.2176/nmc.cr2012-0440, 24257498.
176. Santer M. Joseph Lister: first use of a bacterium as a 'model organism' to illustrate the cause of infectious disease of humans. Notes Rec R Soc Lond 2010, 64:59-65. 10.1098/rsnr.2009.0029, 20503823.
177. Zwielehner J, Handschur M, Michaelsen A, Irez S, Demel M, Denner EBM, Haslberger AG. DGGE and real-time PCR analysis of lactic acid bacteria in bacterial communities of the phyllosphere of lettuce. Mol Nutr Food Res 2008, 52:614-623. 10.1002/mnfr.200700158, 18398868.
178. Braem G, De Vliegher S, Verbist B, Piessens V, Van Coillie E, De Vuyst L, Leroy F. Unraveling the microbiota of teat apices of clinically healthy lactating dairy cows, with special emphasis on coagulase-negative staphylococci. J Dairy Sci 2013, 96:1499-1510. 10.3168/jds.2012-5493, 23313004.
179. Bayjanov JR, Starrenburg MJC, van der Sijde MR, Siezen RJ, van Hijum SAFT. Genotype-phenotype matching analysis of 38 Lactococcus lactis strains using random forest methods. BMC Microbiol 2013, 13:68. 10.1186/1471-2180-13-68, 3637802, 23530958.
180. McCutcheon JP, Moran NA. Extreme genome reduction in symbiotic bacteria. Nat Rev Micro 2012, 10:13-26.
181. Bolotin A, Quinquis B, Renault P, Sorokin A, Ehrlich SD, Kulakauskas S, Lapidus A, Goltsman E, Mazur M, Pusch GD, et al. Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus. Nat Biotechnol 2004, 22:1554-1558. 10.1038/nbt1034, 15543133.
182. Pittet V, Abegunde T, Marfleet T, Haakensen M, Morrow K, Jayaprakash T, Schroeder K, Trost B, Byrns S, Bergsveinson J, et al. Complete genome sequence of the beer spoilage organism Pediococcus claussenii ATCC BAA-344T. J Bacteriol 2012, 194:1271-1272. 10.1128/JB.06759-11, 3294761, 22328764.
183. Broadbent JR, Neeno-Eckwall EC, Stahl B, Tandee K, Cai H, Morovic W, Horvath P, Heidenreich J, Perna NT, Barrangou R, Steele JL. Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation. BMC Genomics 2012, 13:533. 10.1186/1471-2164-13-533, 3496567, 23035691.
184. Nicolas P, Bessieres P, Ehrlich SD, Maguin E, van de Guchte M. Extensive horizontal transfer of core genome genes between two Lactobacillus species found in the gastrointestinal tract. BMC Evol Biol 2007, 7:141. 10.1186/1471-2148-7-141, 1994166, 17708761.
185. Cai H, Thompson R, Budinich MF, Broadbent JR, Steele JL. Genome sequence and comparative genome analysis of Lactobacillus casei: insights into their niche-associated evolution. Genome Biol Evol 2009, 1:239-257. 2817414, 20333194.
186. Douillard FP, Kant R, Ritari J, Paulin L, Palva A, de Vos WM. Comparative genome analysis of Lactobacillus casei strains isolated from Actimel and Yakult products reveals marked similarities and points to a common origin. Microb Biotechnol 2013, 6:576-587. 10.1111/1751-7915.12062, 3918159, 23815335.
187. Linares DM, Geertsma ER, Poolman B. Evolved Lactococcus lactis strains for enhanced expression of recombinant membrane proteins. J Mol Biol 2010, 401:45-55. 10.1016/j.jmb.2010.06.002, 20542040.
188. Bachmann H, Starrenburg MJ, Molenaar D, Kleerebezem M, van Hylckama Vlieg JET. Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution. Genome Res 2012, 22:115-124. 10.1101/gr.121285.111, 3246198, 22080491.
189. Bachmann H, Fischlechner M, Rabbers I, Barfa N, Branco dos Santos F, Molenaar D, Teusink B. Availability of public goods shapes the evolution of competing metabolic strategies. Proc Natl Acad Sci USA 2013, 110:14302-14307. 10.1073/pnas.1308523110, 3761572, 23940318.
190. Kleerebezem M, Hols P, Bernard E, Rolain T, Zhou M, Siezen RJ, Bron PA. The extracellular biology of the lactobacilli. FEMS Microbiol Rev 2010, 34:199-230. 10.1111/j.1574-6976.2009.00208.x, 20088967.
191. Brown J, de Vos WM, DiStefano PS, Dore J, Huttenhower C, Knight R, Lawley TD, Raes J, Turnbaugh P. Translating the human microbiome. Nat Biotechnol 2013, 31:304-308. 10.1038/nbt.2543, 23563424.
192. Kuipers OP, Beerthuyzen MM, de Ruyter PG, Luesink EJ, de Vos WM. Autoregulation of nisin biosynthesis in Lactococcus lactis by signal transduction. J Biol Chem 1995, 270:27299-27304. 10.1074/jbc.270.45.27299, 7592991.
193. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P. CRISPR provides acquired resistance against viruses in prokaryotes. Science 2007, 315:1709-1712. 10.1126/science.1138140, 17379808.
194. Desguin B, Goffin P, Viaene E, Kleerebezem M, Martin-Diaconescu V, Maroney MJ, Declercq J-P, Soumillion P, Hols P. Lactate racemase is a nickel-dependent enzyme activated by a widespread maturation system. Nat Commun 2014, 5.
195. Kant R, Paulin L, Alatalo E, de Vos WM, Palva A. Genome sequence of Lactobacillus amylovorus GRL1112. J Bacteriol 2011, 193:789-790. 10.1128/JB.01365-10, 3021218, 21131492.
196. Maze´ A, Boe¨l G, Zu´ñiga M, Bourand A, Loux V, Yebra MJ, Monedero V, Correia K, Jacques N, Beaufils S, et al. Complete genome sequence of the probiotic Lactobacillus casei strain BL23. J Bacteriol 2010, 192:2647-2648. 10.1128/JB.00076-10, 2863562, 20348264.
197. Morita H, Toh H, Fukuda S, Horikawa H, Oshima K, Suzuki T, Murakami M, Hisamatsu S, Kato Y, Takizawa T, et al. Comparative genome analysis of Lactobacillus reuteri and Lactobacillus fermentum reveal a genomic island for reuterin and cobalamin production. DNA Res 2008, 15:151-161. 10.1093/dnares/dsn009, 2650639, 18487258.
198. Pridmore RD, Berger B, Desiere F, Vilanova D, Barretto C, Pittet AC, Zwahlen MC, Rouvet M, Altermann E, Barrangou R, et al. The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533. Proc Natl Acad Sci USA 2004, 101:2512-2517. 10.1073/pnas.0307327101, 356981, 14983040.
199. Wang Y, Wang J, Ahmed Z, Bai X, Wang J. Complete genome sequence of Lactobacillus kefiranofaciens ZW3. J Bacteriol 2011, 193:4280-4281. 10.1128/JB.05306-11, 3147695, 21705607.
200. Wang S, Zhu H, He F, Luo Y, Kang Z, Lu C, Feng L, Lu X, Xue Y, Wang H. Whole genome sequence of the probiotic strain Lactobacillus paracasei N1115, isolated from traditional chinese fermented milk. Genome Announc 2014, 2. 3953185, 24625864.
201. Siezen RJ, Francke C, Renckens B, Boekhorst J, Wels M, Kleerebezem M, van Hijum SAFT. Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome. J Bacteriol 2012, 194:195-196. 10.1128/JB.06275-11, 3256602, 22156394.
202. Chaillou S, Champomier-Verge`s MC, Cornet M, Crutz-Le Coq AM, Dudez AM, Martin V, Beaufils S, Darbon-Rongere E, Bossy R, Loux V, Zagorec M. The complete genome sequence of the meat-borne lactic acid bacterium Lactobacillus sakei 23K. Nat Biotechnol 2005, 23:1527-1533. 10.1038/nbt1160, 16273110.
203. Wegmann U, O'Connell-Motherway M, Zomer A, Buist G, Shearman C, Canchaya C, Ventura M, Goesmann A, Gasson MJ, Kuipers OP, et al. Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363. J Bacteriol 2007, 189:3256-3270. 10.1128/JB.01768-06, 1855848, 17307855.
204. Paulsen IT, Banerjei L, Myers GS, Nelson KE, Seshadri R, Read TD, Fouts DE, Eisen JA, Gill SR, Heidelberg JF, et al. Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science 2003, 299:2071-2074. 10.1126/science.1080613, 12663927.
205. Qin X, Galloway-Peña JR, Sillanpaa J, Roh JH, Nallapareddy SR, Chowdhury S, Bourgogne A, Choudhury T, Muzny DM, Buhay CJ, et al. Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes. BMC Microbiol 2012, 12:135. 10.1186/1471-2180-12-135, 3433357, 22769602.
206. Jung JY, Lee SH, Jeon CO. Complete genome sequence of Leuconostoc gelidum strain JB7, isolated from kimchi. J Bacteriol 2012, 194:6665. 10.1128/JB.01806-12, 3497507, 23144409.
207. Jung JY, Lee SH, Jeon CO. Complete genome sequence of Leuconostoc carnosum strain JB16, isolated from kimchi. J Bacteriol 2012, 194:6672-6673. 10.1128/JB.01805-12, 3497485, 23144413.
208. Oh HM, Cho YJ, Kim BK, Roe JH, Kang SO, Nahm BH, Jeong G, Han HU, Chun J. Complete genome sequence analysis of Leuconostoc kimchii IMSNU 11154. J Bacteriol 2010, 192:3844-3845. 10.1128/JB.00508-10, 2897357, 20494991.
209. Johansson P, Paulin L, Sa¨de E, Salovuori N, Alatalo ER, Bjo¨rkroth KJ, Auvinen P. Genome sequence of a food spoilage lactic acid bacterium, Leuconostoc gasicomitatum LMG 18811T, in association with specific spoilage reactions. Appl Environ Microbiol 2011, 77:4344-4351. 10.1128/AEM.00102-11, 3127722, 21571876.
210. Dereeper A, Audic S, Claverie JM, Blanc G. BLAST-EXPLORER helps you building datasets for phylogenetic analysis. BMC Evol Biol 2010, 10:8. 10.1186/1471-2148-10-8, 2821324, 20067610.
211. Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, et al. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 2008, 36:W465-469. 10.1093/nar/gkn180, 2447785, 18424797.
212. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797. 10.1093/nar/gkh340, 390337, 15034147.
213. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000, 17:540-552. 10.1093/oxfordjournals.molbev.a026334, 10742046.
214. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003, 52:696-704. 10.1080/10635150390235520, 14530136.
215. Anisimova M, Gascuel O. Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst Biol 2006, 55:539-552. 10.1080/10635150600755453, 16785212.
216. Chevenet F, Brun C, Bañuls AL, Jacq B, Christen R. TreeDyn: towards dynamic graphics and annotations for analyses of trees. BMC Bioinformatics 2006, 7:439. 10.1186/1471-2105-7-439, 1615880, 17032440.
217. Charif D, Lobry J. SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. Structural Approaches to Sequence Evolution 2007, 207-232. Springer Berlin Heidelberg, Bastolla U, Porto M, Roman HE, Vendruscolo M, Biological and Medical Physics, Biomedical Engineering.
218. Pages H, Aboyoun P, Gentleman R, DebRoy S. Biostrings: String objects representing biological sequences, and matching algorithms. 2013, R package version 2.28.0. edition.
219. Stuben C. genomes: Genome sequencing project metadata. 2013, R package version 2.6.0. edition.
220. Bik EM, Eckburg PB, Gill SR, Nelson KE, Purdom EA, Francois F, Perez-Perez G, Blaser MJ, Relman DA. Molecular analysis of the bacterial microbiota in the human stomach. Proc Natl Acad Sci USA 2006, 103:732-737. 10.1073/pnas.0506655103, 1334644, 16407106.
221. Booijink CCGM, Zoetendal EG, Kleerebezem M, de Vos WM. Microbial communities in the human small intestine: coupling diversity to metagenomics. Future Microbiol 2007, 2:285-295. 10.2217/17460913.2.3.285, 17661703.