Tannock GW: Normal microflora: an introduction to microbes inhabiting the human body. 1995, Springer
Google Scholar
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.
CAS
Google Scholar
Zoetendal EG, Rajilić-Stojanović M, de Vos WM: High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut. 2008, 57: 1605-1615.
CAS
Google Scholar
Human Microbiome Project Consortium: Structure, function and diversity of the healthy human microbiome. Nature. 2012, 486: 207-214.
Google Scholar
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T: A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010, 464: 59-65.
CAS
Google Scholar
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.
CAS
Google Scholar
Frese SA, MacKenzie DA, Peterson DA, Schmaltz R, Fangman T, Zhou Y, Zhang C, Benson AK, Cody LA, Mulholland F: Molecular characterization of host-specific biofilm formation in a vertebrate gut symbiont. PLoS Genet. 2013, 9: e1004057-
Google Scholar
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.
CAS
Google Scholar
Petschow B, Dore J, Hibberd P, Dinan T, Reid G, Blaser M, Cani PD, Degnan FH, Foster J, Gibson G: Probiotics, prebiotics, and the host microbiome: the science of translation. Ann N Y Acad Sci. 2013, 1306: 1-17.
CAS
Google Scholar
Tannock GW: A special fondness for lactobacilli. Appl Environ Microbiol. 2004, 70: 3189-3194.
CAS
Google Scholar
Douglas LM: The bacillus of long life. 1911, London: TC & EC Jack
Google Scholar
Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, et al.: Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 1995, 269: 496-512.
CAS
Google Scholar
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.
CAS
Google Scholar
Kleerebezem M, Boekhorst J, van Kranenburg R, Molenaar D, Kuipers OP, Leer R, Tarchini R, Peters SA, Sandbrink HM, Fiers MWEJ: Complete genome sequence of Lactobacillus plantarum WCFS1. Proc Natl Acad Sci USA. 2003, 100: 1990-1995.
CAS
Google Scholar
Johnson BR, Klaenhammer TR: Impact of genomics on the field of probiotic research: historical perspectives to modern paradigms. Antonie Van Leeuwenhoek. 2014
Google Scholar
de Vos WM: Systems solutions by lactic acid bacteria: from paradigms to practice. Microb Cell Fact. 2011, 10 (Suppl 1): S2-
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
Makarova K, Slesarev A, Wolf Y, Sorokin A, Mirkin B, Koonin E, Pavlov A, Pavlova N, Karamychev V, Polouchine N: Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci USA. 2006, 103: 15611-15616.
Google Scholar
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.
CAS
Google Scholar
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:
Google Scholar
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-
Google Scholar
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.
CAS
Google Scholar
Settanni L, Moschetti G: Non-starter lactic acid bacteria used to improve cheese quality and provide health benefits. Food Microbiol. 2010, 27: 691-697.
CAS
Google Scholar
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.
CAS
Google Scholar
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:
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
Loll B, Saenger W, Biesiadka J: Structure of full-length transcription regulator CcpA in the apo form. Biochim Biophys Acta. 2007, 1774: 732-736.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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-
CAS
Google Scholar
McLeod A, Snipen L, Naterstad K, Axelsson L: Global transcriptome response in Lactobacillus sakei during growth on ribose. BMC Microbiol. 2011, 11: 145-
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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-
CAS
Google Scholar
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-
CAS
Google Scholar
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-
Google Scholar
Larsen R, Kloosterman TG, Kok J, Kuipers OP: GlnR-mediated regulation of nitrogen metabolism in Lactococcus lactis. J Bacteriol. 2006, 188: 4978-4982.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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-
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
McDowell EJ, Callegari EA, Malke H, Chaussee MS: CodY-mediated regulation of Streptococcus pyogenes exoproteins. BMC Microbiol. 2012, 12: 114-
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
Cretenet M, Laroute V, Ulve V, Jeanson S, Nouaille S, Even S, Piot M, Girbal L, Le Loir Y, Loubiere P: 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.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
Aguado-Urda M, Gibello A, Blanco Mdel M, Fernández-Garayzábal JF, López-Alonso V, López-Campos GH: Global transcriptome analysis of Lactococcus garvieae strains in response to temperature. PLoS One. 2013, 8: e79692-
CAS
Google Scholar
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-
Google Scholar
Jääskeläinen E, Johansson P, Kostiainen O, Nieminen T, Schmidt G, Somervuo P, Mohsina M, Vanninen P, Auvinen P, Björkroth J: Significance of heme-based respiration in meat spoilage caused by Leuconostoc gasicomitatum. Appl Environ Microbiol. 2013, 79: 1078-1085.
Google Scholar
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.
CAS
Google Scholar
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.
Google Scholar
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.
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
Portela CAF, Smart KF, Tumanov S, Cook GM, Villas-Boas SG: The global metabolic response of Enterococcus faecalis to oxygen. J Bacteriol. 2014
Google Scholar
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.
CAS
Google Scholar
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-
CAS
Google Scholar
Kankainen M, Paulin L, Tynkkynen S, von Ossowski I, Reunanen J, Partanen P, Satokari R, Vesterlund S, Hendrickx APA, Lebeer S: Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein. Proc Natl Acad Sci USA. 2009, 106: 17193-17198.
CAS
Google Scholar
Segers ME, Lebeer S: Lactobacillus rhamnosus GG - host interactions. Microb Cell Fact. 2014,
Google Scholar
Meyrand M, Guillot A, Goin M, Furlan S, Armalyte J, Kulakauskas S, Cortes-Perez NG, Thomas G, Chat S, Pechoux C: 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.
CAS
Google Scholar
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.
CAS
Google Scholar
Walter J: Ecological role of lactobacilli in the gastrointestinal tract: implications for fundamental and biomedical research. Appl Environ Microbiol. 2008, 74: 4985-4996.
CAS
Google Scholar
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.
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
Molin G, Jeppsson B, Johansson ML, Ahrné 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.
CAS
Google Scholar
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.
CAS
Google Scholar
David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA: Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014, 505: 559-563.
CAS
Google Scholar
Douillard FP, Ribbera A, Kant R, Pietila TE, Jarvinen HM, Messing M, Randazzo CL, Paulin L, Laine P, Ritari J: Comparative genomic and functional analysis of 100 Lactobacillus rhamnosus strains and their comparison with strain GG. PLoS Genet. 2013, 9: e1003683-
CAS
Google Scholar
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-
Google Scholar
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.
Google Scholar
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.
CAS
Google Scholar
de Vos WM, Nieuwdorp M: Genomics: a gut prediction. Nature. 2013, 498: 48-49.
CAS
Google Scholar
Benítez-Páez A, Belda-Ferre P, Simón-Soro A, Mira A: Microbiota diversity and gene expression dynamics in human oral biofilms. BMC Genomics. 2014, 15: 311-
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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-
Google Scholar
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T: A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010, 464: 59-65.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
Booijink CCGM, El-Aidy S, Rajilić-Stojanović 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.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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:
Google Scholar
Selle K, Klaenhammer TR: Genomic and phenotypic evidence for probiotic influences of Lactobacillus gasseri on human health. FEMS Microbiol Rev. 2013, 37: 915-935.
CAS
Google Scholar
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.
CAS
Google Scholar
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-
CAS
Google Scholar
Cai H, Rodríguez 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.
CAS
Google Scholar
Raftis EJ, Salvetti E, Torriani S, Felis GE, O'Toole PW: Genomic diversity of Lactobacillus salivarius. Appl Environ Microbiol. 2011, 77: 954-965.
CAS
Google Scholar
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.
CAS
Google Scholar
Claesson MJ, Li Y, Leahy S, Canchaya C, van Pijkeren JP, Cerdeño-Tárraga AM, Parkhill J, Flynn S, O'Sullivan GC, Collins JK: Multireplicon genome architecture of Lactobacillus salivarius. Proc Natl Acad Sci USA. 2006, 103: 6718-6723.
CAS
Google Scholar
Naito S, Hayashidani H, Kaneko K, Ogawa M, Benno Y: Development of intestinal lactobacilli in normal piglets. J Appl Bacteriol. 1995, 79: 230-236.
CAS
Google Scholar
Molin G, Johansson ML, Ståhl M, Ahrné 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.
CAS
Google Scholar
Frese SA, Benson AK, Tannock GW, Loach DM, Kim J, Zhang M, Oh PL, Heng NCK, Patil PB, Juge N: The Evolution of host specialization in the vertebrate gut symbiont Lactobacillus reuteri. PLoS Genet. 2011, 7: e1001314-
CAS
Google Scholar
Moran NA, Plague GR: Genomic changes following host restriction in bacteria. Curr Opin Genet Dev. 2004, 14: 627-633.
CAS
Google Scholar
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-
Google Scholar
Altermann E, Russell WM, Azcarate-Peril MA, Barrangou R, Buck BL, McAuliffe O, Souther N, Dobson A, Duong T, Callanan M: Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM. Proc Natl Acad Sci USA. 2005, 102: 3906-3912.
CAS
Google Scholar
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.
CAS
Google Scholar
Douillard FP, Ribbera A, Järvinen HM, Kant R, Pietilä TE, Randazzo C, Paulin L, Laine PK, Caggia C, von Ossowski I: Comparative genomic and functional analysis of Lactobacillus casei and Lactobacillus rhamnosus strains marketed as probiotics. Appl Environ Microbiol. 2013, 79: 1923-1933.
CAS
Google Scholar
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.
CAS
Google Scholar
Call EK, Klaenhammer TR: Relevance and application of sortase and sortase-dependent proteins in lactic acid bacteria. Front Microbiol. 2013, 4: 73-
Google Scholar
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-
CAS
Google Scholar
Azcarate-Peril MA, Altermann E, Goh YJ, Tallon R, Sanozky-Dawes RB, Pfeiler EA, O'Flaherty S, Buck BL, Dobson A, Duong T: 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.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
Koskenniemi K, Laakso K, Koponen J, Kankainen M, Greco D, Auvinen P, Savijoki K, Nyman TA, Surakka A, Salusjärvi T: Proteomics and transcriptomics characterization of bile stress response in probiotic Lactobacillus rhamnosus GG. Mol Cell Prot. 2011, 10:
Google Scholar
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.
CAS
Google Scholar
Alcántara C, Zúñiga M: Proteomic and transcriptomic analysis of the response to bile stress of Lactobacillus casei BL23. Microbiology. 2012, 158: 1206-1218.
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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-
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
Reverón I, de las Rivas B, Muñoz R, López 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.
Google Scholar
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.
CAS
Google Scholar
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-
Google Scholar
van Bokhorst-van de Veen H, 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.
Google Scholar
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.
CAS
Google Scholar
Lee K, Pi K: Effect of transient acid stress on the proteome of intestinal probiotic Lactobacillus reuteri. Biochemistry (Mosc). 2010, 75: 460-465.
CAS
Google Scholar
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.
CAS
Google Scholar
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-
Google Scholar
Martínez-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-
Google Scholar
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.
CAS
Google Scholar
Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SSK, McCulle SL, Karlebach S, Gorle R, Russell J, Tacket CO: Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci USA. 2011, 108 (Suppl 1): 4680-4687.
CAS
Google Scholar
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.
CAS
Google Scholar
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-
CAS
Google Scholar
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.
Google Scholar
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.
CAS
Google Scholar
Shipitsyna E, Roos A, Datcu R, Hallén 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-
CAS
Google Scholar
O'Hanlon DE, Moench TR, Cone RA: Vaginal pH and microbicidal lactic acid when lactobacilli dominate the microbiota. PLoS One. 2013, 8: e80074-
Google Scholar
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.
Google Scholar
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.
CAS
Google Scholar
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.
Google Scholar
Mastromarino P, Vitali B, Mosca L: Bacterial vaginosis: a review on clinical trials with probiotics. New Microbiol. 2013, 36: 229-238.
Google Scholar
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.
Google Scholar
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.
CAS
Google Scholar
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.
Google Scholar
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.
CAS
Google Scholar
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.
Google Scholar
Osset J, Bartolomé RM, García 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.
CAS
Google Scholar
Saunders S, Bocking A, Challis J, Reid G: Effect of Lactobacillus challenge on Gardnerella vaginalis biofilms. Colloids Surf B Biointerfaces. 2007, 55: 138-142.
CAS
Google Scholar
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.
CAS
Google Scholar
Malik S, Petrova MI, Claes IJJ, Verhoeven TLA, Busschaert P, Vaneechoutte M, Lievens B, Lambrichts I, Siezen RJ, Balzarini J: The highly autoaggregative and adhesive phenotype of the vaginal Lactobacillus plantarum strain CMPG5300 is sortase dependent. Appl Environ Microbiol. 2013, 79: 4576-4585.
CAS
Google Scholar
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-
CAS
Google Scholar
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.
CAS
Google Scholar
Colodner R, Edelstein H, Chazan B, Raz R: Vaginal colonization by orally administered Lactobacillus rhamnosus GG. Isr Med Assoc J. 2003, 5: 767-769.
Google Scholar
EFSA BIOHAZ Panel (EFSA Panel on Biological Hazards): 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-
Google Scholar
Foulquié 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.
Google Scholar
Lebreton F, Willems RJL, Gilmore MS: Enterococcus Diversity, Origins in Nature, and Gut Colonization. Enterococci: From commensals to leading causes of drug resistant infection. Edited by: Gilmore MS, Clewell DB, Ike Y, Shankar N. 2014, Boston
Google Scholar
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.
Google Scholar
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-
Google Scholar
Lukjancenko O, Ussery DW, Wassenaar TM: Comparative genomics of Bifidobacterium, Lactobacillus and related probiotic genera. Microb Ecol. 2012, 63: 651-673.
CAS
Google Scholar
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.
CAS
Google Scholar
Salminen MK, Tynkkynen S, Rautelin H, Saxelin M, Vaara M, Ruutu P, Sarna S, Valtonen V, Järvinen A: Lactobacillus bacteremia during a rapid increase in probiotic use of Lactobacillus rhamnosus GG in Finland. Clin Infect Dis. 2002, 35: 1155-1160.
Google Scholar
Plumed-Ferrer C, Uusikyla K, Korhonen J, von Wright A: Characterization of Lactococcus lactis isolates from bovine mastitis. Vet Microbiol. 2013, 167: 592-599.
CAS
Google Scholar
Hadjisymeou S, Loizou P, Kothari P: Lactococcus lactis cremoris infection: not rare anymore?. BMJ Case Rep. 2013, 2013:
Google Scholar
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.
Google Scholar
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.
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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-
Google Scholar
McCutcheon JP, Moran NA: Extreme genome reduction in symbiotic bacteria. Nat Rev Micro. 2012, 10: 13-26.
CAS
Google Scholar
Bolotin A, Quinquis B, Renault P, Sorokin A, Ehrlich SD, Kulakauskas S, Lapidus A, Goltsman E, Mazur M, Pusch GD: Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus. Nat Biotechnol. 2004, 22: 1554-1558.
CAS
Google Scholar
Pittet V, Abegunde T, Marfleet T, Haakensen M, Morrow K, Jayaprakash T, Schroeder K, Trost B, Byrns S, Bergsveinson J: Complete genome sequence of the beer spoilage organism Pediococcus claussenii ATCC BAA-344T. J Bacteriol. 2012, 194: 1271-1272.
CAS
Google Scholar
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-
CAS
Google Scholar
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-
Google Scholar
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.
Google Scholar
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.
Google Scholar
Linares DM, Geertsma ER, Poolman B: Evolved Lactococcus lactis strains for enhanced expression of recombinant membrane proteins. J Mol Biol. 2010, 401: 45-55.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar
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:
Google Scholar
Kant R, Paulin L, Alatalo E, de Vos WM, Palva A: Genome sequence of Lactobacillus amylovorus GRL1112. J Bacteriol. 2011, 193: 789-790.
CAS
Google Scholar
Mazé A, Boël G, Zúñiga M, Bourand A, Loux V, Yebra MJ, Monedero V, Correia K, Jacques N, Beaufils S: Complete genome sequence of the probiotic Lactobacillus casei strain BL23. J Bacteriol. 2010, 192: 2647-2648.
Google Scholar
Morita H, Toh H, Fukuda S, Horikawa H, Oshima K, Suzuki T, Murakami M, Hisamatsu S, Kato Y, Takizawa T: Comparative genome analysis of Lactobacillus reuteri and Lactobacillus fermentum reveal a genomic island for reuterin and cobalamin production. DNA Res. 2008, 15: 151-161.
CAS
Google Scholar
Pridmore RD, Berger B, Desiere F, Vilanova D, Barretto C, Pittet AC, Zwahlen MC, Rouvet M, Altermann E, Barrangou R: The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533. Proc Natl Acad Sci USA. 2004, 101: 2512-2517.
CAS
Google Scholar
Wang Y, Wang J, Ahmed Z, Bai X, Wang J: Complete genome sequence of Lactobacillus kefiranofaciens ZW3. J Bacteriol. 2011, 193: 4280-4281.
CAS
Google Scholar
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:
Google Scholar
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.
CAS
Google Scholar
Chaillou S, Champomier-Vergès 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.
CAS
Google Scholar
Wegmann U, O'Connell-Motherway M, Zomer A, Buist G, Shearman C, Canchaya C, Ventura M, Goesmann A, Gasson MJ, Kuipers OP: Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363. J Bacteriol. 2007, 189: 3256-3270.
CAS
Google Scholar
Paulsen IT, Banerjei L, Myers GS, Nelson KE, Seshadri R, Read TD, Fouts DE, Eisen JA, Gill SR, Heidelberg JF: Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science. 2003, 299: 2071-2074.
CAS
Google Scholar
Qin X, Galloway-Peña JR, Sillanpaa J, Roh JH, Nallapareddy SR, Chowdhury S, Bourgogne A, Choudhury T, Muzny DM, Buhay CJ: Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes. BMC Microbiol. 2012, 12: 135-
CAS
Google Scholar
Jung JY, Lee SH, Jeon CO: Complete genome sequence of Leuconostoc gelidum strain JB7, isolated from kimchi. J Bacteriol. 2012, 194: 6665-
CAS
Google Scholar
Jung JY, Lee SH, Jeon CO: Complete genome sequence of Leuconostoc carnosum strain JB16, isolated from kimchi. J Bacteriol. 2012, 194: 6672-6673.
CAS
Google Scholar
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.
CAS
Google Scholar
Johansson P, Paulin L, Säde E, Salovuori N, Alatalo ER, Björkroth 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.
CAS
Google Scholar
Dereeper A, Audic S, Claverie JM, Blanc G: BLAST-EXPLORER helps you building datasets for phylogenetic analysis. BMC Evol Biol. 2010, 10: 8-
Google Scholar
Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M: Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 2008, 36: W465-469.
CAS
Google Scholar
Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32: 1792-1797.
CAS
Google Scholar
Castresana J: Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000, 17: 540-552.
CAS
Google Scholar
Guindon S, Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003, 52: 696-704.
Google Scholar
Anisimova M, Gascuel O: Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst Biol. 2006, 55: 539-552.
Google Scholar
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-
Google Scholar
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. Edited by: Bastolla U, Porto M, Roman HE, Vendruscolo M. 2007, 207-232. Biological and Medical Physics, Biomedical Engineering, Springer Berlin Heidelberg
Google Scholar
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
Google Scholar
Stuben C: genomes: Genome sequencing project metadata. 2013, R package version 2.6.0. edition
Google Scholar
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.
CAS
Google Scholar
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.
CAS
Google Scholar