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Chapter 2 : The Genomic Basis of Lactobacilli as Health-Promoting Organisms

Authors: Elisa Salvetti1, Paul W. O’Toole2
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Affiliations: 1: School of Microbiology and APC Microbiome Institute, University College Cork, Ireland; 2: School of Microbiology and APC Microbiome Institute, University College Cork, Ireland
Content Type: Monograph
Publication Year: 2018

Category: Clinical Microbiology; General Interest

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Abstract:

The genus includes 177 species (http://www.bacterio.net/lactobacillus.html): they are non-spore-forming, mostly nonmotile, and rod-shaped (although coccobacilli are observed). They generally have a fermentative metabolism (although genome sequence analysis has provided evidence of potential for respiration [ ]) with lactic acid as the main fermentation product.

Citation: Salvetti E, O’Toole P. 2018. The Genomic Basis of Lactobacilli as Health-Promoting Organisms, p 49-71. In Britton R, Cani P (ed), Bugs as Drugs. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.BAD-0011-2016
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The Genomic Basis of Lactobacilli as Health-Promoting Organisms
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Citation: Salvetti E, O’Toole P. 2018. The Genomic Basis of Lactobacilli as Health-Promoting Organisms, p 49-71. In Britton R, Cani P (ed), Bugs as Drugs. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.BAD-0011-2016
/content/10.1128/9781555819705.chap2.fig2-1
Figure 1

Publication numbers by year using search terms (lactobacillus probiotic) in PubMed. Search performed 13 July 2016.

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10.1128/9781555819705/fig2-1.gif
Image of Figure 1
Figure 1

Publication numbers by year using search terms (lactobacillus probiotic) in PubMed. Search performed 13 July 2016.

Citation: Salvetti E, O’Toole P. 2018. The Genomic Basis of Lactobacilli as Health-Promoting Organisms, p 49-71. In Britton R, Cani P (ed), Bugs as Drugs. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.BAD-0011-2016
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References

/content/book/10.1128/9781555819705.chap2
1. Brooijmans RJ,, de Vos WM,, Hugenholtz J . 2009. Lactobacillus plantarum WCFS1 electron transport chains. Appl Environ Microbiol 75 : 3580– 3585.[CrossRef] [PubMed]
2. Salvetti E,, Torriani S,, Felis GE . 2012. The genus Lactobacillus: a taxonomic update. Probiotics Antimicrob Proteins 4 : 217– 226.[CrossRef]
3. EFSA Panel on Biological Hazards . 2015. Statement on the update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA. 2: suitability of taxonomic units notified to EFSA until March 2015. EFSA J 13 : 4138.[CrossRef]
4. Bourdichon F,, Casaregola S,, Farrokh C,, Frisvad JC,, Gerds ML,, Hammes WP,, Harnett J,, Huys G,, Laulund S,, Ouwehand A,, Powell IB,, Prajapati JB,, Seto Y,, Ter Schure E,, Van Boven A,, Vankerckhoven V,, Zgoda A,, Tuijtelaars S,, Hansen EB . 2012. Food fermentations: microorganisms with technological beneficial use. Int J Food Microbiol 154 : 87– 97. (Erratum, 156:301.)[CrossRef]
5. Lebeer S,, Vanderleyden J,, De Keersmaecker SC . 2008. Genes and molecules of lactobacilli supporting probiotic action. Microbiol Mol Biol Rev 72 : 728– 764.[CrossRef]
6. Papadimitriou K,, Zoumpopoulou G,, Foligné B,, Alexandraki V,, Kazou M,, Pot B,, Tsakalidou E . 2015. Discovering probiotic microorganisms: in vitro, in vivo, genetic and omics approaches. Front Microbiol 6 : 58.[CrossRef] [PubMed]
7. Hill C,, Guarner F,, Reid G,, Gibson GR,, Merenstein DJ,, Pot B,, Morelli L,, Canani RB,, Flint HJ,, Salminen S,, Calder PC,, Sanders ME . 2014. Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol 11 : 506– 514.[CrossRef]
8. Hemarajata P,, Versalovic J . 2013. Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation. Therap Adv Gastroenterol 6 : 39– 51.[CrossRef]
9. EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA) . 2010. Scientific opinion on the substantiation of health claims related to Lactobacillus plantarum 299 (DSM 6595, 67B) (ID 1078) and decreasing potentially pathogenic intestinal microorganisms pursuant to Article 13(1) of Regulation (EC) No 1924/20061. EFSA J 8 : 1726.[CrossRef]
10. EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA) . 2011. Scientific opinion on the substantiation of health claims related to various foods/food constituents and “immune function/immune system” (ID 573, 586, 1374, 1566, 1628, 1778, 1793, 1817, 1829, 1939, 2155, 2485, 2486, 2859, 3521, 3774, 3896), “contribution to body defences against external agents” (ID 3635), stimulation of immunological responses (ID 1479, 2064, 2075, 3139), reduction of inflammation (ID 546, 547, 641, 2505, 2862), increase in renal water elimination (ID 2505), treatment of diseases (ID 500), and increasing numbers of gastrointestinal microorganisms (ID 762, 764, 884) pursuant to Article 13(1) of Regulation (EC) No 1924/20061. EFSA J 9 : 2061.[CrossRef]
11. EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA) . 2012. Scientific opinion on the substantiation of health claims related to Lactobacillus paracasei LPC 01 (CNCM I-1390) and treatment of disease (ID 3055, further assessment) pursuant to Article 13(1) of Regulation (EC) No 1924/20061. EFSA J 10 : 2850.[CrossRef]
12. Sun Z,, Harris HM,, McCann A,, Guo C,, Argimón S,, Zhang W,, Yang X,, Jeffery IB,, Cooney JC,, Kagawa TF,, Liu W,, Song Y,, Salvetti E,, Wrobel A,, Rasinkangas P,, Parkhill J,, Rea MC,, O’Sullivan O,, Ritari J,, Douillard FP,, Paul Ross R,, Yang R,, Briner AE,, Felis GE,, de Vos WM,, Barrangou R,, Klaenhammer TR,, Caufield PW,, Cui Y,, Zhang H,, O’Toole PW . 2015. Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera. Nat Commun 6 : 8322.[CrossRef]
13. Zheng J,, Ruan L,, Sun M,, Gänzle M . 2015. A genomic view of lactobacilli and pediococci demonstrates that phylogeny matches ecology and physiology. Appl Environ Microbiol 81 : 7233– 7243.[CrossRef]
14. Kant R,, Blom J,, Palva A,, Siezen RJ,, de Vos WM . 2011. Comparative genomics of Lactobacillus . Microb Biotechnol 4 : 323– 332.[CrossRef]
15. Morita H,, Toh H,, Fukuda S,, Horikawa H,, Oshima K,, Suzuki T,, Murakami M,, Hisamatsu S,, Kato Y,, Takizawa T,, Fukuoka H,, Yoshimura T,, Itoh K,, O’Sullivan DJ,, McKay LL,, Ohno H,, Kikuchi J,, Masaoka T,, Hattori M . 2008. Comparative genome analysis of Lactobacillus reuteri and Lactobacillus fermentum reveal a genomic island for reuterin and cobalamin production. DNA Res 15 : 151– 161.[CrossRef]
16. Santos F,, Vera JL,, van der Heijden R,, Valdez G,, de Vos WM,, Sesma F,, Hugenholtz J . 2008. The complete coenzyme B12 biosynthesis gene cluster of Lactobacillus reuteri CRL1098. Microbiology 154 : 81– 93.[CrossRef]
17. Lee IC,, Tomita S,, Kleerebezem M,, Bron PA . 2013. The quest for probiotic effector molecules–unraveling strain specificity at the molecular level. Pharmacol Res 69 : 61– 74.[CrossRef]
18. Pokusaeva K,, Fitzgerald GF,, van Sinderen D . 2011. Carbohydrate metabolism in Bifidobacteria. Genes Nutr 6 : 285– 306.[CrossRef]
19. Xu J,, Bjursell MK,, Himrod J,, Deng S,, Carmichael LK,, Chiang HC,, Hooper LV,, Gordon JI . 2003. A genomic view of the human- Bacteroides thetaiotaomicron symbiosis. Science 299 : 2074– 2076.[CrossRef]
20. Kleerebezem M,, Boekhorst J,, van Kranenburg R,, Molenaar D,, Kuipers OP,, Leer R,, Tarchini R,, Peters SA,, Sandbrink HM,, Fiers MW,, Stiekema W,, Lankhorst RM,, Bron PA,, Hoffer SM,, Groot MN,, Kerkhoven R,, de Vries M,, Ursing B,, de Vos WM,, Siezen RJ . 2003. Complete genome sequence of Lactobacillus plantarum WCFS1. Proc Natl Acad Sci USA 100 : 1990– 1995.[CrossRef]
21. Ruas-Madiedo P,, Gueimonde M,, Fernández-García M,, de los Reyes-Gavilán CG,, Margolles A . 2008. Mucin degradation by Bifidobacterium strains isolated from the human intestinal microbiota. Appl Environ Microbiol 74 : 1936– 1940.[CrossRef]
22. Berg J-O,, Lindqvist L,, Nord CE . 1980. Purification of glycoside hydrolases from Bacteroides fragilis . Appl Environ Microbiol 40 : 40– 47.[PubMed]
23. van Passel MW,, Kant R,, Zoetendal EG,, Plugge CM,, Derrien M,, Malfatti SA,, Chain PS,, Woyke T,, Palva A,, de Vos WM,, Smidt H . 2011. The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes. PLoS One 6 : e16876.[CrossRef]
24. Tailford LE,, Crost EH,, Kavanaugh D,, Juge N . 2015. Mucin glycan foraging in the human gut microbiome. Front Genet 6 : 81.[CrossRef]
25. Fanning S,, Hall LJ,, Cronin M,, Zomer A,, MacSharry J,, Goulding D,, Motherway MO,, Shanahan F,, Nally K,, Dougan G,, van Sinderen D . 2012. Bifidobacterial surface-exopolysaccharide facilitates commensal-host interaction through immune modulation and pathogen protection. Proc Natl Acad Sci USA 109 : 2108– 2113.[CrossRef]
26. Denou E,, Pridmore RD,, Berger B,, Panoff JM,, Arigoni F,, Brüssow H . 2008. 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 190 : 3161– 3168.[CrossRef]
27. Lee IC,, Caggianiello G,, van Swam II,, Taverne N,, Meijerink M,, Bron PA,, Spano G,, Kleerebezem M . 2016. Strain-specific features of extracellular polysaccharides and their impact on Lactobacillus plantarum-host interactions. Appl Environ Microbiol 82 : 3959– 3970.[CrossRef]
28. Raftis EJ,, Salvetti E,, Torriani S,, Felis GE,, O’Toole PW . 2011. Genomic diversity of Lactobacillus salivarius . Appl Environ Microbiol 77 : 954– 965.[CrossRef]
29. Sánchez JI,, Martínez B,, Guillén R,, Jiménez-Díaz R,, Rodríguez A . 2006. Culture conditions determine the balance between two different exopolysaccharides produced by Lactobacillus pentosus LPS26. Appl Environ Microbiol 72 : 7495– 7502.[CrossRef]
30. Bergman M,, Del Prete G,, van Kooyk Y,, Appelmelk B . 2006. Helicobacter pylori phase variation, immune modulation and gastric autoimmunity. Nat Rev Microbiol 4 : 151– 159.[CrossRef]
31. Kleerebezem M,, Hols P,, Bernard E,, Rolain T,, Zhou M,, Siezen RJ,, Bron PA . 2010. The extracellular biology of the lactobacilli. FEMS Microbiol Rev 34 : 199– 230.[CrossRef]
32. von Schillde MA,, Hörmannsperger G,, Weiher M,, Alpert CA,, Hahne H,, Bäuerl C,, van Huynegem K,, Steidler L,, Hrncir T,, Pérez-Martínez G,, Kuster B,, Haller D . 2012. Lactocepin secreted by Lactobacillus exerts anti-inflammatory effects by selectively degrading proinflammatory chemokines. Cell Host Microbe 11 : 387– 396.[CrossRef]
33. Bäuerl C,, Pérez-Martínez G,, Yan F,, Polk DB,, Monedero V . 2010. Functional analysis of the p40 and p75 proteins from Lactobacillus casei BL23. J Mol Microbiol Biotechnol 19 : 231– 241.[CrossRef]
34. Dramsi S,, Bierne H . 2016. Spatial organization of cell wall-anchored proteins at the surface of Gram-positive bacteria. Curr Top Microbiol Immunol.[CrossRef]
35. Collins J,, van Pijkeren JP,, Svensson L,, Claesson MJ,, Sturme M,, Li Y,, Cooney JC,, van Sinderen D,, Walker AW,, Parkhill J,, Shannon O,, O’Toole PW . 2012. Fibrinogen-binding and platelet-aggregation activities of a Lactobacillus salivarius septicaemia isolate are mediated by a novel fibrinogen-binding protein. Mol Microbiol 85 : 862– 877.[CrossRef]
36. Vargas García CE,, Petrova M,, Claes IJ,, De Boeck I,, Verhoeven TL,, Dilissen E,, von Ossowski I,, Palva A,, Bullens DM,, Vanderleyden J,, Lebeer S . 2015. Piliation of Lactobacillus rhamnosus GG promotes adhesion, phagocytosis, and cytokine modulation in macrophages. Appl Environ Microbiol 81 : 2050– 2062.[CrossRef]
37. Bull M,, Plummer S,, Marchesi J,, Mahenthiralingam E . 2013. The life history of Lactobacillus acidophilus as a probiotic: a tale of revisionary taxonomy, misidentification and commercial success. FEMS Microbiol Lett 349 : 77– 87.[CrossRef]
38. Di Cerbo A,, Palmieri B,, Aponte M,, Morales-Medina JC,, Iannitti T . 2016. Mechanisms and therapeutic effectiveness of lactobacilli. J Clin Pathol 69 : 187– 203.[CrossRef]
39. Salvetti E,, Torriani S,, Felis GE, . 2015. A survey on established and novel strains for probiotic applications, p 26– 44. In Foerst P,, Santivarangkna C (ed), Advances in Probiotic Technology. CRC Press, Boca Raton, FL.[CrossRef]
40. Altermann E,, Russell WM,, Azcarate-Peril MA,, Barrangou R,, Buck BL,, McAuliffe O,, Souther N,, Dobson A,, Duong T,, Callanan M,, Lick S,, Hamrick A,, Cano R,, Klaenhammer TR . 2005. Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM. Proc Natl Acad Sci USA 102 : 3906– 3912.[CrossRef] [PubMed]
41. Bull MJ,, Jolley KA,, Bray JE,, Aerts M,, Vandamme P,, Maiden MC,, Marchesi JR,, Mahenthiralingam E . 2014. The domestication of the probiotic bacterium Lactobacillus acidophilus . Sci Rep 4 : 7202.[CrossRef]
42. Makarova K,, Slesarev A,, Wolf Y,, Sorokin A,, Mirkin B,, Koonin E,, Pavlov A,, Pavlova N,, Karamychev V,, Polouchine N,, Shakhova V,, Grigoriev I,, Lou Y,, Rohksar D,, Lucas S,, Huang K,, Goodstein DM,, Hawkins T,, Plengvidhya V,, Welker D,, Hughes J,, Goh Y,, Benson A,, Baldwin K,, Lee JH,, Díaz-Muñiz I,, Dosti B,, Smeianov V,, Wechter W,, Barabote R,, Lorca G,, Altermann E,, Barrangou R,, Ganesan B,, Xie Y,, Rawsthorne H,, Tamir D,, Parker C,, Breidt F,, Broadbent J,, Hutkins R,, O’Sullivan D,, Steele J,, Unlu G,, Saier M,, Klaenhammer T,, Richardson P,, Kozyavkin S,, Weimer B,, Mills D . 2006. Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci USA 103 : 15611– 15616.[CrossRef]
43. Boekhorst J,, Helmer Q,, Kleerebezem M,, Siezen RJ . 2006. Comparative analysis of proteins with a mucus-binding domain found exclusively in lactic acid bacteria. Microbiology 152 : 273– 280.[CrossRef]
44. Yakabe T,, Moore EL,, Yokota S,, Sui H,, Nobuta Y,, Fukao M,, Palmer H,, Yajima N . 2009. Safety assessment of Lactobacillus brevis KB290 as a probiotic strain. Food Chem Toxicol 47 : 2450– 2453.[CrossRef]
45. Murakami K,, Habukawa C,, Nobuta Y,, Moriguchi N,, Takemura T . 2012. The effect of Lactobacillus brevis KB290 against irritable bowel syndrome: a placebo-controlled double-blind crossover trial. Biopsychosoc Med 6 : 16.[CrossRef]
46. Fukao M,, Oshima K,, Morita H,, Toh H,, Suda W,, Kim SW,, Suzuki S,, Yakabe T,, Hattori M,, Yajima N . 2013. Genomic analysis by deep sequencing of the probiotic Lactobacillus brevis KB290 harboring nine plasmids reveals genomic stability. PLoS One 8 : e60521.[CrossRef]
47. Bao Q,, Song Y,, Xu H,, Yu J,, Zhang W,, Menghe B,, Zhang H,, Sun Z . 2016. Multilocus sequence typing of Lactobacillus casei isolates from naturally fermented foods in China and Mongolia. J Dairy Sci 99 : 5202– 5213.[CrossRef]
48. Broadbent JR,, Neeno-Eckwall EC,, Stahl B,, Tandee K,, Cai H,, Morovic W,, Horvath P,, Heidenreich J,, Perna NT,, Barrangou R,, Steele JL . 2012. Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation. BMC Genomics 13 : 533.[CrossRef]
49. Cai H,, Rodríguez BT,, Zhang W,, Broadbent JR,, Steele JL . 2007. Genotypic and phenotypic characterization of Lactobacillus casei strains isolated from different ecological niches suggests frequent recombination and niche specificity. Microbiology 153 : 2655– 2665.[CrossRef]
50. Cai H,, Thompson R,, Budinich MF,, Broadbent JR,, Steele JL . 2009. Genome sequence and comparative genome analysis of Lactobacillus casei: insights into their niche-associated evolution. Genome Biol Evol 1 : 239– 257.[CrossRef]
51. Smokvina T,, Wels M,, Polka J,, Chervaux C,, Brisse S,, Boekhorst J,, van Hylckama Vlieg JE,, Siezen RJ . 2013. Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity. PLoS One 8 : e68731.[CrossRef] [PubMed]
52. Ravel J,, Gajer P,, Abdo Z,, Schneider GM,, Koenig SS,, McCulle SL,, Karlebach S,, Gorle R,, Russell J,, Tacket CO,, Brotman RM,, Davis CC,, Ault K,, Peralta L,, Forney LJ . 2011. Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci USA 108( Suppl 1) : 4680– 4687.[CrossRef]
53. Zárate G,, Nader-Macias ME . 2006. Influence of probiotic vaginal lactobacilli on in vitro adhesion of urogenital pathogens to vaginal epithelial cells. Lett Appl Microbiol 43 : 174– 180.[CrossRef]
54. Stapleton AE,, Au-Yeung M,, Hooton TM,, Fredricks DN,, Roberts PL,, Czaja CA,, Yarova-Yarovaya Y,, Fiedler T,, Cox M,, Stamm WE . 2011. Randomized, placebo-controlled phase 2 trial of a Lactobacillus crispatus probiotic given intravaginally for prevention of recurrent urinary tract infection. Clin Infect Dis 52 : 1212– 1217.[CrossRef]
55. Ojala T,, Kankainen M,, Castro J,, Cerca N,, Edelman S,, Westerlund-Wikström B,, Paulin L,, Holm L,, Auvinen P . 2014. Comparative genomics of Lactobacillus crispatus suggests novel mechanisms for the competitive exclusion of Gardnerella vaginalis . BMC Genomics 15 : 1070.[CrossRef]
56. Rajan N,, Cao Q,, Anderson BE,, Pruden DL,, Sensibar J,, Duncan JL,, Schaeffer AJ . 1999. Roles of glycoproteins and oligosaccharides found in human vaginal fluid in bacterial adherence. Infect Immun 67 : 5027– 5032.[PubMed]
57. El Kafsi H,, Binesse J,, Loux V,, Buratti J,, Boudebbouze S,, Dervyn R,, Kennedy S,, Galleron N,, Quinquis B,, Batto JM,, Moumen B,, Maguin E,, van de Guchte M . 2014. Lactobacillus delbrueckii ssp. lactis and ssp. bulgaricus: a chronicle of evolution in action. BMC Genomics 15 : 407.[CrossRef] [PubMed]
58. van de Guchte M,, Penaud S,, Grimaldi C,, Barbe V,, Bryson K,, Nicolas P,, Robert C,, Oztas S,, Mangenot S,, Couloux A,, Loux V,, Dervyn R,, Bossy R,, Bolotin A,, Batto JM,, Walunas T,, Gibrat JF,, Bessières P,, Weissenbach J,, Ehrlich SD,, Maguin E . 2006. The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution. Proc Natl Acad Sci USA 103 : 9274– 9279.[CrossRef]
59. Hao P,, Zheng H,, Yu Y,, Ding G,, Gu W,, Chen S,, Yu Z,, Ren S,, Oda M,, Konno T,, Wang S,, Li X,, Ji ZS,, Zhao G . 2011. Complete sequencing and pan-genomic analysis of Lactobacillus delbrueckii subsp. bulgaricus reveal its genetic basis for industrial yogurt production. PLoS One 6 : e15964.[CrossRef]
60. Mañé J,, Lorén V,, Pedrosa E,, Ojanguren I,, Xaus J,, Cabré E,, Domènech E,, Gassull MA . 2009. Lactobacillus fermentum CECT 5716 prevents and reverts intestinal damage on TNBS-induced colitis in mice. Inflamm Bowel Dis 15 : 1155– 1163.[CrossRef]
61. Olivares M,, Díaz-Ropero MP,, Sierra S,, Lara-Villoslada F,, Fonollá J,, Navas M,, Rodríguez JM,, Xaus J . 2007. Oral intake of Lactobacillus fermentum CECT5716 enhances the effects of influenza vaccination. Nutrition 23 : 254– 260.[CrossRef]
62. Mikelsaar M,, Zilmer M . 2009. Lactobacillus fermentum ME - 3-an antimicrobial and antioxidative probiotic. Microb Ecol Health Dis 21 : 1– 27.[CrossRef]
63. Archer AC,, Halami PM . 2015. Probiotic attributes of Lactobacillus fermentum isolated from human feces and dairy products. Appl Microbiol Biotechnol 99 : 8113– 8123.[CrossRef]
64. Jiménez E,, Langa S,, Martín V,, Arroyo R,, Martín R,, Fernández L,, Rodríguez JM . 2010. Complete genome sequence of Lactobacillus fermentum CECT 5716, a probiotic strain isolated from human milk. J Bacteriol 192 : 4800.[CrossRef]
65. Sun Z,, Zhang W,, Bilige M,, Zhang H . 2015. Complete genome sequence of the probiotic Lactobacillus fermentum F-6 isolated from raw milk. J Biotechnol 194 : 110– 111.[CrossRef]
66. Dan T,, Liu W,, Song Y,, Xu H,, Menghe B,, Zhang H,, Sun Z . 2015. The evolution and population structure of Lactobacillus fermentum from different naturally fermented products as determined by multilocus sequence typing (MLST). BMC Microbiol 15 : 107. (Erratum, 2016.)[CrossRef]
67. Azcarate-Peril MA,, Altermann E,, Goh YJ,, Tallon R,, Sanozky-Dawes RB,, Pfeiler EA,, O’Flaherty S,, Buck BL,, Dobson A,, Duong T,, Miller MJ,, Barrangou R,, Klaenhammer TR . 2008. Analysis of the genome sequence of Lactobacillus gasseri ATCC 33323 reveals the molecular basis of an autochthonous intestinal organism. Appl Environ Microbiol 74 : 4610– 4625.[CrossRef]
68. Mendes-Soares H,, Suzuki H,, Hickey RJ,, Forney LJ . 2014. Comparative functional genomics of Lactobacillus spp. reveals possible mechanisms for specialization of vaginal lactobacilli to their environment. J Bacteriol 196 : 1458– 1470.[CrossRef]
69. Pridmore RD,, Berger B,, Desiere F,, Vilanova D,, Barretto C,, Pittet AC,, Zwahlen MC,, Rouvet M,, Altermann E,, Barrangou R,, Mollet B,, Mercenier A,, Klaenhammer T,, Arigoni F,, Schell MA . 2004. The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533. Proc Natl Acad Sci USA 101 : 2512– 2517.[CrossRef]
70. Buhnik-Rosenblau K,, Matsko-Efimov V,, Jung M,, Shin H,, Danin-Poleg Y,, Kashi Y . 2012. Indication for co-evolution of Lactobacillus johnsonii with its hosts. BMC Microbiol 12 : 149.[CrossRef]
71. Liu CJ,, Wang R,, Gong FM,, Liu XF,, Zheng HJ,, Luo YY,, Li XR . 2015. Complete genome sequences and comparative genome analysis of Lactobacillus plantarum strain 5-2 isolated from fermented soybean. Genomics 106 : 404– 411.[CrossRef]
72. van den Nieuwboer M,, van Hemert S,, Claassen E,, de Vos WM . 2016. Lactobacillus plantarum WCFS1 and its host interaction: a dozen years after the genome. Microb Biotechnol 9 : 452– 465.[CrossRef]
73. Siezen RJ,, van Hylckama Vlieg JET . 2011. Genomic diversity and versatility of Lactobacillus plantarum, a natural metabolic engineer. Microb Cell Fact 10( Suppl 1) : S3.[CrossRef]
74. Martino ME,, Bayjanov JR,, Caffrey BE,, Wels M,, Joncour P,, Hughes S,, Gillet B,, Kleerebezem M,, van Hijum SA,, Leulier F . 2016. Nomadic lifestyle of Lactobacillus plantarum revealed by comparative genomics of 54 strains isolated from different habitats. Environ Microbiol 18 : 4974– 4989.[CrossRef]
75. Oh PL,, Benson AK,, Peterson DA,, Patil PB,, Moriyama EN,, Roos S,, Walter J . 2010. Diversification of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution. ISME J 4 : 377– 387.[CrossRef]
76. Frese SA,, Mackenzie DA,, Peterson DA,, Schmaltz R,, Fangman T,, Zhou Y,, Zhang C,, Benson AK,, Cody LA,, Mulholland F,, Juge N,, Walter J . 2013. Molecular characterization of host-specific biofilm formation in a vertebrate gut symbiont. PLoS Genet 9 : e1004057.[CrossRef]
77. Spinler JK,, Sontakke A,, Hollister EB,, Venable SF,, Oh PL,, Balderas MA,, Saulnier DM,, Mistretta TA,, Devaraj S,, Walter J,, Versalovic J,, Highlander SK . 2014. From prediction to function using evolutionary genomics: human-specific ecotypes of Lactobacillus reuteri have diverse probiotic functions. Genome Biol Evol 6 : 1772– 1789.[CrossRef]
78. Douillard FP,, Ribbera A,, Xiao K,, Ritari J,, Rasinkangas P,, Paulin L,, Palva A,, Hao Y,, de Vos WM . 2016. Polymorphisms, chromosomal rearrangements, and mutator phenotype development during experimental evolution of Lactobacillus rhamnosus GG. Appl Environ Microbiol 82 : 3783– 3792.[CrossRef]
79. Kankainen M,, Paulin L,, Tynkkynen S,, von Ossowski I,, Reunanen J,, Partanen P,, Satokari R,, Vesterlund S,, Hendrickx AP,, Lebeer S,, De Keersmaecker SC,, Vanderleyden J,, Hämäläinen T,, Laukkanen S,, Salovuori N,, Ritari J,, Alatalo E,, Korpela R,, Mattila-Sandholm T,, Lassig A,, Hatakka K,, Kinnunen KT,, Karjalainen H,, Saxelin M,, Laakso K,, Surakka A,, Palva A,, Salusjärvi T,, Auvinen P,, de Vos WM . 2009. Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein. Proc Natl Acad Sci USA 106 : 17193– 17198.[CrossRef]
80. Douillard FP,, Ribbera A,, Kant R,, Pietilä TE,, Järvinen HM,, Messing M,, Randazzo CL,, Paulin L,, Laine P,, Ritari J,, Caggia C,, Lähteinen T,, Brouns SJ,, Satokari R,, von Ossowski I,, Reunanen J,, Palva A,, de Vos WM . 2013. Comparative genomic and functional analysis of 100 Lactobacillus rhamnosus strains and their comparison with strain GG. PLoS Genet 9 : e1003683.[CrossRef]
81. Douillard FP,, Ribbera A,, Järvinen HM,, Kant R,, Pietilä TE,, Randazzo C,, Paulin L,, Laine PK,, Caggia C,, von Ossowski I,, Reunanen J,, Satokari R,, Salminen S,, Palva A,, de Vos WM . 2013. Comparative genomic and functional analysis of Lactobacillus casei and Lactobacillus rhamnosus strains marketed as probiotics. Appl Environ Microbiol 79 : 1923– 1933.[CrossRef]
82. Ceapa C,, Davids M,, Ritari J,, Lambert J,, Wels M,, Douillard FP,, Smokvina T,, de Vos WM,, Knol J,, Kleerebezem M . 2016. The variable regions of Lactobacillus rhamnosus genomes reveal the dynamic evolution of metabolic and host-adaptation repertoires. Genome Biol Evol 8 : 1889– 1905.[CrossRef]
83. Nyquist OL,, McLeod A,, Brede DA,, Snipen L,, Aakra Å,, Nes IF . 2011. Comparative genomics of Lactobacillus sakei with emphasis on strains from meat. Mol Genet Genomics 285 : 297– 311.[CrossRef]
84. Chaillou S,, Champomier-Vergès MC,, Cornet M,, Crutz-Le Coq AM,, Dudez AM,, Martin V,, Beaufils S,, Darbon-Rongère E,, Bossy R,, Loux V,, Zagorec M . 2005. The complete genome sequence of the meat-borne lactic acid bacterium Lactobacillus sakei 23K. Nat Biotechnol 23 : 1527– 1533.[CrossRef]
85. McLeod A,, Nyquist OL,, Snipen L,, Naterstad K,, Axelsson L . 2008. Diversity of Lactobacillus sakei strains investigated by phenotypic and genotypic methods. Syst Appl Microbiol 31 : 393– 403.[CrossRef]
86. Neville BA,, O’Toole PW . 2010. Probiotic properties of Lactobacillus salivarius and closely related Lactobacillus species. Future Microbiol 5 : 759– 774.[CrossRef]
87. Li Y,, Raftis E,, Canchaya C,, Fitzgerald GF,, van Sinderen D,, O’Toole PW . 2006. Polyphasic analysis indicates that Lactobacillus salivarius subsp. salivarius and Lactobacillus salivarius subsp. salicinius do not merit separate subspecies status. Int J Syst Evol Microbiol 56 : 2397– 2403.[CrossRef]
88. Corr SC,, Li Y,, Riedel CU,, O’Toole PW,, Hill C,, Gahan CG . 2007. Bacteriocin production as a mechanism for the antiinfective activity of Lactobacillus salivarius UCC118. Proc Natl Acad Sci USA 104 : 7617– 7621.[CrossRef]
89. Claesson MJ,, Li Y,, Leahy S,, Canchaya C,, van Pijkeren JP,, Cerdeño-Tárraga AM,, Parkhill J,, Flynn S,, O’Sullivan GC,, Collins JK,, Higgins D,, Shanahan F,, Fitzgerald GF,, van Sinderen D,, O’Toole PW . 2006. Multireplicon genome architecture of Lactobacillus salivarius . Proc Natl Acad Sci USA 103 : 6718– 6723.[CrossRef]
90. Pot B,, Felis GE,, De Bruyne K,, Tsakalidou E,, Papadimitriou K,, Leisner J,, Vandamme P, . 2014. The genus Lactobacillus, p 249– 353. In Holzapfel WH,, Wood EJB (ed). Lactic Acid Bacteria: Biodiversity and Taxonomy. John Wiley & Sons, Hoboken, NJ.
91. van Loveren H,, Sanz Y,, Salminen S . 2012. Health claims in Europe: probiotics and prebiotics as case examples. Annu Rev Food Sci Technol 3 : 247– 261.[CrossRef] [PubMed]
92. EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA) . 2016. General scientific guidance for stakeholders on health and claim applications. EFSA J 14 : 4367.[CrossRef]
93. Bron PA,, Grangette C,, Mercenier A,, de Vos WM,, Kleerebezem M . 2004. Identification of Lactobacillus plantarum genes that are induced in the gastrointestinal tract of mice. J Bacteriol 186 : 5721– 5729.[CrossRef]
94. Fang F,, Li Y,, Bumann M,, Raftis EJ,, Casey PG,, Cooney JC,, Walsh MA,, O’Toole PW . 2009. Allelic variation of bile salt hydrolase genes in Lactobacillus salivarius does not determine bile resistance levels. J Bacteriol 191 : 5743– 5757.[CrossRef] [PubMed]
95. Voltan S,, Castagliuolo I,, Elli M,, Longo S,, Brun P,, D’Incà R,, Porzionato A,, Macchi V,, Palù G,, Sturniolo GC,, Morelli L,, Martines D . 2007. Aggregating phenotype in Lactobacillus crispatus determines intestinal colonization and TLR2 and TLR4 modulation in murine colonic mucosa. Clin Vaccine Immunol 14 : 1138– 1148.[CrossRef]
96. Nishiyama K,, Nakazato A,, Ueno S,, Seto Y,, Kakuda T,, Takai S,, Yamamoto Y,, Mukai T . 2015. Cell surface-associated aggregation-promoting factor from Lactobacillus gasseri SBT2055 facilitates host colonization and competitive exclusion of Campylobacter jejuni . Mol Microbiol 98 : 712– 726.[PubMed]
97. Vélez MP,, De Keersmaecker SC,, Vanderleyden J . 2007. Adherence factors of Lactobacillus in the human gastrointestinal tract. FEMS Microbiol Lett 276 : 140– 148.[CrossRef]
98. Yan F,, Cao H,, Cover TL,, Whitehead R,, Washington MK,, Polk DB . 2007. Soluble proteins produced by probiotic bacteria regulate intestinal epithelial cell survival and growth. Gastroenterology 132 : 562– 575.[CrossRef]
99. Seth A,, Yan F,, Polk DB,, Rao RK . 2008. Probiotics ameliorate the hydrogen peroxide-induced epithelial barrier disruption by a PKC- and MAP kinase-dependent mechanism. Am J Physiol Gastrointest Liver Physiol 294 : G1060– G1069.[CrossRef]
100. Konstantinov SR,, Smidt H,, de Vos WM,, Bruijns SC,, Singh SK,, Valence F,, Molle D,, Lortal S,, Altermann E,, Klaenhammer TR,, van Kooyk Y . 2008. S layer protein A of Lactobacillus acidophilus NCFM regulates immature dendritic cell and T cell functions. Proc Natl Acad Sci USA 105 : 19474– 19479.[CrossRef]
101. Gao C,, Major A,, Rendon D,, Lugo M,, Jackson V,, Shi Z,, Mori-Akiyama Y,, Versalovic J . 2015. Histamine H2 receptor-mediated suppression of intestinal inflammation by probiotic Lactobacillus reuteri . MBio 6 : e01358-15.[CrossRef]
102. Kristensen NB,, Bryrup T,, Allin KH,, Nielsen T,, Hansen TH,, Pedersen O . 2016. Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: a systematic review of randomized controlled trials. Genome Med 8 : 52.[CrossRef]

Tables

The Genomic Basis of Lactobacilli as Health-Promoting Organisms
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Citation: Salvetti E, O’Toole P. 2018. The Genomic Basis of Lactobacilli as Health-Promoting Organisms, p 49-71. In Britton R, Cani P (ed), Bugs as Drugs. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.BAD-0011-2016
/content/10.1128/9781555819705.chap2.tab2-1
TABLE 1

Selected examples of probiotic traits in lactobacilli

Generic image for table
TABLE 1

Selected examples of probiotic traits in lactobacilli

Citation: Salvetti E, O’Toole P. 2018. The Genomic Basis of Lactobacilli as Health-Promoting Organisms, p 49-71. In Britton R, Cani P (ed), Bugs as Drugs. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.BAD-0011-2016
/content/10.1128/9781555819705.chap2.tab2-2
TABLE 2

Species for which strains have been ascribed probiotic properties and related applications (according to references and )

Generic image for table
TABLE 2

Species for which strains have been ascribed probiotic properties and related applications (according to references and )

Citation: Salvetti E, O’Toole P. 2018. The Genomic Basis of Lactobacilli as Health-Promoting Organisms, p 49-71. In Britton R, Cani P (ed), Bugs as Drugs. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.BAD-0011-2016

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