Use of Natural Selection and Evolution to Develop New Starter Cultures for Fermented Foods

Literature Cited

1. Achigar R, Magadán AH, Tremblay DM, Pianzzola MJ, Moineau S. 2017. Phage-host interactions in Streptococcus thermophilus: genome analysis of phages isolated in Uruguay and ectopic spacer acquisition in CRISPR array. Sci. Rep. 7:43438 [Google Scholar]
2. Ahmed FE. 2003. Genetically modified probiotics in foods. Trends Biotechnol 21:491–97 [Google Scholar]
3. Bachmann H, Molenaar D, dos Santos FB, Teusink B. 2017. Experimental evolution and the adjustment of metabolic strategies in lactic acid bacteria. FEMS Microbiol. Rev. 41:Suppl. 1S201–19 [Google Scholar]
4. Bachmann H, Starrenburg MJC, Molenaar D, Kleerebezem M, van Hylckama Vlieg JET. 2012. Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution. Genome Res. 22:115–24 [Google Scholar]
5. Bassi D, Cappa F, Gazzola D, Orrù L, Cocconcelli PS. 2017. Biofilm formation on stainless steel by Streptococcus thermophilus UC8547 in milk environments is mediated by the proteinase PrtS. Appl. Environ. Microbiol. 83:e02840–16 [Google Scholar]
6. Bennedsen M, Stuer-Lauridsen B, Danielsen M, Johansen E. 2011. Screening for antimicrobial resistance genes and virulence factors via genome sequencing. Appl. Environ. Microbiol. 77:2785–87 [Google Scholar]
7. Bolotin A, Quinquis B, Renault P, Sorokin A, Ehrlich SD. et al. 2004. Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus. Nat. Biotechnol. 22:1554–58 [Google Scholar]
8. Bourdichon F, Casaregola S, Farrokh C, Frisvad JC, Gerds ML. et al. 2012. Food fermentations: microorganisms with technological beneficial use. Int. J. Food Microbiol. 154:87–97 [Google Scholar]
9. Cavanagh D, Fitzgerald GF, McAuliffe O. 2014. From field to fermentation: the origins of Lactococcus lactis and its domestication to the dairy environment. Food Microbiol 47:45–61 [Google Scholar]
10. Chen J, Shen J, Hellgren LI, Jensen PR, Solem C. 2015. Adaptation of Lactococcus lactis to high growth temperature leads to a dramatic increase in acidification rate. Sci. Rep. 5:14199 [Google Scholar]
11. Chen J, Vestergaard M, Jensen TG, Shen J, Dufva M. et al. 2017. Finding the needle in the haystack: the use of microfluidic droplet technology to identify vitamin-secreting lactic acid bacteria. mBio 8:e00526–17 [Google Scholar]
12. Dandoy D, Fremaux C, de Frahan MH, Horvath P, Boyaval P. et al. 2011. The fast milk acidifying phenotype of Streptococcus thermophilus can be acquired by natural transformation of the genomic island encoding the cell-envelope proteinase PrtS. Microb. Cell Fact. 10:Suppl. 1S21 [Google Scholar]
13. Danielsen M, Johansen E. 2009. Functional genomics of dairy micro-organisms and probiotics in the era of low-cost genome sequencing. Aust. J. Dairy Technol. 64:102–5 [Google Scholar]
14. Derkx PMF, Janzen T, Sørensen KI, Christensen JE, Stuer-Lauridsen B, Johansen E. 2014. The art of strain improvement of industrial lactic acid bacteria without the use of recombinant DNA technology. Microb. Cell Factories 13:Suppl. 1S5 [Google Scholar]
15. Deveau H, Barrangou R, Garneau JE, Labonté J, Fremaux C. et al. 2008. Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J. Bacteriol. 190:1390–400 [Google Scholar]
16. Douillard FP, Ribbera A, Xiao K, Ritari J, Rasinkangas P. et al. 2016. Polymorphisms, chromosomal rearrangements, and mutator phenotype development during experimental evolution of Lactobacillus rhamnosus GG. Appl. Environ. Microbiol. 82:3783–92 [Google Scholar]
17. EFSA BIOHAZ Panel. 2017. Statement on the update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 5: suitability of taxonomic units notified to EFSA until. September 2016 EFSA J 15:4663 [Google Scholar]
18. Eur. Parliam. Counc. 2001. Directive 2001/18/EC of the European Parliament and of the Council of 12 March 2001 on the deliberate release into the environment of genetically modified organisms and repealing Council Directive 90/220/EEC. Off. J. Eur. Communities L106:1–38 [Google Scholar]
19. Eur. Parliam. Counc. 2002. Regulation (EC) No 178/2002 of 28 January 2002 laying down the general principles and requirements of food law, establishing the European Food Safety Authority and laying down procedures in matters of food safety. Off. J. Eur. Communities L31:1–24 [Google Scholar]
20. Eur. Parliam. Counc. 2009. Directive 2009/41/EC of the European Parliament and of the Council of 6 May 2009 on the contained use of genetically modified micro-organisms. Off. J. Eur. Union L125:75–97 [Google Scholar]
21. Eur. Parliam. Counc. 2015. Regulation (EU) 2015/2283 of the European Parliament and of the Council of 25 November 2015 on novel foods, amending Regulation (EU) No 1169/2011 of the European Parliament and of the Council and repealing Regulation (EC) No 258/97 of the European Parliament and of the Council and Commission Regulation (EC) No 1852/2001. Off. J. Eur. Union L327:1–22 [Google Scholar]
22. Frantzen CA, Kot W, Pedersen TB, Ardö YM, Broadbent JR. et al. 2017. Genomic characterization of dairy associated Leuconostoc species and diversity of Leuconostocs in undefined mixed mesophilic starter cultures. Front. Microbiol. 8:132 [Google Scholar]
23. Garrigues C, Johansen E, Crittenden R. 2013. Pangenomics: an avenue to improved industrial starter cultures and probiotics. Curr. Opin. Biotechnol. 24:187–91 [Google Scholar]
24. Gibbons D. 2016. Hansen, Christian D.A. The Oxford Companion to Cheese C Donnelly 341–43 New York: Oxford Univ. Press [Google Scholar]
25. Høier E, Janzen T, Rattray F, Sørensen K, Børsting M. et al. 2010. The production, application and action of lactic cheese starter cultures. The Technology of Cheesemaking B Law, A Tamime 166–92 Oxford: Blackwell Publ. 2nd ed [Google Scholar]
26. Horinouchi T, Minamoto T, Suzuki S, Shimizu H, Furusawa C. 2014. Development of an automated culture system for laboratory evolution. J. Lab. Autom. 19:478–82 [Google Scholar]
27. Hutkins R. 2006. Microbiology and Technology of Fermented Foods Oxford, UK: Wiley-Blackwell [Google Scholar]
28. Johansen E. 2003. Challenges when transferring technology from Lactococcus laboratory strains to industrial strains. Genet. Mol. Res. 2:112–16 [Google Scholar]
29. Johansen E, Øregaard G, Sørensen K, Derkx P. 2015. Modern approaches for isolation, selection and improvement of bacterial strains for fermentation applications. Advances in Fermented Foods and Beverages: Improving Quality, Technologies and Health Benefits W Holzapfel 227–48 Cambridge, UK: Woodhead Publ [Google Scholar]
30. Ju SY, Kim JH, Lee PC. 2016. Long-term adaptive evolution of Leuconostoc mesenteroides for enhancement of lactic acid tolerance and production. Biotechnol. Biofuels 9:240 [Google Scholar]
31. Kankainen M, Paulin L, Tynkkynen S, von Ossowskic I, Reunanen J. et al. 2009. Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human mucus binding protein. PNAS 106:17193–98 [Google Scholar]
32. Kibenich A, Sørensen KI, Johansen E. 2016. Texturizing lactic acid bacteria strains. US Patent 9,453,231 B2 [Google Scholar]
33. Kuipers OP. 2015. Back to nature: a revival of natural strain improvement methodologies. Microb. Biotechnol. 8:17–18 [Google Scholar]
34. Laulund S, Wind A, Derkx PMF, Zuliani V. 2017. Regulatory and safety requirements for food cultures. Microorganisms 5:28 [Google Scholar]
35. Mahony J, Cambillau C, van Sinderen D. 2017. Host recognition by lactic acid bacterial phages. FEMS Microbiol. Rev. 41:Suppl. 1S16–26 [Google Scholar]
36. McDonnell B, Mahony J, Neve H, Hanemaaijer L, Noben J-P. et al. 2016. Identification and analysis of a novel group of bacteriophages infecting the lactic acid bacterium Streptococcus thermophilus. Appl. Environ. Microbiol. 82:5153–65 [Google Scholar]
37. Meyer M. 1909. A Treatise on Commercial Starters in Butter and Cheese Making Little Falls, NY: Chr. Hansen Lab [Google Scholar]
38. Nat. News. 2017. Gene editing in legal limbo in Europe. Nature 542:392 [Google Scholar]
39. Oh J-H, van Pijkeren J-P. 2014. CRISPR-Cas9-assisted recombineering in Lactobacillus reuteri. Nucleic Acids Res 42:e131 [Google Scholar]
40. Patnaik R, Louie S, Gavrilovic V, Perry K, Stemmer WPC. et al. 2002. Genome shuffling of Lactobacillus for improved acid tolerance. Nat. Biotechnol. 20:707–12 [Google Scholar]
41. Robyt JF. 1998. Sweetness. Essentials of Carbohydrate Chemistry JF Robyt 142–56 New York: Springer-Verlag [Google Scholar]
42. Sanders ME, Klaenhammer TR, Ouwehand AC, Pot B, Johansen E. et al. 2014. Effects of genetic, processing or product formulation changes on efficacy and safety of probiotics. Ann. N. Y. Acad. Sci. 1309:1–18 [Google Scholar]
43. Selle K, Klaenhammer TR, Barrangou R. 2015. CRISPR-based screening of genomic island excision events in bacteria. PNAS 112:8076–81 [Google Scholar]
44. Sørensen K, Curic-Bawden M, Junge MP, Janzen T, Johansen E. 2016. Enhancing the sweetness of yoghurt through metabolic remodeling of carbohydrate metabolism in Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus. Appl. Environ. Microbiol. 82:3683–92 [Google Scholar]
45. Sprink T, Eriksson D, Schiemann J, Hartung F. 2016. Regulatory hurdles for genome editing: process- vs. product-based approaches in different regulatory contexts. Plant Cell Rep 35:1493–506 [Google Scholar]
46. Spus M, Liub H, Wels M, Abee T, Smid EJ. 2017. Isolation and characterization of Lactobacillus helveticus DSM 20075 variants with improved autolytic capacity. Int. J. Food Microbiol. 241:173–80 [Google Scholar]
47. Stout E, Klaenhammer T, Barrangou R. 2017. CRISPR-Cas technologies and applications in food bacteria. Annu. Rev. Food Sci. Technol. 8:413–37 [Google Scholar]
48. Stuer-Lauridsen B, Janzen T. 2011. Bacteriophage resistant lactic acid bacteria. Eur. Patent EP 1 838 839 B1 [Google Scholar]
49. Sturino JM, Klaenhammer TR. 2005. Bacteriophage defense systems and strategies for lactic acid bacteria. Advances in Applied Microbiology 56 A Laskin, J Bennett, G Gadd 331–78 San Diego: Academic [Google Scholar]
50. Szymczak P, Janzen T, Neves AR, Kot W, Hansen LH. et al. 2017. Novel variants of Streptococcus thermophilus bacteriophages are indicative of genetic recombination among phages from different bacterial species. Appl. Environ. Microbiol. 83:e02748–16 [Google Scholar]
51. Tamang JP, Watanabe K, Holzapfel WH. 2016. Review: Diversity of microorganisms in global fermented foods and beverages. Front. Microbiol. 7:377 [Google Scholar]
52. Triratna L, Saksono B, Sukmarini L, Suparman A. 2011. Genome-shuffling-improved acid tolerance and lactic acid production in Lactobacillus plantarum for commercialization. Microbiol. Indones. 5:21–26 [Google Scholar]
53. van de Guchte M, Penaud S, Grimaldi C, Barbe V, Bryson K. et al. 2006. The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution. PNAS 103:9274–79 [Google Scholar]
54. van Pijkeren J-P, Britton RA. 2012. High efficiency recombineering in lactic acid bacteria. Nucleic Acids Res 40:e76 [Google Scholar]
55. van Pijkeren J-P, Britton RA. 2014. Precision genome engineering in lactic acid bacteria. Microb. Cell Fact. 13:Suppl. 1S10 [Google Scholar]
56. Villion M, Moineau S. 2013. Phages hijack a host's defense mechanism. Nature 494:433–34 [Google Scholar]
57. Waltz E. 2016. Gene-edited CRISPR mushroom escapes US regulation. Nature 532:293 [Google Scholar]
58. Wang H, La Russa M, Qi LS. 2016. CRISPR/Cas9 in genome editing and beyond. Annu. Rev. Biochem. 85:227–64 [Google Scholar]
59. Wang H, Sun Y, Chen C, Sun Z, Zhou Y. et al. 2013. Genome shuffling of Lactobacillus plantarum for improving antifungal activity. Food Control 32:341–47 [Google Scholar]
60. Wang Y, Li Y, Pei X, Yu L, Feng Y. 2007. Genome-shuffling improved acid tolerance and l-lactic acid volumetric productivity in Lactobacillus rhamnosus. J. Biotechnol. 129:510–15 [Google Scholar]
61. Zago M, Orrù L, Rossetti L, Lamontanara A. , Fornasari, et al. 2017. Survey on the phage resistance mechanisms displayed by a dairy Lactobacillus helveticus strain. Food Microbiol 66:110–16 [Google Scholar]
62. Zeidan AA, Poulsen VK, Janzen T, Buldo P, Derkx PMF. et al. 2017. Polysaccharide production by LAB: from genes to industrial application. FEMS Microbiol. Rev. 41:Suppl. 1S168–200 [Google Scholar]
63. Zhang J, Wu C, Du G, Chen J. 2012. Enhanced acid tolerance in Lactobacillus casei by adaptive evolution and compared stress response during acid stress. Biotechnol. Bioprocess Eng. 17:283–89 [Google Scholar]
64. Zhang Y, Liu J-Z, Huang J-S, Mao Z-W. 2010. Genome shuffling of Propionibacterium shermanii for improving vitamin B12 production and comparative proteome analysis. J. Biotechnol. 148:139–43 [Google Scholar]
65. Zhang YF, Liu SY, Du YH, Feng WJ, Liu JH, Qiao JJ. 2014. Genome shuffling of Lactococcus lactis subspecies lactis YF11 for improving nisin Z production and comparative analysis. J. Dairy Sci. 97:2528–41 [Google Scholar]
66. Zhang Y-X, Perry K, Vinci VA, Powell K, Stemmer WPC, del Cardayré SB. 2002. Genome shuffling leads to rapid phenotypic improvement in bacteria. Nature 415:644–46 [Google Scholar]