Evolutionary engineering to enhance starter culture performance in food fermentations

Current Opinion in Biotechnology

Volumn 32, Issue , 2015, Pages 1-7

  Bachmann, Herwig ^a,b   Pronk, Jack T ^c,d   Kleerebezem, Michiel ^a,b,d,e   Teusink, Bas ^d,f  

^a NIZO FOOD RESEARCH   (Netherlands)

^b TOP INSTITUTE FOOD AND NUTRITION   (Netherlands)

^c DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

^d KLUYVER CENTRE FOR GENOMICS OF INDUSTRIAL FERMENTATION   (Netherlands)

^e WAGENINGEN UNIVERSITY   (Netherlands)

^f AMSTERDAM INSTITUTE FOR MOLECULES   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

EVOLUTIONARY ENGINEERING; FOOD FERMENTATION; STARTER CULTURES;

CAROTENOID;

BACTERIAL METABOLISM; BACTERIAL STRAIN; BATCH CELL CULTURE; BIOENGINEERING; BIOMASS FERMENTATION; CONTINUOUS CULTURE; EMULSION; ENERGY METABOLISM; EVOLUTIONARY ENGINEERING; FERMENTATION; FUNGAL METABOLISM; FUNGAL STRAIN; LACTOBACILLUS PLANTARUM; LACTOCOCCUS LACTIS; METAGENOMICS; MICROBIAL BIOMASS; MICROBIAL CONSORTIUM; MOLECULAR EVOLUTION; NONHUMAN; PHENOTYPE; PROCESS OPTIMIZATION; REVIEW; SACCHAROMYCES CEREVISIAE; STARTER CULTURE; STREPTOCOCCUS THERMOPHILUS; SUSPENSION CELL CULTURE; YEAST; ANIMAL; FOOD CONTROL; HUMAN; TASTE;

ANIMALS; BIOENGINEERING; FERMENTATION; FOOD MICROBIOLOGY; HUMANS; PHENOTYPE; TASTE;

EID: 84907855872     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2014.09.003     Document Type: Review

References (51)

1. Smid E.J., Kleerebezem M. Production of aroma compounds in lactic fermentations. Annu Rev Food Sci Technol 2014, 5:313-326.
2. Barrick J.E., Lenski R.E. Genome dynamics during experimental evolution. Nat Rev Genet 2013, 14:827-839.
3. Sauer U. Evolutionary engineering of industrially important microbial phenotypes. Adv Biochem Eng Biotechnol 2001, 73:129-169.
4. Solopova A., Bachmann H., Teusink B., Kok J., Neves A.R., Kuipers O.P. A specific mutation in the promoter region of the silent cel cluster accounts for the appearance of lactose-utilizing Lactococcus lactis MG1363. Appl Environ Microbiol 2012, 78:5612-5621.
5. Margolles A., Sánchez B. Selection of a Bifidobacterium animalis subsp. lactis strain with a decreased ability to produce acetic acid. Appl Environ Microbiol 2012, 78:3338-3342.
6. Oud B., Guadalupe-Medina V., Nijkamp J.F., de Ridder D., Pronk J.T., van Maris A.J., Daran J-M. Genome duplication and mutations in ACE2 cause multicellular, fast-sedimenting phenotypes in evolved Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2013, 110:E4223-E4231.
7. Ekberg J., Rautio J., Mattinen L., Vidgren V., Londesborough J., Gibson B.R. Adaptive evolution of the lager brewing yeast Saccharomyces pastorianus for improved growth under hyperosmotic conditions and its influence on fermentation performance. FEMS Yeast Res 2013, 13:335-349.
8. Tilloy V., Ortiz-Julien A., Dequin S. Reduction of ethanol yield and improvement of glycerol formation by adaptive evolution of the wine yeast Saccharomyces cerevisiae under hyperosmotic conditions. Appl Environ Microbiol 2014, 80:2623-2632.
9. Bachmann H., Starrenburg M.J.C., Molenaar D., Kleerebezem M., van Hylckama Vlieg J.E.T. Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution. Genome Res 2012, 22:115-124.
10. Cadière A., Ortiz-Julien A., Camarasa C., Dequin S. Evolutionary engineered Saccharomyces cerevisiae wine yeast strains with increased in vivo flux through the pentose phosphate pathway. Metab Eng 2011, 13:263-271.
11. Cadière A., Aguera E., Caillé S., Ortiz-Julien A., Dequin S. Pilot-scale evaluation the enological traits of a novel, aromatic wine yeast strain obtained by adaptive evolution. Food Microbiol 2012, 32:332-337.
12. Jansen M.L., Diderich J.A., Mashego M., Hassane A., de Winde J.H., Daran-Lapujade P., Pronk J.T. Prolonged selection in aerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae causes a partial loss of glycolytic capacity. Microbiology 2005, 151:1657-1669.
13. Heavner B.D., Smallbone K., Price N.D., Walker L.P. Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance. Database (Oxford) 2013, 2013:bat059.
14. Racle J., Picard F., Girbal L., Cocaign-Bousquet M., Hatzimanikatis V. A genome-scale integration and analysis of Lactococcus lactis translation data. PLoS Comput Biol 2013, 9:e1003240.
15. Hamilton J.J., Reed J.L. Software platforms to facilitate reconstructing genome-scale metabolic networks. Environ Microbiol 2014, 16:49-59.
16. Berkhout J., Bruggeman F.J., Teusink B. Optimality principles in the regulation of metabolic networks. Metabolites 2012, 2:529-552.
17. Lewis N.E., Nagarajan H., Palsson B.O. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol 2012, 10:291-305.
18. Ibarra R.U., Edwards J.S., Palsson B.O. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 2002, 420:186-189.
19. Ren S., Zeng B., Qian X. Adaptive bi-level programming for optimal gene knockouts for targeted overproduction under phenotypic constraints. BMC Bioinform 2013, 14(Suppl 2):S17.
20. Imai T., Ohno T. The relationship between viability and intracellular pH in the yeast Saccharomyces cerevisiae. Appl Environ Microbiol 1995, 61:3604-3608.
21. Choon Y.W., Mohamad M.S., Deris S., Illias R.M., Chong C.K., Chai L.E. A hybrid of bees algorithm and flux balance analysis with OptKnock as a platform for in silico optimization of microbial strains. Bioprocess Biosyst Eng 2014, 37:521-532.
22. Brochado A.R., Patil K.R. Model-guided identification of gene deletion targets for metabolic engineering in Saccharomyces cerevisiae. Methods Mol Biol 2014, 1152:281-294.
23. McCloskey D., Palsson B.Ø., Feist A.M. Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli. Mol Syst Biol 2013, 9:661.
24. MacLean R.C. The tragedy of the commons in microbial populations: insights from theoretical, comparative and experimental studies. Heredity (Edinb) 2008, 100:233-239.
25. Brown C.J., Todd K.M., Rosenzweig R.F. Multiple duplications of yeast hexose transport genes in response to selection in a glucose-limited environment. Mol Biol Evol 1998, 15:931-942.
26. Reyes L.H., Gomez J.M., Kao K.C. Improving carotenoids production in yeast via adaptive laboratory evolution. Metab Eng 2014, 21:26-33.
27. 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 U S A 2013, 110:14302-14307.
28. Kojima T., Nagao N., Ando D., Ojima T., Kawarasaki Y., Kobayashi I., Nakajima M., Nakano H. Emulsion culture: a miniaturized library screening system based on micro-droplets in an emulsified medium. J Biosci Bioeng 2011, 112:299-303.
29. Wang B.L., Ghaderi A., Zhou H., Agresti J., Weitz D.A., Fink G.R., Stephanopoulos G. Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption. Nat Biotechnol 2014, 32:473-478.
30. Joensson H.N., Andersson Svahn H. Droplet microfluidics-a tool for single-cell analysis. Angew Chem Int Ed Engl 2012, 51:12176-12192.
31. Herrgård M., Panagiotou G. Analyzing the genomic variation of microbial cell factories in the era of "New Biotechnology". Comput Struct Biotechnol J 2012, 3:e201210012.
32. Oud B., van Maris A.J., Daran J-M., Pronk J.T. Genome-wide analytical approaches for reverse metabolic engineering of industrially relevant phenotypes in yeast. FEMS Yeast Res 2012, 12:183-196.
33. Hong K-K., Vongsangnak W., Vemuri G.N., Nielsen J. Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis. Proc Natl Acad Sci U S A 2011, 108:12179-12184.
34. González-Ramos D., van den Broek M., van Maris A.J., Pronk J.T., Daran J-M.G. Genome-scale analyses of butanol tolerance in Saccharomyces cerevisiae reveal an essential role of protein degradation. Biotechnol Biofuels 2013, 6:48.
35. Parts L., Cubillos F.A., Warringer J., Jain K., Salinas F., Bumpstead S.J., Molin M., Zia A., Simpson J.T., Quail M.A., et al. Revealing the genetic structure of a trait by sequencing a population under selection. Genome Res 2011, 21:1131-1138.
36. Cubillos F.A., Parts L., Salinas F., Bergström A., Scovacricchi E., Zia A., Illingworth C.J.R., Mustonen V., Ibstedt S., Warringer J., et al. High-resolution mapping of complex traits with a four-parent advanced intercross yeast population. Genetics 2013, 195:1141-1155.
37. Paez-Espino D., Morovic W., Sun C.L., Thomas B.C., Ueda K., Stahl B., Barrangou R., Banfield J.F. Strong bias in the bacterial CRISPR elements that confer immunity to phage. Nat Commun 2013, 4:1430.
38. Barrangou R., Marraffini L.A. CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity. Mol Cell 2014, 54:234-244.
39. Van Bokhorst-van de Veen H., van Swam I., Wels M., Bron P.A., Kleerebezem M. Congruent strain specific intestinal persistence of Lactobacillus plantarum in an intestine-mimicking in vitro system and in human volunteers. PLoS ONE 2012, 7:e44588.
40. Bron P.A., Wels M., Bongers R.S., van Bokhorst-van de Veen H., Wiersma A., Overmars L., Marco M.L., Kleerebezem M. Transcriptomes reveal genetic signatures underlying physiological variations imposed by different fermentation conditions in Lactobacillus plantarum. PLoS ONE 2012, 7:e38720.
41. Van Bokhorst-van de Veen H., Smelt M.J., Wels M., van Hijum S.A., de Vos P., Kleerebezem M., Bron P.A. Genotypic adaptations associated with prolonged persistence of Lactobacillus plantarum in the murine digestive tract. Biotechnol J 2013, 8:895-904.
42. Erkus O., de Jager V.C., Spus M., van Alen-Boerrigter I.J., van Rijswijck I.M., Hazelwood L., Janssen P.W., van Hijum S.A., Kleerebezem M., Smid E.J. Multifactorial diversity sustains microbial community stability. ISME J 2013, 7:2126-2136.
43. Rodriguez-Valera F., Martin-Cuadrado A-B., Rodriguez-Brito B., Pasić L., Thingstad T.F., Rohwer F., Mira A. Explaining microbial population genomics through phage predation. Nat Rev Microbiol 2009, 7:828-836.
44. Smid E.J., Lacroix C. Microbe-microbe interactions in mixed culture food fermentations. Curr Opin Biotechnol 2013, 24:148-154.
45. Pande S., Merker H., Bohl K., Reichelt M., Schuster S., de Figueiredo L.F., Kaleta C., Kost C. Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria. ISME J 2014, 8:953-962.
46. Harcombe W. Novel cooperation experimentally evolved between species. Evolution 2010, 64:2166-2172.
47. Molenaar D., van Berlo R., de Ridder D., Teusink B. Shifts in growth strategies reflect tradeoffs in cellular economics. Mol Syst Biol 2009, 5:323.
48. Peña M.I., Davlieva M., Bennett M.R., Olson J.S., Shamoo Y. Evolutionary fates within a microbial population highlight an essential role for protein folding during natural selection. Mol Syst Biol 2010, 6:387.
49. Smith W.M., Pham T.H., Lei L., Dou J., Soomro A.H., Beatson S.A., Dykes G.A., Turner M.S. Heat resistance and salt hypersensitivity in Lactococcus lactis due to spontaneous mutation of llmg_1816 (gdpP) induced by high-temperature growth. Appl Environ Microbiol 2012, 78:7753-7759.
50. Maharjan R., Nilsson S., Sung J., Haynes K., Beardmore R.E., Hurst L.D., Ferenci T., Gudelj I. The form of a trade-off determines the response to competition. Ecol Lett 2013, 16:1267-1276.
51. Solopova A., van Gestel J., Weissing F.J., Bachmann H., Teusink B., Kok J., Kuipers O.P. Bet-hedging during bacterial diauxic shift. Proc Natl Acad Sci U S A 2014, 111:7427-7432.