1,865
Views
71
CrossRef citations to date
0
Altmetric
Review Article

Genomics of lactic acid bacteria: Current status and potential applications

, &
Pages 393-404 | Received 21 Jul 2015, Accepted 13 Apr 2016, Published online: 02 Mar 2017

References

  • Abdullah-Al-Mahin, Sugimoto S, Higashi C, et al. (2010). Improvement of multiple-stress tolerance and lactic acid production in Lactococcus lactis NZ9000 under conditions of thermal stress by heterologous expression of Escherichia coli dnaK. Appl Environ Microb 76:4277–85.
  • Ainsworth S, Stockdale S, Bottacini F, et al. (2014). The Lactococcus lactis plasmidome: much learnt, yet still lots to discover. FEMS Microbiol Rev 38:1066–88.
  • Alcántara C, Zúñiga M. (2012). Proteomic and transcriptomic analysis of the response to bile stress of Lactobacillus casei BL23. Microbiology (Reading, Engl) 158:1206–18.
  • An H, Douillard FP, Wang G, et al. (2014). Integrated transcriptomic and proteomic analysis of the bile stress response in a centenarian-originated probiotic Bifidobacterium longum BBMN68. Mol Cell Proteomics 13:2558–72.
  • Ardö Y. (2006). Flavour formation by amino acid catabolism. Biotechnol Adv 24:238–42.
  • Arena M, Landete J, Manca de Nadra M, et al. (2008). Factors affecting the production of putrescine from agmatine by Lactobacillus hilgardii XB isolated from wine. J Appl Microbiol 105:158–65.
  • Becker J, Wittmann C. (2012). Systems and synthetic metabolic engineering for amino acid production – the heartbeat of industrial strain development. Curr Opin Biotechnol 23:718–26.
  • Boghigian BA, Armando J, Salas D, Pfeifer BA. (2012). Computational identification of gene over-expression targets for metabolic engineering of taxadiene production. Appl Microbiol Biotechnol 93:2063–73.
  • Bolotin A, Quinquis B, Renault P, et al. (2004). Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus. Nat Biotechnol 22:1554–8.
  • Broadbent J, Oberg T, Hughes J, et al. (2014). Influence of polysorbate 80 and cyclopropane fatty acid synthase activity on lactic acid production by Lactobacillus casei ATCC 334 at low pH. J Ind Microbiol Biotechnol 41:545–53.
  • Broadbent JR, Larsen RL, Deibel V, Steele JL. (2010). Physiological and transcriptional response of Lactobacillus casei ATCC 334 to acid stress. J Bacteriol 192:2445–58.
  • Bron PA, Kleerebezem M. (2011). Engineering lactic acid bacteria for increased industrial functionality. Bioeng Bugs 2:80–7.
  • Burgess CM, Smid EJ, Rutten G, Van Sinderen D. (2006). A general method for selection of riboflavin-overproducing food grade micro-organisms. Microb Cell Fact 5:24.
  • Capozzi V, Menga V, Digesu AM, et al. (2011). Biotechnological production of vitamin B2-enriched bread and pasta. J Agric Food Chem 59:8013–20.
  • Capozzi V, Russo P, Dueñas MT, et al. (2012). Lactic acid bacteria producing B-group vitamins: a great potential for functional cereals products. Appl Microbiol Biotechnol 96:1383–94.
  • Carvalho AL, Cardoso FS, Bohn A, et al. (2011). Engineering trehalose synthesis in Lactococcus lactis for improved stress tolerance. Appl Environ Microbiol 77:4189–99.
  • Carvalho AL, Turner DL, Fonseca LL, et al. (2013). Metabolic and transcriptional analysis of acid stress in Lactococcus lactis, with a focus on the kinetics of lactic acid pools. PLoS One 8:e68470.
  • Claesson MJ, Li Y, Leahy S, et al. (2006). Multireplicon genome architecture of Lactobacillus salivarius. Proc Natl Acad Sci USA 103:6718–23.
  • Crowley S, Bottacini F, Mahony J, van Sinderen D. (2013). Complete genome sequence of Lactobacillus plantarum strain 16, a broad-spectrum antifungal-producing lactic acid bacterium. Genome Announcements 1:e00533–13.
  • da Silva Sabo S, Vitolo M, González JMD, de Souza Oliveira RP. (2014). Overview of Lactobacillus plantarum as a promising bacteriocin producer among lactic acid bacteria. Food Res Int 64:527–36.
  • De Angelis M, Gobbetti M. (2004). Environmental stress responses in Lactobacillus: a review. Proteomics 4:106–22.
  • de Cadiñanos LPG, García-Cayuela T, Yvon M, et al. (2013). Inactivation of the panE gene in Lactococcus lactis enhances formation of cheese aroma compounds. Appl Environ Microb 79:3503–6.
  • De Felipe FL, Kleerebezem M, de Vos WM, Hugenholtz J. (1998). Cofactor engineering: a novel approach to metabolic engineering in Lactococcus lactis by controlled expression of NADH oxidase. J Bacteriol 180:3804–8.
  • Delorme C. (2008). Safety assessment of dairy microorganisms: Streptococcus thermophilus. Int J Food Microbiol 126:274–7.
  • Dijkstra AR, Alkema W, Starrenburg MJ, et al. (2014). Fermentation-induced variation in heat and oxidative stress phenotypes of Lactococcus lactis MG1363 reveals transcriptome signatures for robustness. Microb Cell Fact 13:148.
  • Douillard FP, de Vos WM. (2014). Functional genomics of lactic acid bacteria: from food to health. Microb Cell Fact 13:S8.
  • Douillard FP, Ribbera A, Kant R, et al. (2013). Comparative genomic and functional analysis of 100 Lactobacillus rhamnosus strains and their comparison with strain GG. PLoS Genet 9:e1003683.
  • El-Semman IE, Karlsson FH, Shoaie S, et al. (2014). Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction. BMC Syst Biol 8:41.
  • El Kafsi H, Binesse J, Loux V, et al. (2014). Lactobacillus delbrueckii ssp. lactis and ssp. bulgaricus: a chronicle of evolution in action. BMC Genomics 15:407.
  • Fang S-H, Lai Y-J, Chou C-C. (2013). The susceptibility of Streptococcus thermophilus 14085 to organic acid, simulated gastric juice, bile salt and disinfectant as influenced by cold shock treatment. Food Microbiol 33:55–60.
  • Fernández M, Del Río B, Linares D, et al. (2006). Real-time polymerase chain reaction for quantitative detection of histamine-producing bacteria: use in cheese production. J Dairy Sci 89:3763–9.
  • Fernández M, Zú iga M. (2006). Amino acid catabolic pathways of lactic acid bacteria. Crit Rev Microbiol 32:155–83.
  • Filannino P, Cardinali G, Rizzello C, et al. (2014). Metabolic responses of Lactobacillus plantarum strains during fermentation and storage of vegetable and fruit juices. Appl Environ Microb 80:2206–15.
  • Fukao M, Oshima K, Morita H, et al. (2013). Genomic analysis by deep sequencing of the probiotic Lactobacillus brevis KB290 harboring nine plasmids reveals genomic stability. PLoS One 8:e60521.
  • Gaspar P, Carvalho AL, Vinga S, et al. (2013). From physiology to systems metabolic engineering for the production of biochemicals by lactic acid bacteria. Biotechnol Adv 31:764–88.
  • Ghalfi H, Benkerroum N, Ongena M, et al. (2010). Production of three anti-listerial peptides by Lactobacillus curvatus in MRS broth. Food Res Int 43:33–9.
  • Goh YJ, Goin C, O’Flaherty S, et al. (2011). Specialized adaptation of a lactic acid bacterium to the milk environment: the comparative genomics of Streptococcus thermophilus LMD-9. Microb Cell Fact 10:S22.
  • Hagi T, Kobayashi M, Kawamoto S, et al. (2013). Expression of novel carotenoid biosynthesis genes from Enterococcus gilvus improves the multistress tolerance of Lactococcus lactis. J Appl Microbiol 114:1763–71.
  • Heunis T, Deane S, Smit S, Dicks LM. (2014). Proteomic profiling of the acid stress response in Lactobacillus plantarum 423. J Proteome Res 13:4028–39.
  • Higuchi T, Hayashi HU, Abe K. (1997). Exchange of glutamate and gamma-aminobutyrate in a Lactobacillus strain. J Bacteriol 179:3362–4.
  • Hols P, Kleerebezem M, Schanck AN, et al. (1999). Conversion of Lactococcus lactis from homolactic to homoalanine fermentation through metabolic engineering. Nat Biotechnol 17:588–92.
  • Kim JE, Eom H-J, Kim Y, et al. (2012). Enhancing acid tolerance of Leuconostoc mesenteroides with glutathione. Biotechnol Lett 34:683–7.
  • Kim JE, Eom H-J, Li L, et al. (2014). Induction of the acid tolerance response in Leuconostoc mesenteroides ATCC 8293 by pre-adaptation in acidic condition. Food Sci Biotechnol 23:221–4.
  • Kleerebezem M, Boekhorst J, van Kranenburg R, et al. (2003). Complete genome sequence of Lactobacillus plantarum WCFS1. Proc Natl Acad Sci USA 100:1990–5.
  • Ladero V, Ramos A, Wiersma A, et al. (2007). High-level production of the low-calorie sugar sorbitol by Lactobacillus plantarum through metabolic engineering. Appl Environ Microb 73:1864–72.
  • Li B, Tian F, Liu X, et al. (2011). Effects of cryoprotectants on viability of Lactobacillus reuteri CICC6226. Appl Microbiol Biotechnol 92:609–16.
  • Li H, Cao Y. (2010). Lactic acid bacterial cell factories for gamma-aminobutyric acid. Amino Acids 39:1107–16.
  • Li H, Lu M, Guo H, et al. (2010). Protective effect of sucrose on the membrane properties of Lactobacillus casei Zhang subjected to freeze-drying. J Food Protect 73:715–19.
  • Li Y, Wei G, Chen J. (2004). Glutathione: a review on biotechnological production. Appl Microbiol Biotechnol 66:233–42.
  • Maitre M, Weidmann S, Dubois-Brissonnet F, et al. (2014). Adaptation of the wine bacterium Oenococcus oeni to ethanol stress: role of the small heat shock protein Lo18 in membrane integrity. Appl Environ Microbiol 80:2973–80.
  • Makarova K, Slesarev A, Wolf Y, et al. (2006). Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci USA 103:15611–6.
  • Makarova KS, Koonin EV. (2007). Evolutionary genomics of lactic acid bacteria. J Bacteriol 189:1199–208.
  • Mayo B, Van Sinderen D, Ventura M. (2008). Genome analysis of food grade lactic acid-producing bacteria: from basics to applications. Curr Genomics 9:169.
  • Mazzoli R, Bosco F, Mizrahi I, et al. (2014). Towards lactic acid bacteria-based biorefineries. Biotechnol Adv 32:1216–36.
  • Moraïs S, Shterzer N, Grinberg IR, et al. (2013). Establishment of a simple Lactobacillus plantarum cell consortium for cellulase-xylanase synergistic interactions. Appl Environ Microb 79:5242–9.
  • Motherway MOC, Zomer A, Leahy SC, et al. (2011). Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor. Proc Natl Acad Sci USA 108:11217–22.
  • Muller J, Ross R, Sybesma W, et al. (2011). Modification of the technical properties of Lactobacillus johnsonii NCC 533 by supplementing the growth medium with unsaturated fatty acids. Appl Environ Microbiol 77:6889–98.
  • Mykytczuk NCS, Trevors JT, Leduc LG, Ferroni GD. (2007). Fluorescence polarization in studies of bacterial cytoplasmic membrane fluidity under environmental stress. Prog Biophys Mol Biol 95:60–82.
  • Ng CY, Jung M-Y, Lee J, Oh M-K. (2012). Production of 2,3-butanediol in Saccharomyces cerevisiae by in silico aided metabolic engineering. Microb Cell Fact 11:68.
  • O’Shea EF, Cotter PD, Ross RP, Hill C. (2013). Strategies to improve the bacteriocin protection provided by lactic acid bacteria. Curr Opin Biotechnol 24:130–4.
  • Oddone GM, Mills DA, Block DE. (2009). A dynamic, genome-scale flux model of Lactococcus lactis to increase specific recombinant protein expression. Metab Eng 11:367–81.
  • Okano K, Kimura S, Narita J, et al. (2007). Improvement in lactic acid production from starch using alpha-amylase-secreting Lactococcus lactis cells adapted to maltose or starch. Appl Microbiol Biotechnol 75:1007–13.
  • Okano K, Zhang Q, Shinkawa S, et al. (2009). Efficient production of optically pure d-lactic acid from raw corn starch by using a genetically modified l-lactate dehydrogenase gene-deficient and α-amylase-secreting Lactobacillus plantarum strain. Appl Environ Microb 75:462–7.
  • Oliveira AP, Nielsen J, Förster J. (2005). Modeling Lactococcus lactis using a genome-scale flux model. BMC Microbiol 5:39.
  • Papadimitriou K, Anastasiou R, Maistrou E, et al. (2015). Acquisition through horizontal gene transfer of plasmid pSMA198 by Streptococcus macedonicus ACA-DC 198 points towards the dairy origin of the species. PLoS One 10:e0116337.
  • Pastink MI, Teusink B, Hols P, et al. (2009). Genome-scale model of Streptococcus thermophilus LMG18311 for metabolic comparison of lactic acid bacteria. Appl Environ Microbiol 75:3627–33.
  • Perez RH, Zendo T, Sonomoto K. (2014). Novel bacteriocins from lactic acid bacteria (LAB): various structures and applications. Microb Cell Fact 13:S3.
  • Pfeiler EA, Klaenhammer TR. (2007). The genomics of lactic acid bacteria. Trends Microbiol 15:546–53.
  • Raha A, Chang L, Sipat A, et al. (2006). Expression of a thermostable xylanase gene from Bacillus coagulans ST-6 in Lactococcus lactis. Lett Appl Microbiol 42:210–4.
  • Sánchez B, Champomier-Vergès MC, Collado MC, et al. (2007). Low-pH adaptation and the acid tolerance response of Bifidobacterium longum biotype longum. Appl Environ Microbiol 73:6450–9.
  • Saha R, Chowdhury A, Maranas CD. (2014). Recent advances in the reconstruction of metabolic models and integration of omics data. Curr Opin Biotechnol 29:39–45.
  • Santiago B, MacGilvray M, Faustoferri RC, Quivey RG. (2012). The branched-chain amino acid aminotransferase encoded by ilvE is involved in acid tolerance in Streptococcus mutans. J Bacteriol 194:2010–9.
  • Schroeter J, Klaenhammer T. (2009). Genomics of lactic acid bacteria. FEMS Microbiol Lett 292:1–6.
  • Senan S, Prajapati JB, Joshi CG, Bell J. (2014). Comparative genome-scale analysis of niche-based stress-responsive genes in Lactobacillus helveticus strains. Genome 57:999, 1–8.
  • Serrazanetti DI, Ndagijimana M, Sado-Kamdem SL, et al. (2011). Acid stress-mediated metabolic shift in Lactobacillus sanfranciscensis LSCE1. Appl Environ Microb 77:2656–66.
  • Smit G, Smit BA, Engels WJ. (2005). Flavour formation by lactic acid bacteria and biochemical flavour profiling of cheese products. FEMS Microbiol Rev 29:591–610.
  • Solem C, Dehli T, Jensen PR. (2013). Rewiring Lactococcus lactis for ethanol production. Appl Environ Microbiol 79:2512–8.
  • Song D-F, Zhu M-Y, Gu Q. (2014). Purification and characterization of Plantaricin ZJ5, a new bacteriocin produced by Lactobacillus plantarum ZJ5. PLoS One 9:e105549.
  • Sybesma W, Starrenburg M, Kleerebezem M, et al. (2003). Increased production of folate by metabolic engineering of Lactococcus lactis. Appl Environ Microb 69:3069–76.
  • Tabanelli G, Montanari C, Bargossi E, et al. (2014). Control of tyramine and histamine accumulation by lactic acid bacteria using bacteriocin forming lactococci. Int J Food Microbiol. 190:14--23
  • Tabanelli G, Patrignani F, Gardini F, et al. (2014). Effect of a sublethal high-pressure homogenization treatment on the fatty acid membrane composition of probiotic lactobacilli. Lett Appl Microbiol 58:109–17.
  • Teusink B, Smid EJ. (2006). Modelling strategies for the industrial exploitation of lactic acid bacteria. Nat Rev Microbiol 4:46–56.
  • Teusink B, Wiersma A, Molenaar D, et al. (2006). Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model. J Biol Chem 281:40041–8.
  • Tian H, Tan J, Zhang L, et al. (2012). Increase of stress resistance in Lactococcus lactis via a novel food-grade vector expressing a shsp gene from Streptococcus thermophilus. Braz J Microbiol 43:1157–64.
  • Tomar N, De RK. (2013). Comparing methods for metabolic network analysis and an application to metabolic engineering. Gene 521:1–14.
  • Trip H, Mulder NL, Lolkema JS. (2012). Improved acid stress survival of Lactococcus lactis expressing the histidine decarboxylation pathway of Streptococcus thermophilus CHCC1524. J Biol Chem 287:11195–204.
  • Tsuji A, Okada S, Hols P, Satoh E. (2013). Metabolic engineering of Lactobacillus plantarum for succinic acid production through activation of the reductive branch of the tricarboxylic acid cycle. Enzyme Microb Technol 53:97–103.
  • Vaidyanathan H, Kandasamy V, Ramakrishnan GG, et al. (2011). Glycerol conversion to 1, 3-propanediol is enhanced by the expression of a heterologous alcohol dehydrogenase gene in Lactobacillus reuteri. AMB Express 1:1–8.
  • van Bokhorst-van de Veen H, Abee T, Tempelaars M, et al. (2011). Short- and long-term adaptation to ethanol stress and its cross-protective consequences in Lactobacillus plantarum. Appl Environ Microb 77:5247–56.
  • Van de Guchte M, Penaud S, Grimaldi C, et al. (2006). The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution. Proc Natl Acad Sci USA 103:9274–9.
  • Velly H, Bouix M, Passot S, et al. (2015). Cyclopropanation of unsaturated fatty acids and membrane rigidification improve the freeze-drying resistance of Lactococcus lactis subsp. lactis TOMSC161. Appl Microbiol Biotechnol 99:907–18.
  • Wu C, He G, Zhang J. (2014). Physiological and proteomic analysis of Lactobacillus casei in response to acid adaptation. J Ind Microbiol Biotechnol 41:1533–40.
  • Wu C, Zhang J, Chen W, et al. (2012). A combined physiological and proteomic approach to reveal lactic-acid-induced alterations in Lactobacillus casei Zhang and its mutant with enhanced lactic acid tolerance. Appl Microbiol Biotechnol 93:707–22.
  • Wu C, Zhang J, Du G, Chen J. (2013). Heterologous expression of Lactobacillus casei RecO improved the multiple-stress tolerance and lactic acid production in Lactococcus lactis NZ9000 during salt stress. Bioresour Technol 143:238–41.
  • Wu C, Zhang J, Wang M, et al. (2012). Lactobacillus casei combats acid stress by maintaining cell membrane functionality. J Ind Microbiol Biotechnol 39:1031–9.
  • Wu R, Zhang W, Sun T, et al. (2011). Proteomic analysis of responses of a new probiotic bacterium Lactobacillus casei Zhang to low acid stress. Int J Food Microbiol 147:181–7.
  • Xu C, Liu L, Zhang Z, et al. (2013). Genome-scale metabolic model in guiding metabolic engineering of microbial improvement. Appl Microbiol Biotechnol 97:519–39.
  • Zhang J, Du G-C, Zhang Y, et al. (2010). Glutathione protects Lactobacillus sanfranciscensis against freeze-thawing, freeze-drying, and cold treatment. Appl Environ Microb 76:2989–96.
  • Zhang J, Fu R-Y, Hugenholtz J, et al. (2007). Glutathione protects Lactococcus lactis against acid stress. Appl Environ Microbiol 73:5268–75.
  • Zhang J, Li Y, Chen W, et al. (2012). Glutathione improves the cold resistance of Lactobacillus sanfranciscensis by physiological regulation. Food Microbiol 31:285–92.
  • 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 Bioproc Eng 17:283–9.
  • Zhang W, Zhang H. (2014). Genomics of lactic acid bacteria. Dordrecht, Netherlands: Springer.
  • Zhang Y, Li Y. (2013). Engineering the antioxidative properties of lactic acid bacteria for improving its robustness. Curr Opin Biotechnol 24:142–7.
  • Zhang Y, Zhang Y, Zhu Y, et al. (2010). Proteomic analyses to reveal the protective role of glutathione in resistance of Lactococcus lactis to osmotic stress. Appl Environ Microbiol 76:3177–86.
  • Zhang Z-Y, Liu C, Zhu Y-Z, et al. (2012). Safety assessment of Lactobacillus plantarum JDM1 based on the complete genome. Int J Food Microbiol 153:166–70.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.