Applications of plant-based fermented foods and their microbes

Current Opinion in Biotechnology

Volumn 61, Issue , 2020, Pages 45-52

  Wuyts, Sander ^a   Van Beeck, Wannes ^a   Allonsius, Camille Nina ^a   van den Broek, Marianne FL ^a   Lebeer, Sarah ^a  

^a UNIVERSITY OF ANTWERP   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; DNA SEQUENCES; FERMENTATION; GENE ENCODING; LACTIC ACID; PROBIOTICS;

BIOTECHNOLOGICAL APPLICATIONS; CELLULASE ENZYME; COMPARATIVE GENOMICS; GENETIC POTENTIAL; LACTIC ACID BACTERIA; LACTOBACILLUS PLANTARUM; PRODUCTION CAPACITY; RATIONAL DESIGN;

LABORATORIES;

CELLULASE; PROBIOTIC AGENT;

BIOTECHNOLOGICAL PROCEDURES; COMMUNITY DYNAMICS; COMPARATIVE GENOMIC HYBRIDIZATION; FERMENTATION TECHNIQUE; FERMENTED PRODUCT; FOOD INDUSTRY; FOOD INTAKE; HEALTH PROMOTION; HOST PATHOGEN INTERACTION; IMMUNOMODULATION; LACTIC ACID BACTERIUM; LACTOBACILLUS PLANTARUM; MICROBIAL DIVERSITY; MICROBIAL GENOME; MOLECULAR RECOGNITION; NONHUMAN; PHENOTYPE; PLANT BASED FERMENTATION; PRIORITY JOURNAL; REVIEW; SCREENING TEST; FERMENTATION; FOOD CONTROL; LACTOBACILLALES;

FERMENTATION; FERMENTED FOODS AND BEVERAGES; FOOD MICROBIOLOGY; LACTOBACILLALES; PROBIOTICS;

EID: 85074705576     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2019.09.023     Document Type: Review

References (58)

1. Hugenholtz, J., Traditional biotechnology for new foods and beverages. Curr Opin Biotechnol 24 (2013), 155–159.
2. Tamang, J.P., Watanabe, K., Holzapfel, W.H., Review: diversity of microorganisms in global fermented foods and beverages. Front Microbiol, 7, 2016, 377.
3. Gänzle, M.G., Lactic metabolism revisited: metabolism of lactic acid bacteria in food fermentations and food spoilage. Curr Opin Food Sci 2 (2015), 106–117.
4. Duar, R.M., Lin, X.B., Zheng, J., Martino, M.E., Grenier, T., Pérez-Muñoz, M.E., Leulier, F., Gänzle, M., Walter, J., Lifestyles in transition: evolution and natural history of the genus Lactobacillus. FEMS Microbiol Rev 41 (2017), S27–S48 Landmark paper on the evolutionary history and preferred lifestyle of the different phylogenetic groups of Lactobacillus. Plant-associated lactobacilli are considered to be nomadic or free-living.
5. Roh, S.W., Kim, K.-H., Nam, Y.-D., Chang, H.-W., Park, E.-J., Bae, J.-W., Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing. ISME J 4 (2010), 1–16.
6. Marco, M.L., Heeney, D., Binda, S., Cifelli, C.J., Cotter, P.D., Foligné, B., Gänzle, M., Kort, R., Pasin, G., Pihlanto, A., et al. Health benefits of fermented foods: microbiota and beyond. Curr Opin Biotechnol 44 (2017), 94–102.
7. Wuyts, S., Beeck, W., Van, Oerlemans, E.F.M., Carrot juice fermentations as man-made microbial ecosystems. Appl Environ Microbiol 84 (2018), 1–16 84e00134-18.
8. Wolfe, B.E., Dutton, R.J., Fermented foods as experimentally tractable microbial ecosystems. Cell 161 (2015), 49–55 This study highlights how spontaneously fermented foods (such as sourdough) are interesting model ecosystems.
9. De Filippis, F., Parente, E., Ercolini, D., Metagenomics insights into food fermentations. Microb Biotechnol 10 (2017), 91–102.
10. Martins, E.M.F., Ramos, A.M., Vanzela, E.S.L., Stringheta, P.C., de Oliveira Pinto, C.L., Martins, J.M., Products of vegetable origin: a new alternative for the consumption of probiotic bacteria. Food Res Int 51 (2013), 764–770.
11. Ranadheera, C.S., Vidanarachchi, J.K., Rocha, R.S., Cruz, A.G., Ajlouni, S., Probiotic delivery through fermentation: dairy vs. non-dairy beverages. Fermentation, 3, 2017.
12. Lagier, J.C., Dubourg, G., Million, M., Cadoret, F., Bilen, M., Fenollar, F., Levasseur, A., Rolain, J.M., Fournier, P.E., Raoult, D., Culturing the human microbiota and culturomics. Nat Rev Microbiol 16 (2018), 540–550.
13. Sarhan, M.S., Hamza, M.A., Youssef, H.H., Patz, S., Becker, M., ElSawey, H., Nemr, R., Daanaa, H.S.A., Mourad, E.F., Morsi, A.T., et al. Culturomics of the plant prokaryotic microbiome and the dawn of plant-based culture media – a review. J Adv Res 19 (2019), 15–27.
14. Singhal, N., Kumar, M., Kanaujia, P.K., Virdi, J.S., MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis. Front Microbiol, 6, 2015.
15. Forde, B.M., O'Toole, P.W., Next-generation sequencing technologies and their impact on microbial genomics. Brief Funct Genomics 12 (2013), 440–453, 10.1093/bfgp/els062.
16. Wittouck, S., Wuyts, S., Meehan, C.J., van Noort, V., Lebeer, S., A genome-based species taxonomy of the Lactobacillus genus complex. mSystems 4 (2019), e00264–19.
17. Wuyts, S., Wittouck, S., De Boeck, I., Allonsius, C.N., Pasolli, E., Segata, N., Lebeer, S., Large-scale phylogenomics of the Lactobacillus casei group highlights taxonomic inconsistencies and reveals novel clade-associated features. mSystems 2 (2017), e00061–17.
18. Lebeer, S., Bron, P.A., Marco, M.L., Van Pijkeren, J.-P., O’ M, Motherway, C., Hill, C., Pot, B., Roos, S., Klaenhammer, T., et al. Identification of probiotic effector molecules: present state and future perspectives. Curr Opin Biotechnol 49 (2018), 217–223.
19. Kleerebezem, M., Binda, S., Bron, P.A., Gross, G., Hill, C., van Hylckama Vlieg, J.E., Lebeer, S., Satokari, R., Ouwehand, A.C., Understanding mode of action can drive the translational pipeline towards more reliable health benefits for probiotics. Curr Opin Biotechnol 56 (2019), 55–60.
20. Liu, B., Zheng, D., Jin, Q., Chen, L., Yang, J., VFDB 2019: a comparative pathogenomic platform with an interactive web interface. Nucleic Acids Res 47 (2019), D687–D692.
21. Jia, B., Raphenya, A.R., Alcock, B., Waglechner, N., Guo, P., Tsang, K.K., Lago, B.A., Dave, B.M., Pereira, S., Sharma, A.N., et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res 45 (2017), D566–D573.
22. De Boeck, I., van den Broek, M.F.L., Allonsius, C.N., Martens, K., Wuyts, S., Wittouck, S., Cauwenberghs, E., Jokicevic, K., Vandenheuvel, D., Spacova, I., et al. Lactobacilli have a niche in the human nose. SSRN Electron J, 2019, 10.2139/ssrn.3422481.
23. EFSA, Guidance on the assessment of bacterial susceptibility to antimicrobials of human and veterinary importance. EFSA J, 10, 2012.
24. Alakomi, H., Skyttä, E., Saarela, M., Helander, I.M., Lactic acid permeabilizes gram-negative bacteria by disrupting the outer membrane. Appl Environ Microbiol 66 (2005), 2000–2005.
25. De Keersmaecker, S.C.J., Verhoeven, T.L.A., Desair, J., Marchal, K., Vanderleyden, J., Nagy, I., Strong antimicrobial activity of Lactobacillus rhamnosus GG against Salmonella typhimurium is due to accumulation of lactic acid. FEMS Microbiol Lett 259 (2006), 89–96.
26. van den Broek, M.F.L., De Boeck, I., Claes, I.J.J., Nizet, V., Lebeer, S., Multifactorial inhibition of lactobacilli against the respiratory tract pathogen Moraxella catarrhalis. Benef Microbes 9 (2018), 429–439.
27. Collins, F.W.J., O'Connor, P.M., O'Sullivan, O., Gómez-Sala, B., Rea, M.C., Hill, C., Ross, R.P., Bacteriocin gene-trait matching across the complete Lactobacillus Pan-genome. Sci Rep, 7, 2017 Interesting example of large-scale genomic screening for bacteriocin production, including wet-lab validation.
28. van Heel, A.J., de Jong, A., Song, C., Viel, J.H., Kok, J., Kuipers, O.P., BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins. Nucleic Acids Res 46 (2018), W278–W281.
29. Blin, K., Medema, M.H., Kottmann, R., Lee, S.Y., Weber, T., The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters. Nucleic Acids Res 45 (2017), D555–D559 This database and online tool provide interesting opportunities to screen genomes for microbial secondary metabolites.
30. Kankainen, M., Paulin, L., Tynkkynen, S., von Ossowski, I., Reunanen, J., Partanen, P., Satokari, R., Vesterlund, S., Hendrickx, A.P.A., Lebeer, S., et al. Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein. Proc Natl Acad Sci U S A 106 (2009), 17193–17198.
31. Lebeer, S., Claes, I., Tytgat, H.L.P., Verhoeven, T.L.A., Marien, E., von Ossowski, I., Reunanen, J., Palva, A., de Vos, W.M., De Keersmaecker, S.C.J., et al. Functional analysis of Lactobacillus rhamnosus GG pili in relation to adhesion and immunomodulatory interactions with intestinal epithelial cells. Appl Environ Microbiol 78 (2012), 185–193.
32. Petrova, M.I., Lievens, E., Verhoeven, T.L.A., Macklaim, J.M., Gloor, G., Schols, D., Vanderleyden, J., Reid, G., Lebeer, S., The lectin-like protein 1 in Lactobacillus rhamnosus GR-1 mediates tissue-specific adherence to vaginal epithelium and inhibits urogenital pathogens. Sci Rep, 6, 2016, 37437.
33. Fimereli, D.K., Tsirigos, K.D., Litou, Z.I., Liakopoulos, T.D., Bagos, P.G., Hamodrakas, S.J., CW-PRED: A HMM-based method for the classification of cell wall-anchored proteins of Gram-positive bacteria. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2012.
34. Jones, P., Binns, D., Chang, H.Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G., et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30 (2014), 1236–1240.
35. Sun, Z., Harris, H.M.B., McCann, A., Guo, C., Argimón, S., Zhang, W., Yang, X., Jeffery, I.B., Cooney, J.C., Kagawa, T.F., et al. Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera. Nat Commun, 6, 2015, 8322.
36. Douillard, F.P., Mora, D., Eijlander, R.T., Wels, M., de Vos, W.M., Comparative genomic analysis of the multispecies probiotic-marketed product VSL3. PLoS One, 13, 2018, e0192452.
37. Zhang, H., Yohe, T., Huang, L., Entwistle, S., Wu, P., Yang, Z., Busk, P.K., Xu, Y., Yin, Y., dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 46 (2018), W95–W101.
38. Maldonado-Barragán, A., Caballero-Guerrero, B., Lucena-Padrós, H., Ruiz-Barba, J.L., Induction of bacteriocin production by coculture is widespread among plantaricin-producing Lactobacillus plantarum strains with different regulatory operons. Food Microbiol 33 (2013), 40–47.
39. Allonsius, C.N., Vandenheuvel, D., Oerlemans, E.F.M., Petrova, M.I., Donders, G.G.G., Cos, P., Delputte, P., Lebeer, S., Inhibition of Candida albicans morphogenesis by chitinase from Lactobacillus rhamnosus GG. Sci Rep, 9, 2019.
40. Clua, P., Kanmani, P., Zelaya, H., Tada, A., Humayun Kober, A.K.M., Salva, S., Alvarez, S., Kitazawa, H., Villena, J., Peptidoglycan from immunobiotic Lactobacillus rhamnosus improves resistance of infant mice to respiratory syncytial viral infection and secondary pneumococcal pneumonia. Front Immunol, 8, 2017.
41. Riehl, T.E., Alvarado, D., Ee, X., Zuckerman, A., Foster, L., Kapoor, V., Thotala, D., Ciorba, M.A., Stenson, W.F., Lactobacillus rhamnosus GG protects the intestinal epithelium from radiation injury through release of lipoteichoic acid, macrophage activation and the migration of mesenchymal stem cells. Gut 68 (2019), 1003–1013.
42. Malamud, M., Carasi, P., Assandri, M.H., Freire, T., Lepenies, B., De Los Ángeles Serradell, M., S-Layer glycoprotein from Lactobacillus kefiri exerts its immunostimulatory activity through glycan recognition by mincle. Front Immunol, 10, 2019.
43. Tytgat, H.L.P., van Teijlingen, N.H., Sullan, R.M.A., Douillard, F.P., Rasinkangas, P., Messing, M., Reunanen, J., Satokari, R., Vanderleyden, J., Dufrêne, Y.F., et al. Probiotic gut microbiota isolate interacts with dendritic cells via glycosylated heterotrimeric pili. PLoS One, 11, 2016, e0151824.
44. Lebeer, S., Vanderleyden, J., De Keersmaecker, S.C.J., Host interactions of probiotic bacterial surface molecules: comparison with commensals and pathogens. Nat Rev Microbiol 8 (2010), 171–184.
45. Latousakis, D., Juge, N., How sweet are our gut beneficial bacteria? A focus on protein glycosylation in Lactobacillus. Int J Mol Sci, 19, 2018.
46. Vargas García, C.E., Petrova, M., Claes, I.J.J., De Boeck, I., Verhoeven, T.L.A., Dilissen, E., von Ossowski, I., Palva, A., Bullens, D.M., Vanderleyden, J., et al. Piliation of Lactobacillus rhamnosus GG promotes adhesion, phagocytosis, and cytokine modulation in macrophages. Appl Environ Microbiol 81 (2015), 2050–2062.
47. Özçam, M., Tocmo, R., Oh, J.H., Afrazi, A., Mezrich, J.D., Roos, S., Claesen, J., van Pijkeren, J.P., Gut symbionts Lactobacillus reuteri R2lc and 2010 encode a polyketide synthase cluster that activates the mammalian aryl hydrocarbon receptor. Appl Environ Microbiol, 85, 2019.
48. Qi, H., Li, Y., Yun, H., Zhang, T., Huang, Y., Zhou, J., Yan, H., Wei, J., Liu, Y., Zhang, Z., et al. Lactobacillus maintains healthy gut mucosa by producing L-ornithine. Commun Biol, 2, 2019.
49. Peters, A., Krumbholz, P., Jäger, E., Heintz-Buschart, A., Çakir, M.V., Rothemund, S., Gaudl, A., Ceglarek, U., Schöneberg, T., Stäubert, C., Metabolites of lactic acid bacteria present in fermented foods are highly potent agonists of human hydroxycarboxylic acid receptor 3. PLoS Genet, 15, 2019 Detailed study on how metabolites of fermented food microbes can exert immunomodulatory interactions.
50. Wuyts, S., Allonsius, C.N., Wittouck, S., Thys, S., Lievens, B., Weckx, S., De Vuyst, L., Sarah, L., Comparative genome analysis of Lactobacillus mudanjiangensis, an understudied member of the Lactobacillus plantarum group. Microb Genomics, 5, 2019, e000286, 10.1099/mgen.0.000286.
51. Tytgat, H.L.P., Lebeer, S., The sweet tooth of bacteria: common themes in bacterial glycoconjugates. Microbiol Mol Biol Rev 78 (2014), 372–417.
52. Zeidan, A.A., Poulsen, V.K., Janzen, T., Buldo, P., Derkx, P.M.F., Øregaard, G., Neves, A.R., Polysaccharide production by lactic acid bacteria: from genes to industrial applications. FEMS Microbiol Rev 41 (2017), S168–S200.
53. Subathra Devi, C., Reddy, S., Mohanasrinivasan, V., Fermentative production of dextran using Leuconostoc spp. isolated from fermented food products. Front Biol (Beijing) 9 (2014), 244–253.
54. Lombard, V., Golaconda Ramulu, H., Drula, E., Coutinho, P.M., Henrissat, B., The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 42 (2014), D490–D495.
55. Gu, C.T., Li, C.Y., Yang, L.J., Huo, G.C., Lactobacillus mudanjiangensis sp. nov., Lactobacillus songhuajiangensis sp. nov. and Lactobacillus nenjiangensis sp. nov., isolated from Chinese traditional pickle and sourdough. Int J Syst Evol Microbiol 63 (2013), 4698–4706.
56. Majcherczyk, J., Surówka, K., Effects of onion or caraway on the formation of biogenic amines during sauerkraut fermentation and refrigerated storage. Food Chem, 298, 2019.
57. Nilsson, B.O., Persson, L., Beneficial effects of spermidine on cardiovascular health and longevity suggest a cell type-specific import of polyamines by cardiomyocytes. Biochem Soc Trans 47 (2018), 265–272.
58. Thomas, C.M., Hong, T., Pijkeren, J.P., van, Hemarajata, P., Trinh, D.V., Hu, W., Britton, R.A., Kalkum, M., Versalovic, J., Histamine derived from probiotic Lactobacillus reuteri suppresses TNF via Modulation of PKA and ERK Signaling. PLoS One, 7, 2012.