Pretorius, I. S. Tasting the terroir of wine yeast innovation. FEMS Yeast Res. https://doi.org/10.1093/femsyr/foz084 (2020).
Bartle, L., Sumby, K., Sundstrom, J. & Jiranek, V. The microbial challenge of winemaking: yeast-bacteria compatibility. FEMS Yeast Res. https://doi.org/10.1093/femsyr/foz040 (2019).
Fleet, G. H. Yeast interactions and wine flavour. Int. J. Food Microbiol. 86, 11–22 (2003).
Google Scholar
Denby, C. M. et al. Industrial brewing yeast engineered for the production of primary flavor determinants in hopped beer. Nat. Commun. 9, 965 (2018).
Google Scholar
Lee, D., Lloyd, N. D., Pretorius, I. S. & Borneman, A. R. Heterologous production of raspberry ketone in the wine yeast Saccharomyces cerevisiae via pathway engineering and synthetic enzyme fusion. Microbial Cell Factories 15, 49 (2016).
Google Scholar
Timmins, J. B., Kroukamp, H., Paulsen, I. T. & Pretorius, I. S. The sensory significance of apocarotenoids in wine: importance of carotenoid cleavage dioxygenase 1 (CCD1) in the production of beta-ionone. Molecules https://doi.org/10.3390/molecules25122779 (2020).
Goold, H. D. et al. Yeast’s balancing act between ethanol and glycerol production in low-alcohol wines. Microb. Biotechnol. 10, 264–278 (2017).
Google Scholar
Conacher, C. G. et al. The ecology of wine fermentation: a model for the study of complex microbial ecosystems. Appl. Microbiol. Biotechnol. 105, 3027–3043 (2021).
Google Scholar
McCarty, N. S. & Ledesma-Amaro, R. Synthetic biology tools to engineer microbial communities for biotechnology. Trends Biotechnol. 37, 181–197 (2019).
Google Scholar
Stovicek, V., Borodina, I. & Forster, J. CRISPR-Cas system enables fast and simple genome editing of industrial saccharomyces cerevisiae strains. Metabolic Eng. Commun. 2, 13–22 (2015).
Brenner, K., You, L. & Arnold, F. H. Engineering microbial consortia: a new frontier in synthetic biology. Trends Biotechnol. 26, 483–489 (2008).
Google Scholar
Tsoi, R. et al. Metabolic division of labor in microbial systems. Proc. Natl Acad. Sci. USA 115, 2526–2531 (2018).
Google Scholar
Hays, S. G., Patrick, W. G., Ziesack, M., Oxman, N. & Silver, P. A. Better together: engineering and application of microbial symbioses. Curr. Opin. Biotechnol. 36, 40–49 (2015).
Google Scholar
Zhou, K., Qiao, K., Edgar, S. & Stephanopoulos, G. Distributing a metabolic pathway among a microbial consortium enhances production of natural products. Nat. Biotechnol. 33, 377–383 (2015).
Google Scholar
Conacher, C. G., Naidoo-Blassoples, R. K., Rossouw, D. & Bauer, F. F. Real-time monitoring of population dynamics and physical interactions in a synthetic yeast ecosystem by use of multicolour flow cytometry. Appl. Microbiol. Biotechnol. 104, 5547–5562 (2020).
Google Scholar
Vega, N. M. & Gore, J. Simple organizing principles in microbial communities. Curr. Opin. Microbiol. 45, 195–202 (2018).
Google Scholar
Ratzke, C., Barrere, J. & Gore, J. Strength of species interactions determines biodiversity and stability in microbial communities. Nat. Ecol. Evol. 4, 376–383 (2020).
Google Scholar
Gorter, F. A., Manhart, M. & Ackermann, M. Understanding the evolution of interspecies interactions in microbial communities. Phil. Trans. R. Soc. B. 375, 20190256 (2020).
Google Scholar
Rodriguez-Verdugo, A. & Ackermann, M. Rapid evolution destabilizes species interactions in a fluctuating environment. ISME J. 15, 450–460 (2021).
Google Scholar
Avramova, M. et al. Brettanomyces bruxellensis population survey reveals a diploid–triploid complex structured according to substrate of isolation and geographical distribution. Sci. Rep. 8, 4136 (2018).
Google Scholar
Du Toit, M. & Pretorius, I. Microbial spoilage and preservation of wine: using weapons from nature’s own arsenal—a review. S. Afr. J. Enol. Vitic. 21, 74–96 (2000).
Mannazzu, I. et al. Yeast killer toxins: from ecological significance to application. Crit. Rev. Biotechnol. 39, 603–617 (2019).
Google Scholar
Chessa, R. et al. Biotechnological exploitation of Tetrapisispora phaffii killer toxin: heterologous production in Komagataella phaffii (Pichia pastoris). Appl. Microbiol. Biotechnol. 101, 2931–2942 (2017).
Google Scholar
Schoeman, H., Vivier, M. A., Du Toit, M., Dicks, L. M. & Pretorius, I. S. The development of bactericidal yeast strains by expressing the Pediococcus acidilactici pediocin gene (pedA) in Saccharomyces cerevisiae. Yeast 15, 647–656 (1999).
Google Scholar
Borrero, J. et al. Cloning, production, and functional expression of the bacteriocin enterocin A, produced by Enterococcus faecium T136, by the yeasts Pichia pastoris, Kluyveromyces lactis, Hansenula polymorpha, and Arxula adeninivorans. Appl. Environ. Microbiol. 78, 5956–5961 (2012).
Google Scholar
Jayaraman, P., Holowko, M. B., Yeoh, J. W., Lim, S. & Poh, C. L. Repurposing a two-component system-based biosensor for the killing of Vibrio cholerae. ACS Synth. Biol. 6, 1403–1415 (2017).
Google Scholar
Shaw, W. M. et al. Engineering a model cell for rational tuning of GPCR signaling. Cell 177, 782–796.e727 (2019).
Google Scholar
Ostrov, N. et al. A modular yeast biosensor for low-cost point-of-care pathogen detection. Sci. Adv. 3, e1603221 (2017).
Google Scholar
Meng, Q. et al. Optimization of electrotransformation parameters and engineered promoters for Lactobacillus plantarum from wine. ACS Synthetic Biology 10, 1728–1738 (2021).
Google Scholar
Badura, J. et al. Development of genetic modification tools for Hanseniaspora uvarum. Int. J. Mol. Sci. https://doi.org/10.3390/ijms22041943 (2021).
Avbelj, M., Zupan, J. & Raspor, P. Quorum-sensing in yeast and its potential in wine making. Appl. Microbiol. Biotechnol. 100, 7841–7852 (2016).
Google Scholar
Volschenk, H., Viljoen-Bloom, M., Subden, R. E. & van Vuuren, H. J. Malo-ethanolic fermentation in grape must by recombinant strains of Saccharomyces cerevisiae. Yeast 18, 963–970 (2001).
Google Scholar
Carpenter, A. C., Paulsen, I. T. & Williams, T. C. Blueprints for biosensors: Design, limitations, and application. Genes https://doi.org/10.3390/genes9080375 (2018).
Krstic, M. P., Johnson, D. L. & Herderich, M. J. Review of smoke taint in wine: smoke-derived volatile phenols and their glycosidic metabolites in grapes and vines as biomarkers for smoke exposure and their role in the sensory perception of smoke taint. Aust. J. Grape Wine Res. 21, 537–553 (2015).
Google Scholar
Morcillo-Parra, M. Á., Beltran, G., Mas, A. & Torija, M.-J. Determination of melatonin by a whole cell bioassay in fermented beverages. Sci. Rep. 9, 9120 (2019).
Google Scholar
Dixon, T. A., Williams, T. C. & Pretorius, I. S. Bioinformational trends in grape and wine biotechnology. Trends Biotechnol. https://doi.org/10.1016/j.tibtech.2021.05.001 (2021).
Dixon, T. A., Williams, T. C. & Pretorius, I. S. Sensing the future of bio-informational engineering. Nat. Commun. 12, 388 (2021).
Google Scholar
Hardin, G. The competitive exclusion principle. Science 131, 1292–1297 (1960).
Google Scholar
Grandel, N. E., Reyes Gamas, K. & Bennett, M. R. Control of synthetic microbial consortia in time, space, and composition. Trends Microbiol. https://doi.org/10.1016/j.tim.2021.04.001 (2021).
Johns, N. I., Blazejewski, T., Gomes, A. L. & Wang, H. H. Principles for designing synthetic microbial communities. Curr. Opin. Microbiol. 31, 146–153 (2016).
Google Scholar
Chen, M.-T. & Weiss, R. Artificial cell–cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana. Nat. Biotechnol. 23, 1551–1555 (2005).
Google Scholar
Khakhar, A., Bolten, N. J., Nemhauser, J. & Klavins, E. Cell–cell communication in yeast using auxin biosynthesis and auxin responsive CRISPR transcription factors. ACS Synth. Biol. 5, 279–286 (2016).
Google Scholar
Hennig, S. et al. New approaches in bioprocess-control: consortium guidance by synthetic cell–cell communication based on fungal pheromones. Eng. Life Sci. 18, 387–400 (2018).
Google Scholar
Williams, T. C. et al. Quorum-sensing linked RNA interference for dynamic metabolic pathway control in Saccharomyces cerevisiae. Metab. Eng. 29, 124–134 (2015).
Google Scholar
Billerbeck, S. et al. A scalable peptide–GPCR language for engineering multicellular communication. Nat. Commun. 9, 5057 (2018).
Google Scholar
Hennig, S., Clemens, A., Rödel, G. & Ostermann, K. A yeast pheromone-based inter-species communication system. Appl. Microbiol. Biotechnol. 99, 1299–1308 (2015).
Google Scholar
Terrell, J. L. et al. Bioelectronic control of a microbial community using surface-assembled electrogenetic cells to route signals. Nat. Nanotechnol. 16, 688–697 (2021).
Google Scholar
Tschirhart, T. et al. Electronic control of gene expression and cell behaviour in Escherichia coli through redox signalling. Nat. Commun. 8, 14030 (2017).
Google Scholar
Milias-Argeitis, A., Rullan, M., Aoki, S. K., Buchmann, P. & Khammash, M. Automated optogenetic feedback control for precise and robust regulation of gene expression and cell growth. Nat. Commun. 7, 12546 (2016).
Google Scholar
Lalwani, M. A., Kawabe, H., Mays, R. L., Hoffman, S. M. & Avalos, J. L. Optogenetic control of microbial consortia populations for chemical production. ACS Synth. Biol. 10, 2015–2029 (2021).
Google Scholar
Bhokisham, N. et al. A redox-based electrogenetic CRISPR system to connect with and control biological information networks. Nat. Commun. 11, 2427 (2020).
Google Scholar
Dozon, N. M. & Noble, A. C. Sensory study of the effect of fluorescent light on a sparkling wine and its base wine. Am. J. Enol. Viticult. 40, 265 (1989).
Shou, W., Ram, S. & Vilar, J. M. Synthetic cooperation in engineered yeast populations. Proc. Natl Acad. Sci. USA 104, 1877–1882 (2007).
Google Scholar
Rovner, A. J. et al. Recoded organisms engineered to depend on synthetic amino acids. Nature 518, 89–93 (2015).
Google Scholar
Biava, H. D. Tackling Achilles’ heel in synthetic biology: pairing intracellular synthesis of noncanonical amino acids with genetic-code expansion to foster biotechnological applications. ChemBioChem 21, 1265–1273 (2020).
Google Scholar
Yang, Y., Nemhauser, J. L. & Klavins, E. Synthetic bistability and differentiation in yeast. ACS Synth. Biol. 8, 929–936 (2019).
Google Scholar
Aditya, C., Bertaux, F., Batt, G. & Ruess, J. A light tunable differentiation system for the creation and control of consortia in yeast. Nat. Commun. 12, 5829 (2021).
Google Scholar
Del Vecchio, D., Dy, A. J. & Qian, Y. Control theory meets synthetic biology. J. Roy. Soc. Interface https://doi.org/10.1098/rsif.2016.0380 (2021).
Perrino, G., Hadjimitsis, A., Ledesma-Amaro, R. & Stan, G. B. Control engineering and synthetic biology: working in synergy for the analysis and control of microbial systems. Curr. Opin. Microbiol. 62, 68–75 (2021).
Google Scholar
Markley, L. & Crassidis, J. Fundamentals of Spacecraft Attitude Determination and Control (Springer, 2014).
Briat, C., Gupta, A. & Khammash, M. Antithetic integral feedback ensures robust perfect adaptation in noisy biomolecular networks. Cell Systems 2, 15–26 (2016).
Google Scholar
Lindemann, S. R. et al. Engineering microbial consortia for controllable outputs. ISME J. 10, 2077–2084 (2016).
Google Scholar
Fedorec, A. J. H., Karkaria, B. D., Sulu, M. & Barnes, C. P. Single strain control of microbial consortia. Nat. Commun. 12, 1977 (2021).
Google Scholar
Swiegers, J. H. & Pretorius, I. S. Modulation of volatile sulfur compounds by wine yeast. Appl. Microbiol. Biotechnol. 74, 954–960 (2007).
Google Scholar
Bell, S.-J. & Henschke, P. A. Implications of nitrogen nutrition for grapes, fermentation and wine. Aust. J. Grape Wine Res. 11, 242–295 (2005).
Google Scholar
Pretorius, I. S. Conducting wine symphonics with the aid of yeast genomics. Beverages https://doi.org/10.3390/beverages2040036 (2016).
Det-udom, R. et al. Towards semi-synthetic microbial communities: enhancing soy sauce fermentation properties in B. subtilis co-cultures. Microb. Cell Fact. 18, 101 (2019).
Google Scholar

