Seeding the idea of encapsulating a representative synthetic metagenome in a single yeast cell

Belda, Ignacio; Williams, Thomas; Celis, Miguel de; Paulsen, Ian T.; Pretorius, Isak S.

doi:10.1038/s41467-021-21877-y

Cited by 13 publications

(16 citation statements)

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“…Though we may solve today's urgent problems based on yesterday's scientific discoveries, we cannot solve today's problems with yesterday's thinking. To be forward-thinking, we have a responsibility to imagine future challenges and potential solutions alongside new opportunities and possible benefits to producers and consumers alike [21][22][23]. In this context, our contention here is that the convergence of information technology and synthetic biology will enable the translation of bioinformational data into practical applications that would assist with the mitigation of future risks, finding solutions to unforeseen challenges and creating new opportunities for the global grape and wine industry.…”

Section: Glossarymentioning

confidence: 99%

“…Across the longer term, the data availability heuristic could facilitate bioinformation being stored and accessed in biological substrates. With the building of the first synthetic yeast genome nearing finalisation [36], a key example here is the idea of a synthetic metagenome, or the concept of a ready-to-use 'ecosystem in a cell' [21]. A synthetic yeast metagenome could theoretically store a representation of the yeast ecology of a local terroir within a single synthetic organism, Saccharomyces cerevisiae.…”

Section: Trends Trends In In Biotechnology Biotechnologymentioning

confidence: 99%

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Bioinformational trends in grape and wine biotechnology

Dixon

Williams

Pretorius

2022

Trends in Biotechnology

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The creative destruction caused by the coronavirus pandemic is yielding immense opportunity for collaborative innovation networks. The confluence of biosciences, information sciences, and the engineering of biology, is unveiling promising bioinformational futures for a vibrant and sustainable bioeconomy. Bioinformational engineering, underpinned by DNA reading, writing, and editing technologies, has become a beacon of opportunity in a world paralysed by uncertainty. This article draws on lessons from the current pandemic and previous agricultural blights, and explores bioinformational research directions aimed at future-proofing the grape and wine industry against biological shocks from global blights and climate change. The shock and awe of the pandemic's creative destructionThe years of global pandemic outbreaks, 1346, 1918, and 2020, loom large in history because these low-probability, high-impact disasters have devastating impacts on people's lives with tranquilising effects on society as a whole. In this regard, the 2020 coronavirus outbreak was no less damaging than previous once-in-a-century pandemics, global blights (see Glossary), and other catastrophes. This paper explores the future of grape and wine biotechnology with future global biological shocks in mind. These shocks include both the potential for global blights but also the disruptive potential of climate change. It is important to note that these two shocks combine in a layered manner; temperature change combined with existing land use patterns can contribute to the likelihood of a new global blight emerging. COVID-19 exemplifies the power of a global biological shock. The virus has infected millions of people and reset the trajectory of macro political, economic, sociological, technological, legal, and environmental (PESTLE) forces that shape the modern world. Such powerful forces are of course not solely the province of human biological shocks, and global blights harbour similar levels of disruptive potential. This paper explores the emerging science and technologies that might mitigate the risks of a global blight in the grape and wine sector. HighlightsUncertainty caused by pandemics, global blights, and climate change, tends to heighten the focus on how biotechnological advances can mitigate challenges to public safety, cyberbio resilience, environmental sustainability, and bioeconomic security.Convergence of cyberbio technologies and high-throughput automation in biofoundries offers future-shaping bioinformational engineering opportunities with transformational potential to the wine industry.Consumer preferences, biosecurity, and bioethical considerations, must guide research directions and adoption of new bioinformational engineering technologies at the levels of both problem selection and experimental design.

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Section: Glossarymentioning

confidence: 99%

Section: Trends Trends In In Biotechnology Biotechnologymentioning

confidence: 99%

Bioinformational trends in grape and wine biotechnology

Dixon

Williams

Pretorius

2022

Trends in Biotechnology

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“…Given the impact of seasonal weather conditions and other environmental factors, it is less complicated to test the aforementioned conceptual framework in a more controlled model system, such as an uninoculated wine fermentation. A spontaneous wine fermentation represents an ephemeral microbial ecosystem, defined by a deterministic microbial succession where a keystone species, S. cerevisiae , will ultimately become the dominant species (Belda et al 2021 ). Using fermenting grape must as a model ecological system has the advantage that fermentation conditions can be controlled and the keystone species is a well-studied model organism.…”

Section: Synthetic Metagenomes Encapsulating Ecosystems In a Cellmentioning

confidence: 99%

“…With the creation of a physiologically fit Sc2.0 strain nearing completion, it might be possible to move our research from a synthetic S. cerevisiae genome to the de novo synthesis of metagenomes that represent a whole yeast community in spontaneously fermenting grape must. Recently, the idea of encapsulating a representative synthetic metagenome in a single cell was proposed (Belda et al 2021 ). This idea is not without risks, limitations, and challenges.…”

Section: Synthetic Metagenomes Encapsulating Ecosystems In a Cellmentioning

confidence: 99%

Visualizing the next frontiers in wine yeast research

Pretorius

2022

FEMS Yeast Research

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A range of game-changing biodigital and biodesign technologies are coming of age all around us, transforming our world in complex ways that are hard to predict. Not a day goes by without news of how data-centric engineering, algorithm-driven modelling and biocyber technologies—including the convergence of artificial intelligence, machine learning, automated robotics, quantum computing, and genome editing—will change our world. If we are to be better at expecting the unexpected in the world of wine, we need to gain deeper insights into the potential and limitations of these technological developments and advances along with their promise and perils. This article anticipates how these fast-expanding bioinformational and biodesign toolkits might lead to the creation of synthetic organisms and model systems, and ultimately new understandings of biological complexities could be achieved. Four future frontiers in wine yeast research are discussed in this article: the construction of fully synthetic yeast genomes, including minimal genomes; supernumerary pan-genome neochromosomes; synthetic metagenomes; and synthetic yeast communities. These four concepts are at varying stages of development with plenty of technological pitfalls to overcome before such model chromosomes, genomes, strains and yeast communities could illuminate some of the ill-understood aspects of yeast resilience, fermentation performance, flavour biosynthesis, and ecological interactions in vineyard and winery settings. From a winemaker's perspective, some of these ideas might be considered as far-fetched and, as such, tempting to ignore. However, synthetic biologists know that by exploring these futuristic concepts in the laboratory could well forge new research frontiers to deepen our understanding of the complexities of consistently producing fine wines with different fermentation processes from distinctive viticultural terroirs. As the saying goes in the disruptive technology industry, it take years to create an overnight success. The purpose of this article is neither to glorify any of these concepts as a panacea to all ills nor to crucify them as a danger to winemaking traditions. Rather, this article suggests that these proposed research endeavours deserve due consideration because they are likely to cast new light on the genetic blind spots of wine yeasts and how they interact as communities in vineyards and wineries. Future-focussed research is, of course, designed to be subject to revision as new data and technologies become available. Successful dislodging of old paradigms with transformative innovations will require open-mindedness and pragmatism, not dogmatism―and this can make for a catch-22 situation in an archetypal traditional industry, such as the wine industry, with its rich territorial and socio-cultural connotations.

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“…Minor metagenomes can be customized by including specific transcripts or sequence variants serving specific purposes. Synthetic metagenomics could be used to gather metabolic networks from various members into a single yeast species, then used as a chassis (Belda et al, 2021). Systems and synthetic biology could be used to enhance KMC's biotechnological features.…”

Section: Perspectivesmentioning

confidence: 99%

To Other Planets With Upgraded Millennial Kombucha in Rhythms of Sustainability and Health Support

Kozyrovska

Reva

Podolich

et al. 2021

Front. Astron. Space Sci.

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Humankind has entered a new era of space exploration: settlements on other planetary bodies are foreseen in the near future. Advanced technologies are being developed to support the adaptation to extraterrestrial environments and, with a view on the longer term, to support the viability of an independent economy. Biological processes will likely play a key role and lead to the production of life-support consumables, and other commodities, in a way that is cheaper and more sustainable than exclusively abiotic processes. Microbial communities could be used to sustain the crews’ health as well as for the production of consumables, for waste recycling, and for biomining. They can self-renew with little resources from Earth, be highly productive on a per-volume basis, and be highly versatile—all of which will be critical in planetary outposts. Well-defined, semi-open, and stress-resistant microecosystems are particularly promising. An instance of it is kombucha, known worldwide as a microbial association that produces an eponymous, widespread soft drink that could be valuable for sustaining crews’ health or as a synbiotic (i.e., probiotic and prebiotic) after a rational assemblage of defined probiotic bacteria and yeasts with endemic or engineered cellulose producers. Bacterial cellulose products offer a wide spectrum of possible functions, from leather-like to innovative smart materials during long-term missions and future activities in extraterrestrial settlements. Cellulose production by kombucha is zero-waste and could be linked to bioregenerative life support system (BLSS) loops. Another advantage of kombucha lies in its ability to mobilize inorganic ions from rocks, which may help feed BLSS from local resources. Besides outlining those applications and others, we discuss needs for knowledge and other obstacles, among which is the biosafety of microbial producers.

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Seeding the idea of encapsulating a representative synthetic metagenome in a single yeast cell

Cited by 13 publications

References 60 publications

Bioinformational trends in grape and wine biotechnology

Bioinformational trends in grape and wine biotechnology

Visualizing the next frontiers in wine yeast research

To Other Planets With Upgraded Millennial Kombucha in Rhythms of Sustainability and Health Support

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