Overall sensitivity analysis of synthetic co-cultures. Credit: Natural microbiology (2024). DOI: 10.1038/s41564-023-01596-4
Microbes such as bacteria and yeast are increasingly used to produce components of medicines, biofuels and foods. Indeed, baker’s yeast, also called brewer’s yeast or Saccharomyces cerevisiae, is responsible for the fermentation process used in the manufacture of beer or bread, but it is also used on a large scale to produce other valuable molecules for the industry.
Using microbes could be key to producing these materials more sustainably, but there is still much we don’t understand about how microbial communities, particularly yeasts, form and persist.
To answer these questions, researchers at Imperial College London have created a molecular toolbox that uses a new way to produce useful compounds. Their work is published in the journal Natural microbiology.
The toolbox consists of 15 different yeast strains that overproduce key cellular building blocks – amino acids and nucleotides – but lack the ability to make other building blocks. Unlike traditional synthetic biology communities, strains have been divided into “donors” – strains that donate the building blocks of growth to others, and recipients – strains that receive them.
To test the kit, researchers studied the effectiveness of the donor-recipient system on the communities’ ability to produce resveratrol, an antioxidant compound found in red wine, and certain dietary supplements that are being studied for their potential medicinal properties.
Using the new donor-receptor system, the researchers created yeast communities each composed of two or three different strains and observed how they interacted and grew together. The toolkit allowed them to split the resveratrol production pathway in two, placing each half into a selection of donor and recipient yeast strains.
As a control, they also produced resveratrol using standard methods with a single yeast strain.
Effect of varied metabolite supplements and initial cell densities on growth and population size in three-member cocultures. ASchematic of a three-member AKH_III co-culture via one-way communication. b,vsThe growth of co-culture (b) and the population percentage (vs) of each member of the AKH_III co-culture with and without supplementation of exchanged metabolite (em) (mg l−1) at 48 hours. em_0 means no em supplementation; supplementation (final concentration, mg l−1) of ade, Lys, His and Trp were 2.5, 5, 10; 12.5, 25, 50; 10, 20, 40 and 10, 20, 40, respectively. NOT = 3 biologically independent samples and data are presented as mean ± standard deviation. One-way ANOVA, followed by Bonferroni’s multiple comparisons test with 95% confidence intervals, were performed using GraphPad Prism 9.5.0 and P. the values are noted. dSchematic of a three-member co-culture AKW_VI via two-way communication. e,FThe growth of co-culture (e) and the population percentage (F) of each member in AKW_VI co-culture with and without em supplementation at 48 h. NOT = 3 biologically independent samples and data are presented as mean ± standard deviation. One-way ANOVA, followed by Bonferroni’s multiple comparisons test with 95% confidence intervals, were performed using GraphPad Prism 9.5.0 and P. the values are noted. gThe growth curves of AKW_VI co-culture (OD) and the estimated growths of three members, including GOD, BOD and ROD, at different initial cell densities of OD700 0.067, 0.078, 0.102 and 0.148 in 72 hours. OD indicates the total OD700 values of co-culture. GOD, BOD and ROD represent the estimated OD values for the GFP, BFP and RFP labeled populations, respectively. The initial ratio was 1:1:1 for each member of these co-cultures. NOT= 3 biologically independent samples and data are presented as mean ± standard deviation. Credit : Natural microbiology(2024). DOI: 10.1038/s41564-023-01596-4
They then measured the effects of variables such as adding additional nutrients, changing the initial mixture of different yeast strains, and changing cell density on how the communities behaved and how quickly they produced resveratrol.
They found that spitting the path between two yeast strains resulted in increased resveratrol production compared to the traditional production platform. Mathematical modeling showed that the system also enabled more stable and specific partnerships between yeast strains.
Lead author Dr Rodrigo Ledesma-Amaro, from Imperial’s Department of Bioengineering, said: “Our results, if replicated in other yeasts and metabolites, could have a significant impact on how we understand and use microbial communities in sustainable bioproduction, from food to bioproduction. biofuels.”
Although tested so far using one strain producing one compound, the new system could allow researchers to create diverse combinations of yeast communities that work together and make various products more efficiently and sustainably.
The ability to engineer and improve the efficiency of yeast communities could improve our production of pharmaceuticals, food, beverages, bioplastics and biofuels. Efficiency could also lead to less waste, lower energy consumption and lower costs of producing valuable compounds.
First author Dr Huadong Peng, who led the work at Imperial’s Department of Bioengineering, said: “Our study is the first of its kind to use both mathematical modeling and practical experiments to understand how Factors inside and outside yeast cells affect community growth. Our results present exciting possibilities for further study. »
Next, researchers will refine the toolbox and expand its scope to include a broader range of small molecules beyond the current 15 amino acids and nucleotides. They will also extend testing to understand the long-term stability of the kit, which will be essential for practical applications where these communities might be used for extended periods. They will also introduce different types of yeast and monitor for mutations and adaptations that could affect the results.
More information:
Huadong Peng et al, A molecular toolbox of cross-feeding strains for engineering synthetic yeast communities, Natural microbiology(2024). DOI: 10.1038/s41564-023-01596-4
Provided by Imperial College London
Quote: Creating a toolbox of yeast strains that overproduce key cellular building blocks (February 7, 2024) retrieved February 7, 2024 from
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