Periodic Reporting for period 1 - FastMicrobes (Enhancing Industrial Cultivation: A Breakthrough Approach Using Methylated Compounds to Expedite Microbial Growth)
Okres sprawozdawczy: 2024-07-01 do 2025-12-31
Microbial cultivation is essential for producing pharmaceuticals, industrial enzymes, chemicals, and alternative food proteins. However, it remains a major contributor to production costs, with fermentation accounting for 20 to 40% of the final product price. Current optimization strategies mainly focus on improving growth during the exponential phase, while the lag phase, an early adaptation period with little visible growth, is largely overlooked. This is a critical gap, as the lag phase can represent up to 20 percent of total cultivation time and significantly increases costs and energy use.
Recent results from our ERC funded research reveal a previously unknown mechanism that controls the duration of the microbial lag phase. We discovered that adding naturally occurring methylated compounds during this early phase can significantly shorten the time required for microorganisms to begin active growth. Compounds such as choline, betaine, and dimethylsulfoniopropionate are abundant in nature, safe, commercially available, and effective at very low concentrations. Their targeted application creates a metabolic shortcut that allows cells to adapt faster, accelerating growth by up to 10 hours without reducing final yield.
The objective of this project is to translate this breakthrough biological insight into a practical and scalable solution for industrial microbial cultivation. By optimizing the use of methylated compounds in bacteria and yeast and validating their performance under industrially relevant conditions, we aim to reduce cultivation time, improve process efficiency, and lower production costs.
The expected impact is significant. Shortening the lag phase alone can reduce final product costs by an estimated 4 to 8%, and no existing technology directly targets this phase of growth. Given that microbial based industries are projected to reach a global value of 130 to 180 billion dollars by 2030, even modest improvements will have major economic effects. In addition, lower production costs can increase access to affordable medicines, sustainable foods, and bio based products, delivering broad societal and environmental benefits.
Recent results from our ERC funded research reveal a previously unknown mechanism that controls the duration of the microbial lag phase. We discovered that adding naturally occurring methylated compounds during this early phase can significantly shorten the time required for microorganisms to begin active growth. Compounds such as choline, betaine, and dimethylsulfoniopropionate are abundant in nature, safe, commercially available, and effective at very low concentrations. Their targeted application creates a metabolic shortcut that allows cells to adapt faster, accelerating growth by up to 10 hours without reducing final yield.
The objective of this project is to translate this breakthrough biological insight into a practical and scalable solution for industrial microbial cultivation. By optimizing the use of methylated compounds in bacteria and yeast and validating their performance under industrially relevant conditions, we aim to reduce cultivation time, improve process efficiency, and lower production costs.
The expected impact is significant. Shortening the lag phase alone can reduce final product costs by an estimated 4 to 8%, and no existing technology directly targets this phase of growth. Given that microbial based industries are projected to reach a global value of 130 to 180 billion dollars by 2030, even modest improvements will have major economic effects. In addition, lower production costs can increase access to affordable medicines, sustainable foods, and bio based products, delivering broad societal and environmental benefits.
1. The aim of this effort was to test whether methylated compounds that shorten the bacterial lag phase can also reduce the lag phase in yeast, using Saccharomyces cerevisiae as a model organism. We focused on the laboratory strain S288c (ATCC 204508, internal ID yMS1412), a haploid wild type strain without auxotrophies, making it well suited for physiological growth studies.
The strain was revived from a frozen glycerol stock and plated on SD complete agar plates containing yeast nitrogen base with amino acids and 2 percent glucose. Plates were incubated at 30 degrees Celsius for two days. Single colonies were then used to inoculate preculture tubes containing 5 mL of the same medium without agar. These precultures were grown overnight at 30 degrees Celsius until they reached stationary phase, with optical density values around 12.0.
Stationary phase precultures were used to inoculate main cultures at a starting optical density of 0.001. This very low inoculation density was chosen to clearly capture the lag phase and early growth dynamics. Main cultures consisted of yeast nitrogen base without amino acids and were supplemented with a single carbon source. Three carbon sources were tested to cover distinct metabolic states: 5 mM glucose, 5 mM galactose, or 15 mM acetate.
To assess the effect of methylated compounds on yeast growth, cultures were supplemented with one of the following compounds at a final concentration of 10 micromolar: dimethylsulfoniopropionate, betaine, choline, stachydrine (dimethylproline), or S methylmethionine. Water was used as a control. These compounds were selected based on their strong lag phase shortening effects in Phaeobacter inhibens. In addition, S methylmethionine was included because S. cerevisiae encodes a known S methylmethionine demethylase, while no demethylases for the other compounds have been reported in yeast according to BioCyc and KEGG databases.
Results: none of the selected methylated compounds shortened the lag phase in yeast.
2. The aim of this effort was to assess lag phase shortening in E. coli from lab scale cultures to industrial size cultures.
The study was commissioned by Yeda based on preliminary evidence suggesting that certain additives may accelerate early growth of Escherichia coli. The tested organism was E. coli BL21(DE3), a widely used laboratory strain suitable for research and development work
The experimental design involved shake flask cultivation in LB medium, comparing a control condition with six additive supplemented conditions. The additives tested were trigonelline hydrochloride, choline chloride, L carnitine, L carnitine hydrochloride, S methylmethionine, and betaine, all applied at a final concentration of 20 micromolar. Cultures were inoculated from an overnight starter and grown at 37 degrees Celsius with agitation. Optical density at 600 nm was measured every 30 minutes over a six hour period to generate detailed growth curves
The results showed typical bacterial growth behavior, with clearly defined lag, log, and late log phases. However, comparison of growth curves revealed no significant differences in growth rate or lag phase duration between the control and any of the additive treated conditions. All cultures entered exponential growth at similar times and reached comparable optical density values by the end of the experiment
In summary, under the tested conditions, none of the additives produced a measurable effect on the lag phase or growth kinetics of E. coli BL21(DE3). The study confirms the robustness of the experimental setup while indicating that further optimization or alternative conditions may be required to observe lag phase shortening effects.
The strain was revived from a frozen glycerol stock and plated on SD complete agar plates containing yeast nitrogen base with amino acids and 2 percent glucose. Plates were incubated at 30 degrees Celsius for two days. Single colonies were then used to inoculate preculture tubes containing 5 mL of the same medium without agar. These precultures were grown overnight at 30 degrees Celsius until they reached stationary phase, with optical density values around 12.0.
Stationary phase precultures were used to inoculate main cultures at a starting optical density of 0.001. This very low inoculation density was chosen to clearly capture the lag phase and early growth dynamics. Main cultures consisted of yeast nitrogen base without amino acids and were supplemented with a single carbon source. Three carbon sources were tested to cover distinct metabolic states: 5 mM glucose, 5 mM galactose, or 15 mM acetate.
To assess the effect of methylated compounds on yeast growth, cultures were supplemented with one of the following compounds at a final concentration of 10 micromolar: dimethylsulfoniopropionate, betaine, choline, stachydrine (dimethylproline), or S methylmethionine. Water was used as a control. These compounds were selected based on their strong lag phase shortening effects in Phaeobacter inhibens. In addition, S methylmethionine was included because S. cerevisiae encodes a known S methylmethionine demethylase, while no demethylases for the other compounds have been reported in yeast according to BioCyc and KEGG databases.
Results: none of the selected methylated compounds shortened the lag phase in yeast.
2. The aim of this effort was to assess lag phase shortening in E. coli from lab scale cultures to industrial size cultures.
The study was commissioned by Yeda based on preliminary evidence suggesting that certain additives may accelerate early growth of Escherichia coli. The tested organism was E. coli BL21(DE3), a widely used laboratory strain suitable for research and development work
The experimental design involved shake flask cultivation in LB medium, comparing a control condition with six additive supplemented conditions. The additives tested were trigonelline hydrochloride, choline chloride, L carnitine, L carnitine hydrochloride, S methylmethionine, and betaine, all applied at a final concentration of 20 micromolar. Cultures were inoculated from an overnight starter and grown at 37 degrees Celsius with agitation. Optical density at 600 nm was measured every 30 minutes over a six hour period to generate detailed growth curves
The results showed typical bacterial growth behavior, with clearly defined lag, log, and late log phases. However, comparison of growth curves revealed no significant differences in growth rate or lag phase duration between the control and any of the additive treated conditions. All cultures entered exponential growth at similar times and reached comparable optical density values by the end of the experiment
In summary, under the tested conditions, none of the additives produced a measurable effect on the lag phase or growth kinetics of E. coli BL21(DE3). The study confirms the robustness of the experimental setup while indicating that further optimization or alternative conditions may be required to observe lag phase shortening effects.
Key Needs for Further Uptake and Success:
To enable further uptake and eventual industrial success, several needs must be addressed. First, additional research is required to define the biological and environmental conditions under which lag phase shortening occurs, including strain specificity, medium composition, oxygen availability, and inoculation history. Second, systematic demonstration studies are needed in bacterial species and strains that have already shown responsiveness, using pilot scale and industrially relevant fermentation setups. Third, mechanistic understanding should be deepened to enable rational selection of target organisms and compounds, strengthening intellectual property positioning. Finally, engagement with industrial partners will be essential to align experimental design with real world process constraints, facilitate access to markets and finance, and support downstream commercialization.
Overview of Results:
Overall, the project established that the tested methylated compounds did not shorten the lag phase in Saccharomyces cerevisiae or E. coli BL21(DE3) under the examined conditions. These findings refine the scope of the technology, highlight the importance of organism and context specificity, and provide a clear roadmap for focused future development toward bacterial systems where lag phase shortening has already been demonstrated.
To enable further uptake and eventual industrial success, several needs must be addressed. First, additional research is required to define the biological and environmental conditions under which lag phase shortening occurs, including strain specificity, medium composition, oxygen availability, and inoculation history. Second, systematic demonstration studies are needed in bacterial species and strains that have already shown responsiveness, using pilot scale and industrially relevant fermentation setups. Third, mechanistic understanding should be deepened to enable rational selection of target organisms and compounds, strengthening intellectual property positioning. Finally, engagement with industrial partners will be essential to align experimental design with real world process constraints, facilitate access to markets and finance, and support downstream commercialization.
Overview of Results:
Overall, the project established that the tested methylated compounds did not shorten the lag phase in Saccharomyces cerevisiae or E. coli BL21(DE3) under the examined conditions. These findings refine the scope of the technology, highlight the importance of organism and context specificity, and provide a clear roadmap for focused future development toward bacterial systems where lag phase shortening has already been demonstrated.