Technologies for controlling bacterial contamination during fermentation
Summary
We have developed technologies for cost-effective control of bacterial contamination during large-scale yeast fermentation (both aerobic and anaerobic). This is the major problem preventing continuous fermentation using yeast. Instead of adding anti-bacterial substances to a fermenter or using sulfuric acid washes to kill bacteria during yeast recycling, we eliminate nickel leaching and use urea as the sole nitrogen source. Bacteria can’t grow on urea without nickel as a co-factor, but yeasts only need biotin to grow on urea.
This technique allows fermentation without requiring aseptic conditions and is thus much less expensive than traditional fermentation techniques. This also allows continuous fermentation, since aseptic conditions can be ruined by even a single contaminating bacterium.
Example use in Brazil:
This technique can be used in sugarcane ethanol plants in Brazil to improve efficiency, produce more ethanol, reduce foaming and reduce the strong odor from the vinasse.
Minimal changes are needed to integrate our contamination control technique:
Use urea as the only nitrogen source, replacing ammonium sulfate
Use fed-batch feeding of sugars and urea
Make sure heat exchangers use stainless steel grade 316 (not grade 304)
Don’t use acid wash, recycle yeast cream directly from centrifuge
Clean vats with high pressure water spray, without caustic
Without bacterial contamination, contamination by D. bruxellensis and other wild yeasts doesn’t occur when using a fast-growing S. cerevisiae strain like PE-2. Foaming is also reduced because the extracellular protein from Lactobacillus is eliminated.
Eliminating sulfur from the wash and changing ammonium sulfate to urea results in significant reduction of sulfur in the vinasse, which reduces the strong odor from bacteria producing hydrogen sulfide from the vinasse. Not using sulfur dioxide in sugarcane juice clarification can further reduce the strong odor from the vinasse.
Eliminating the sulfuric acid wash eliminates adding soluble calcium sulfate to the distillation columns when recovering ethanol from this wash. Calcium sulfate from the wash also precipitates in the distillation column, causing fouling and requiring more cleaning. This wash water also dilutes the mash being distilled, which increases the energy and time needed for distillation. It’s more efficient to carry this ethanol with the recycled yeast into the next fermentation cycle.
The cost savings are considerable due to reducing the time per batch by 2-4 hours and improving process efficiency.
The Fermentation Cycle in Brazilian Sugarcane Ethanol Production
In Brazil, sugarcane ethanol production typically employs the Melle-Boinot process, a fed-batch fermentation process, which is widely used due to its efficiency and scalability. The process begins with the preparation of a substrate, usually sugarcane juice or molasses, derived from sugarcane processing. This substrate, rich in fermentable sugars like sucrose, glucose, and fructose, is fed into large fermentation vats. The fermentation is carried out by the yeast Saccharomyces cerevisiae, a robust strain well-suited for ethanol production.
Fermentation Phase: The yeast ferments the sugars into ethanol and carbon dioxide over a period typically ranging from 6 to 12 hours, depending on factors like temperature (maintained around 30–34°C), sugar concentration, and yeast activity. The process is "fed-batch," meaning the substrate is added incrementally to avoid overwhelming the yeast with high sugar levels, which could inhibit fermentation.
Harvesting Phase: Once fermentation is complete, the fermented broth (containing ethanol, yeast, water, and residual sugars) is centrifuged. This separates the liquid fraction (called "wine," containing ethanol) from the yeast biomass. The ethanol-rich liquid proceeds to distillation to purify and concentrate the ethanol, while the yeast is collected for reuse.
Yeast Recycling: In the standard process, approximately 90–95% of the centrifuged yeast is recycled to the next fermentation cycle to maintain high productivity and reduce costs. Before recycling, the yeast is often subjected to an acid wash (using sulfuric acid) or a water wash to remove contaminants, particularly bacteria, and to refresh the yeast by reducing the buildup of fermentation byproducts and dead cells.
Vat Cleaning: After each cycle, the fermentation vats are cleaned to remove residues and prevent contamination in the next batch. This cleaning typically involves caustic soda (sodium hydroxide), often heated, to ensure thorough sanitation, followed by rinsing.
This cycle repeats multiple times, leveraging the recycled yeast to maximize efficiency in Brazil’s large-scale ethanol industry, which produces billions of liters annually.
Improvements with No Bacterial Contamination and No Yeast Washing
Now, let’s consider a modified process where no bacterial contamination occurs during fermentation, and no acid or water wash is applied to the centrifuged yeast. Instead, 95% of the yeast is recycled directly without washing. Here’s how this alters and potentially improves the process:
Operational Improvements
Elimination of Ethanol Recovery from Acid Wash:
In the standard process, acid washing the yeast can dilute any residual ethanol clinging to the yeast biomass. This ethanol must be recovered (e.g., via distillation), adding an energy-intensive step. By skipping the wash, no ethanol is lost to a wash solution, eliminating this recovery process and saving energy.
No Acid Neutralization:
Acid washing requires neutralizing the acidic yeast slurry (e.g., with a base like lime) before recycling to avoid harming the yeast or altering the fermentation pH. Skipping the wash eliminates the need for neutralization, reducing chemical inputs, waste treatment, and associated costs.
Simplified Process:
Removing the washing step streamlines operations by reducing the number of unit processes, lowering labor, equipment maintenance, and water usage.
These changes enhance plant efficiency by cutting energy, chemical, and operational expenses.
Equilibrium Concentration of Metabolites and Dead Cells
Without washing, the recycled yeast carries over fermentation metabolites (e.g., organic acids like acetic acid, glycerol, and higher alcohols) and weak or dead yeast cells into each new cycle. Here’s how this stabilizes:
Accumulation: Initially, the concentrations of these components increase with each cycle as 95% of the yeast, including its metabolites and dead cells, is reused.
Removal and Dilution:
5% Yeast Loss: The 5% of yeast not recycled (discarded or lost) removes a small fraction of these components from the system.
Fresh Substrate Addition: Each cycle introduces fresh sugarcane juice or molasses, diluting the metabolite concentration in the fermentation broth.
Equilibrium: Over multiple cycles, an equilibrium concentration is reached where the rate of metabolite production and dead cell accumulation equals their removal (via the 5% yeast loss) and dilution (via fresh substrate). This equilibrium level would be higher than in a washed-yeast system, where washing removes some metabolites and dead cells each cycle. However, since Saccharomyces cerevisiae is tolerant to many of its own byproducts (up to certain thresholds), and no bacterial competition exists, this higher concentration is manageable without significantly impairing fermentation efficiency.
Quantitatively, this equilibrium depends on fermentation conditions (e.g., sugar concentration, cycle duration), but qualitatively, it stabilizes at a level reflecting the balance of production, loss, and dilution.
Cycle Time Improvement with Water-Washed Vats
Finally, consider how not washing the yeast improves the overall cycle time when fermentation vats are cleaned with water instead of caustic:
Standard Cycle Time Components:
Fermentation: 6–12 hours.
Harvesting (centrifugation): ~1–2 hours.
Yeast Washing: In the standard process, acid or water washing, neutralization, and rinsing add 1–2 hours (depending on scale and method).
Vat Cleaning: Caustic cleaning, often heated and followed by rinsing, takes 2–3 hours or more.
Modified Process:
No Yeast Washing: Eliminating the washing step saves 1–2 hours per cycle. After centrifugation, the yeast is immediately recycled, cutting a significant preparation step.
Water-Washed Vats: Cleaning vats with water instead of caustic is faster—potentially reducing cleaning time to 1–2 hours—since it avoids heating, prolonged chemical exposure, and extensive rinsing. Water suffices here because bacterial contamination is absent, and the goal is simply to remove physical residues (yeast, sugars) rather than sanitize deeply.
Combined Effect: Without yeast washing, the time between fermentation cycles shrinks directly. Pairing this with quicker water-based vat cleaning further shortens the downtime, allowing cycles to restart sooner. For example, a cycle that took 12–15 hours (fermentation + harvesting + washing + caustic cleaning) could drop to 10–12 hours, boosting throughput.
The absence of bacterial contamination enables these simplifications without risking fermentation performance, as bacteria—typically controlled by acid washing and caustic cleaning—are not a factor.
Conclusion
In Brazilian sugarcane ethanol production, the standard fed-batch fermentation cycle involves fermenting sugarcane juice or molasses with Saccharomyces cerevisiae, followed by centrifugation, yeast washing, and vat cleaning with caustic. When no bacterial contamination occurs and 95% of the centrifuged yeast is recycled without washing:
Plant operations improve by eliminating ethanol recovery and acid neutralization, saving energy, chemicals, and time.
Metabolite and dead cell concentrations reach a higher but stable equilibrium, balanced by yeast loss and substrate dilution, tolerable due to no bacterial interference.
Cycle time shortens by removing the yeast washing step (1–2 hours saved) and, when vats are water-washed instead of caustic-cleaned, further reducing cleaning time (1–2 hours vs. 2–3+ hours), enhancing overall efficiency.
This optimized process leverages the absence of contamination to simplify and accelerate ethanol production.
Reduces fermentation time:
In the improved process, fermentation time is reduced because the yeast is no longer subjected to the stress of acid washing. Here’s how this works:
Acid Washing in Traditional Processes
In traditional ethanol production, yeast is often recycled between fermentation cycles to maximize efficiency. To control bacterial contamination during this recycling, the yeast is washed with sulfuric acid. However, this acid exposure stresses the yeast cells. The stress can damage their cell membranes, lower their viability, and slow their metabolic activity. When these stressed yeast cells are reused, they need time to recover before they can ferment sugars efficiently. This recovery period, or lag phase, extends the overall fermentation time.
Eliminating Acid Washing in the Improved Process
In the improved process, the acid washing step is skipped entirely. After fermentation, 95% of the yeast is separated using centrifugation and directly reused in the next cycle without being exposed to acid. Since there’s no acid wash, the yeast avoids this stress. As a result:
Higher Viability: The yeast cells remain healthier, with intact membranes and better metabolic function.
No Recovery Time: Without the need to recover from acid stress, the yeast can start fermenting the new batch of sugarcane juice or molasses immediately.
How This Reduces Fermentation Time
The key to shorter fermentation time lies in the yeast’s improved condition:
Faster Start: In the traditional process, acid-washed yeast may enter a lag phase as it recovers from stress, delaying the start of active fermentation. In the improved process, this lag phase is minimized or eliminated because the yeast is unstressed and ready to work right away.
More Efficient Fermentation: Healthier yeast converts sugars into ethanol and carbon dioxide more quickly. Without the burden of repairing acid-induced damage, the yeast ferments at a faster rate, completing the cycle sooner.
How Much Time Is Saved?
The exact reduction in fermentation time depends on factors like the yeast strain, sugar concentration, and fermentation conditions. However, by avoiding acid stress, fermentation could be shortened by approximately 10–20%. For a typical 8–12 hour fermentation cycle, this might mean a savings of 1–2 hours per batch.
Additional Advantages
Beyond reducing fermentation time, skipping acid washing simplifies the process. It eliminates the need for acid, neutralizing agents, and extra steps like treating the wash, which also saves time and resources. With faster fermentation cycles, the plant can process more batches in the same timeframe, increasing overall productivity.
Conclusion
By eliminating acid washing, the improved process keeps the yeast healthier and more active, avoiding the stress that slows fermentation in the traditional method. This leads to a quicker start and more efficient sugar conversion, ultimately reducing the fermentation time while improving the process’s simplicity and efficiency.
Contamination Control
Bacterial contamination is often the biggest technical problem when growing yeasts at an industrial-scale.
We’ve invented a patented technology for preventing contamination by using urea as the sole nitrogen source along with grade 316 stainless steel heat exchangers to reduce leaching of nickel. No acid wash or antibiotics are needed to prevent 100% of all bacterial contamination.
The main yeasts we are using with this invention are Saccharomyces cerevisiae and Candida utilis (Torula)
This technique allows fermentation at pH 5 to pH 7 without bacterial contamination.
Brazil Patent BR112024003499
PCT Patent WO2024092285A2
Low Cost Fermenter
We are developing a low-cost fermenter that takes advantage of our contamination control invention.
This low-cost fermenter is designed for anaerobic fermentation of sugars to produce ethanol and for aerobic fermentation of sugars or waste glycerol to produce single-cell protein.
The building block for a large-scale fermenter is the 1 m3 Intermediate Bulk Carrier (IBC). This enables us to build large fermenters for less than $500/m3, while other fermenters can cost more than $200K/m3. The operating cost of these fermenters is also much lower than traditional submerged fermentation.
Healthier than Soy Protein
Our low-cost fermenter produces single-cell protein from yeast that is significantly healthier than soy protein, at a competitive price.
Growing soybeans uses many unhealthy herbicides and pesticides, and these enter the food chain through soy protein in animal feed.
Soy also contains many anti-nutritional compounds that are unhealthy in fish and animal feed.
Yeast has been shown to be much healthier than soy protein and has a better balance of amino acids than soy protein. It is also more sustainable, needing less land than soybeans.
Omega-3 and Omega-6 fatty acids are essential to human life and are only provided in our diet by plants, animals, some yeasts and some algae.
When people consume too much Omega-6 fatty acid, people are more likely to have heart problems, high blood pressure, dementia and many other health problems.
Our low-cost fermenter can produce Candida utilis (Torula) yeast with tunable amounts of Omega-3 fatty acids, which has been shown to be very nutritious for fish and chicken, and thus makes a more valuable feed for fish and chicken.
Protein from Sugars and Biodiesel Waste Glycerol
Our low-cost fermenter can produce single-cell protein from both sugars and waste glycerol.
A byproduct of biodiesel production is waste glycerol, which is a low-cost feedstock for growing Candida utilis yeast. About 50 million tons of waste glycerol are produced per year.
It’s possible to make low-cost protein from waste glycerol by growing Candida utilis yeast using our low-cost fermenter and our contamination control technique.
This yeast is high in protein and can be tuned to have variable amounts of Omega-3 fatty acids.
A high sulfate growth environment increases the methionine + cysteine content to 2-3% of dry weight, making Candida utilis a complete protein source for humans, poultry and fish.
Who are we?
Hamrick Engineering was founded in 2013 by Edward B. Hamrick.
Edward (Ed) Hamrick graduated with honors from the California Institute of Technology (CalTech) with a degree in Engineering and Applied Science. He worked for three years at NASA/JPL on the International Ultraviolet Explorer and Voyager projects and worked for ten years at Boeing as a Senior Systems Engineer and Engineering Manager. Subsequently, Ed worked for five years at Convex Computer Corporation as a Systems Engineer and Systems Engineering Manager. Ed has been a successful entrepreneur for the past 25 years.
Alex Ablaev, MBA, PhD is Sr. Worldwide Business Developer. Alex previously worked for Genencor's enzymatic hydrolysis division, and is the President of the Russian Biofuels Association as well as General Manager of NanoTaiga, a company in Russia using CelloFuel technologies in Russia.
Alan Pryce, CEng is Chief Engineer. Alan is an experienced professional mechanical engineer - Chartered Engineer (CEng) – Member of the Institute of Mechanical Engineers (IMechE) - with 10+ years’ experience in the mechanical design and project management of factory automation projects in UK and European factories. He has been a Senior Design Consultant and project manager for over 30 years working for Frazer-Nash Consultancy Ltd involved with many design and build contracts in the military, rail, manufacturing, and nuclear industries.
Maria Kharina, PhD, is Sr. Microbiology Scientist. Maria has a PhD in Biotechnology and is a researcher with 10+ years of experience. Maria was a Fulbright Scholar in the USA from 2016-2017.
Beverley Nash is Director of Marketing. Beverley has run Nash Marketing for over 30 years and has extensive experience in marketing planning and development for both new and established businesses. Beverley has worked for many global corporations in the technical marketplace and has been responsible for both the planning and management of many programs dealing with all aspects of company and product growth.
Dr. Ryan P. O'Connor (www.oconnor-company.com) provides intellectual property strategy consulting and patent prosecution. Dr. O'Connor holds a degree in Chemical Engineering from University of Notre Dame and a Ph.D. in Chemical Engineering from University of Minnesota. He has filed more than 1000 U.S. and PCT applications and is admitted to the Patent Bar, United States Patent & Trademark Office.
Hamrick Engineering Patent Portfolio
Contamination control when growing yeasts
U.S. Patent App. No. 18/532,043 status: Received Notice of Allowance
International Patent App. No. PCT/US2023/083031 status: Published
CN118043470A (China) status: Published
RU2826104 (Russia) status: Granted
BR112024003499 (Brazil) status: Granted
Contamination control when growing green algae
US Patent App. No. 18/640,396, (USA) status: Filed
International Patent App. No. PCT/US2024/025597 status: Published
Methods for fermenting carbohydrate-rich crops
US9499839 (USA) status: Granted
RU2642296 (Russia) status: Granted
BR112016005352 (Brazil) status: Granted
CN107109440B (China) status: Granted
EP3140411 (European Union) status: Granted
AR106148A1 (Argentina) status: Granted
IN328228 (India) status: Granted
Notified of grant by Ukraine patent office
Method for fermenting stalks of the Poaceae family
US9631209 (USA) status: Granted
RU2650870 (Russia) status: Granted
EP3277825B1 (EU) status: Granted
MX363750B (Mexico) status: Granted
CN107849585B (China) status: Granted
BR112017008075 (Brazil) status: Granted
Methods and apparatus for separating ethanol from fermented biomass
US10087411 (USA) status: Granted
RU2685209 (Russia) status: Granted
EP3541489A1 (EU) status: Granted
MX371710 (Mexico) status: Granted
BR112018075838A2 (Brazil) status: Granted
IN332722 (India) status: Granted
CA3025016A1 (Canada) status: Granted
UA119630C2 (Ukraine) status: Granted
Methods and systems for producing sugars from carbohydrate-rich substrates
US9194012 (USA) status: Granted
RU9194012 (Russia) status: Granted
CA2884907 (Canada) status: Granted
CN105283468 (China) status: Granted
EP3004178 (European Union) status: Granted