Companies Developing Modified Microorganisms to Produce Biodiesel and Jet Biofuels

In this entry, I’ll profile companies that are using advanced biotechnology to improve microorganisms for production of fuels other than ethanol and butanol. Primarily, these include hydrocarbon or fatty acid based fuels that, when produced from a biological source, resemble or duplicate the chemical composition of common petroleum-based fuels, in particular diesel fuel and jet fuel. 

Much of the interest in alternate biological technologies has been directed towards diesel fuel. Petroleum-derived diesel fuel is produced from the fractional distillation of crude oil, resulting in a mixture of carbon chains that typically contain between 8 and 21 carbon atoms per molecule. The biological alternative, generally called “biodiesel”, can be manufactured from any of numerous sources, including algae, plant biomass, vegetable oil or even animal fats. Biodiesel is usually composed of a mixture of fatty acid methyl esters, with the final product created by a transesterification reaction. Most biodiesel consists of alkyl (usually methyl) esters instead of the alkanes and aromatic hydrocarbons of petroleum derived diesel, but because biodiesel has similar combustion properties to petrodiesel, it has been used as a substitute for diesel fuel, and it is widely believed that newer technologies for biological production of diesel can play an important role in the world’s portfolio of renewable fuels. 

Recent years have also seen enhanced interest in the possibility that petroleum-derived jet fuel and possibly other transportation fuels can instead be produced by biological systems in large quantities at commercially-viable costs. The term jet fuel refers to a type of aviation fuel designed for use in aircraft powered by gas-turbine engines. There are many different types of jet fuels used for commercial or military aviation, that are produced to a number of standardized international specifications. Jet fuel is typically a mixture of many different hydrocarbons, with size ranges that are specified by the requirements for each product. For example, kerosene-type jet fuel (including Jet A and Jet A-1) includes molecules having between about 8 and 16 carbon numbers; wide-cut or naphtha-type jet fuel (including Jet B), between about 5 and 15 carbon numbers. It is possible to produce these different jet fuels biologically, by selecting or designing organisms (generally algae or microorganisms) capable of producing the desired mixture of hydrocarbons, or the fatty acids that can be converted into hydrocarbons. 

Interest in biologically-derived jet fuels seems to have increased dramatically in recent months, with several airlines, including such as Continental, Virgin Atlantic, Japan Airline, and KLM conducing highly-publicized test flights using jet biofuels, and with the announcement of several high-profile research collaborations relating to microbial, algal or biomass-based production of jet fuel. Both the U.S. Department of Energy, through its National Renewable Energy Laboratory, and the Defense Advanced Research Projects Agency have devoted their attention and funding to the development of biological methods for production of jet fuel. 

It seems that commercial interest in biodiesel, jet biofuels, and similar fuels is gaining momentum in recent years, so that there is a real chance that these bio-based fuels can begin to claim a small but significant market share within the next several years. Many companies and individuals have been producing biodiesel for years, but these have generally been small-scale operations, using locally collected organic wastes or other biomass, which generally produce and sell fuel for use only within their immediate geographic area. So, as always, the key to major commercial success will be whether biological production methods can be scaled-up to large, commercial-size production for regional or national distribution at a cost that allows the fuel to be sold at a price competitive to petroleum-derived fuels. If that can be achieved, as seems possible at the moment, the companies producing biodiesel and jet biofuels may meet commercial success. 

The companies I’ll describe below are ones that are focusing their attentions on using microorganisms (generally bacteria) as the production platform. It is important to note that similar goals are being pursued by many of the algae companies that I’ll be profiling in a later entry in this blog. Use of algae for such applications has the advantage of fitting into the established infrastructure and technology for growing algae and processing its products for fuel use; however, in the long term, use of microorganisms may be favored because fine-tuning the fatty acid or hydrocarbon output of an organism is best done using metabolic engineering, synthetic biology, and other advanced methods that are currently more feasible in bacteria than they are in algae. But then again, one of the more prominent firms using synthetic biology to enhance fuel production is Synthetic Genomics, whose R&D is believed to be directed more towards algae than bacteria. It is noteworthy that almost all of the biofuel companies specializing in the use of synthetic biology and similar technologies are directing their efforts to producing biodiesel, jet biofuels, or similar fuels, because such technologies seem so well-suited to create the “designer organisms” needed to produce these fuels. Overall, this is a sector where commercial success seems likely for many of the companies active in the sector, although the timeframes here are likely to be longer than for cellulosic ethanol or even butanol. 

The following are the companies developing modified microorganisms for production of biodiesel, jet fuel and related fuels (some of these companies are also developing other fuels, including ethanol, as noted in their profiles).                                                                                                             

  • Amyris Biotechnologies, Inc.
  • Codexis, Inc.
  • Joule Biotechnologies, Inc.
  • LS9, Inc.
  • Sequesco
  • Verdezyne, Inc.

The following are brief profiles of companies that are developing engineered or modified microorganisms for the production of biodiesel, jet biofuels or fuels other than ethanol or butanol. These profiles have been adapted or excerpted from company websites and/or other publicly available information, and I don’t assume any liability for the accuracy, comprehensiveness or use of the information. 

Amyris Biotechnologies, Inc. is an integrated renewable products company whose strategy is to combine technology, production and distribution with the goal of commercializing and scaling products across the supply chain. Amyris applies synthetic biology to produce a broad range of products, and combines this technology with growing scale up and production capabilities through its subsidiary, Amyris Brasil Pesquisa e Desenvolvimento, Ltda. Amyris is developing fuels it calls No Compromise© fuels – renewable fuels that it says will demand no sacrifice in performance or penalty in price, and will offer a superior environmental profile by reducing lifecycle (GHG) emissions of 80% or more compared to petroleum fuels. They are also delivered to consumers using existing petroleum distribution infrastructure and work in today’s engines. 

Amyris technology makes it possible to alter the metabolic pathways of microorganisms such as yeasts, creating living factories that produce molecules with practical applications. The company’s proprietary technology transforms plant-based feedstocks, such as sugarcane, into 50,000 different isoprenoids –molecules used in a wide variety of energy, pharmaceutical, and chemical applications. The company is developing biodiesel fuels that are expected to work well even at low temperatures, not clog filters, and be stored for a long period of time without degradation. Amyris says that its fuels will solve many of the performance challenges, such as cold flow and stability, associated with conventional biodiesels. The company is also developing a renewable jet fuel which it plans to commercialize as early as 2012. The company says that this fuel performs well at low temperatures, can be produced in the US at competitive economics using sugar cane as a feedstock, and meets initial certification criteria. 

In November 2009, Amyris Biotechnologies announced that it has secured patent protection for its entire line of diesel, jet and gasoline renewable fuel products which have been registered by the U.S. Environmental Protection Agency. Amyris has operated a pilot plant in Campinas, São Paulo, Brazil since the fall of 2008, and plans to commercialize its renewable products starting in 2011.  

Codexis, Inc. uses DNA shuffling to customize “super” enzymes capable of selectively and efficiently performing a desired chemical process, for application to production of cellulosic biofuels and other products. Starting with a diverse set of genes that encode for variations of the enzyme catalyst, Codexis recombines, or shuffles these DNA sequences to create new variants. Using sophisticated high-throughput screening methods, novel biocatalysts with desired improvements are selected and these improved variants can then be put through the process again until a highly efficient biocatalyst is created that meets or exceeds targeted performance  characteristics. 

Codexis has a long term collaboration with Royal Dutch Shell to develop enhanced methods of converting non-food biomass to advanced biofuels. The collaboration began in 2006 and was expanded in 2007 and again in 2009. Shell is the leading worldwide distributor of biofuels. Codexis is using its biocatalytic approach to find critical pathways for developing economically feasible alternative transportation fuels from renewable resources. 

In December 2009, Codexis announced plans for an initial public offering, reportedly seeking up to $100 million in funding.

Joule Biotechnologies, Inc. is tackling the global energy crisis with what it calls a “game-changing” renewable alternative to transportation fuels. Its patent-pending Helioculture™ technology is designed to overcome the limitations of biomass-derived fuel approaches by using sunlight to convert CO2 directly into liquid energy products under the trade name Joule™. Founded in 2007 by Flagship Ventures, Joule is privately held and headquartered in Cambridge, Massachusetts, and is using synthetic biology to design and create organisms to meet these goals. 

Joule recently announced proof of concept for its development of renewable fuels, achieving direct microbial conversion of carbon dioxide (CO2) into hydrocarbons via engineered organisms. The company’s photosynthesis-driven approach avoids the economic and environmental burden of multi-step, cellulosic or algal biomass-derived methods. The company employs a novel SolarConverter™ system, together with proprietary, product-specific organisms and state-of-the-art process design, to harness the power of sunlight while consuming waste CO2. The company says that this technology platform has been proven out with the conversion of CO2 into ethanol at high productivities. The breakthrough was made possible by the discovery of unique genes coding for enzymatic mechanisms that enable the direct synthesis of both alkane and olefin molecules – the chemical composition of diesel. Production was achieved at lab scale, with pilot development slated for early 2011. 

The Joule SolarConverter™ system was engineered to maximize productivity and photon yields with the potential to deliver more than 20,000 gallons of Joule™ ethanol and more than 13,000 gallons of Joule™ diesel per acre per year. It facilitates the entire process in one integrated system: optimizing conditions for the organisms, capturing sunlight, and converting and initially separating the product into specification fuel with far fewer polishing operations than petroleum or biomass-derived approaches. The SolarConverter™ system applies sophisticated optical and thermal engineering to allow its deployment on just minimal amounts of non-agricultural land, and it requires no fresh water. Its modular design means that the same system demonstrated in the laboratory today can easily move to wide-scale production, by adding interconnected assemblies to any size based on land, CO2 availability and desired output. 

In January 2010, Joule announced the signing of a lease agreement to build its first pilot plant in Leander, Texas, where the company will further develop and test its transformative system for the production of renewable solar fuels, beginning with ethanol. The company expects this plant to be operational within six months. 

LS9, Inc. is a privately-held industrial biotechnology company based in South San Francisco, California that is using synthetic biology to develop patent-pending UltraClean™ fuels customized to closely resemble petroleum fuels and engineered to be renewable, low-carbon and cost competitive with crude oil. LS9 UltraClean™ products are a family of fuels produced by microorganisms (trade named DesignerMicrobes™) the company has created using synthetic biology. 

LS9 has perfected a one-step fermentation process that uses patent-pending microorganisms to efficiently convert renewable feedstocks to a portfolio of “drop in compatible” UltraClean™ fuels and sustainable chemicals. LS9 has developed a novel method of efficiently converting fatty acid intermediates into petroleum replacement products via fermentation of renewable sugars. The company has also discovered and engineered a new class of enzymes and their associated genes to efficiently convert fatty acids into hydrocarbons. Starting from low-carbon, natural sources of sugar such as sugar cane and cellulosic biomass, the company hopes these renewable fuels will fundamentally change the transportation fuels landscape and set the stage for petroleum displacement.  LS9 UltraClean™ fuels have higher energetic content than ethanol or butanol and have fuel properties that are essentially indistinguishable from those of gasoline, diesel, and jet fuel. LS9’s technology provides a means to genetically control the structure and function of its fuels, enabling a product portfolio that meets the diverse demands of the petroleum economy. The company has operated a pilot plant at its South San Francisco headquarters since August 2008. 

LS9 has the financial backing of venture capital firms Flagship Ventures, Khosla Ventures, and Lightspeed Venture Partners, as well as funding from Chevron Technology Ventures. LS9 has a partnership arrangement with Procter and Gamble, one of the world’s largest consumer products companies, to jointly develop and commercialize LS9 technology for use in the production of key consumer chemicals. The company also has a research and development collaboration with Lawrence Berkeley National Lab – Joint BioEnergy Institute at University of California – Berkeley. 

In January 2010, LS9 announced that a collaborative team of researchers from the company, the University of California at Berkeley, and the U.S. Department of Energy’s Joint BioEnergy Institute (JBEI) have developed a microbe that can produce an advanced biofuel directly from cellulosic biomass in a one-step process. Using the power of synthetic biology, the team of researchers engineered a microbe that consolidates advanced biofuels production and cellulosic bioprocessing for the first time. This breakthrough enables the production of advanced hydrocarbon fuels and chemicals in a single fermentation process that does not require additional chemical transformations. In February 2010, the company announced the acquisition of the former Biomass Processing Technology production facility in Okeechobee, Florida, which will be retrofitted for production of LS9 UltraClean™ Diesel fuel, with production slated to begin in late 2010. 

Sequesco is developing technology that addresses the two major global energy problems – the rising levels of greenhouse gases in the atmosphere and our continued reliance on non-renewable fossil fuels.  Sequesco uses a microbial process to capture carbon dioxide emissions from industrial flue gases and convert the emissions into biomass which is a feedstock for biofuel. Unlike algal or agricultural approaches to capturing carbon dioxide for biofuel production, Sequesco’s technology does not rely on photosynthesis. This gives it greater potential to scale to meet the world’s growing energy needs without posing a threat to food production or natural habitats. 

Verdezyne, Inc., founded in 2005 as CODA Genomics, a spin-out from the University of Irvine, California, is developing genetic engineering techniques and processes for producing industrial chemicals and fuels from microorganisms.  Verdezyne employs its biological expertise and proprietary advanced computational algorithms to design and synthesize novel, high-diversity gene libraries for engineering proteins, metabolic pathways, and microorganisms. Verdezyne creates and harnesses this unique biological diversity to optimize commercial fermentation processes for the production of petrochemical replacements. 

The company’s technology platform includes proprietary metabolic pathway models, algorithms for protein design, a patented method for self-assembling synthetic genes and translational engineering tools that optimize the expression of these genes in recombinant microbes. The company has applied these technologies to ethanol fermentation, and they claim they have been able to achieve high yields and lower costs for the process. The company is also engineering new pathways to enable the biological synthesis of a number of chemical targets as petrochemical replacements. 

Verdezyne has entered into an agreement with Novozymes, a biotech-based world leader in enzymes and microorganisms. Under the arrangement, Verdezyne will optimize selected genes that encode industrial enzymes. These enzymes will then be manufactured in microbial systems. Verdezyne has raised nearly $3 million of a planned $15.2 million round of venture capital, and has been awarded a $1.7 million Small Business Technology Transfer grant, which will be used to develop gene libraries for its computational and bioinformatics programs.

D. Glass Associates, Inc. is a consulting company specializing in several fields of biotechnology. David Glass, Ph.D. is a veteran of nearly thirty years in the biotech industry, with expertise in patents, technology licensing, industrial biotechnology regulatory affairs, and market and technology assessments. This blog provides back-up and expanded content to complement a presentation Dr. Glass made at the EUEC 2010 conference on February 2, 2010 entitled “Prospects for the Use of Genetic Engineering in Biofuel Production.” The slides from that presentation are available at

8 thoughts on “Companies Developing Modified Microorganisms to Produce Biodiesel and Jet Biofuels

  1. Biotechnology, Biomedical and Bioinformatics News » Companies Developing Modified Microorganisms to Produce Biodiesel …

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  5. I have no training in the field of chemistry or fuel production but I do have an ingenious IDEA for fuel in jetliner to keep the fuel from exploding in the event of a crash.Like I said I have no experience in this field but I know that this idea will work if I can get the right people involved.Can anyone help direct me in the right direction and who I may speak with on this matter.

    Thank You,
    David Latil

  6. I think the idea of biofuels is the best one since the world is facing climate changes and global warming. It will reduce air pollution because it is said to be friendly to the environment.

  7. I would like to be notified via email on posts related to biotechnology since i am currently studying it and would like to be amongst the team that put microorganisms in action to save our world that is polluted by fossil fuels.

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