Posted 10/4/11 by . Filed under RAFT IX.

David Glassner Dr. Glassner will be Keynote Speaker at SIM’s 9th annual Recent Advances in Fermentation Technology. RAFT IX will be held November 6-9 in Marco Island, FL. The meeting theme is “From Concept to Commercialization.” Learn more about RAFT IX.

Many organizations are pursuing the production of industrial biochemicals and fuels using synthetic biology to create magic bugs. However, there are very few examples of success in the industrial biochemical and fuels sector because success is driven by high efficiency, low cost and large scale which is not easily achieved. This contribution will provide insights on meeting the challenges in moving novel, recombinant fermentation technology from concept to commercialization using lactic acid and isobutanol as examples.

The key characteristics of each project are similar and start with the definition of a target product and process forming an economically attractive business opportunity. The business opportunity created by the new product allows the target performance characteristics for the new microorganism to be established from a process economic analysis. Both operating and capital cost for implementation are considered in establishing the microorganism performance targets. However, the performance target is not established by looking at microorganism literature but rather on establishing a low cost, highly efficient manufacturing process that may be equaled but not beaten from an economic standpoint.

After the performance targets are established, resources required to successfully develop the fermentative organism must be assembled. The resources are a combination of funding and technical capabilities. The technical capabilities include personnel, equipment and facilities required to successfully execute the microorganism development project. Capabilities will make or break a project and certainly play a key role in the time required to reach commercialization or the possibility of ever reaching commercialization.

The final component in a successful commercialization is leadership. Strong leadership is required to obtain required resources, communicate how, when and why success will be attained and to inspire the team developing the microorganism to success. The key characteristics outlined will be illustrated by a variety of experiences and lessons learned on the way from concept to commercialization for lactic acid and isobutanol.

Posted 9/29/11 by . Filed under News and Updates, Uncategorized.

Fifteen years ago the SIM annual meeting had loads of talks dealing with natural products (I knew the S. coelicolor ActI gene sequence by heart) and there was barely a talk on fuel ethanol to be found. Now there are plenty of biofuel talks to go along with a healthy dose of natural products (and I no longer remember the ActI sequence). So it begs the question, what will we be listening to at the 2025 annual meeting. As I look into my crystal ball, the answer is…. in vitro meat cultivation.

These are meat products that are grown using tissue culture technologies in the lab and TIME magazine identified in vitro meat production as one of the top 50 breakthrough ideas of 2009. This is not a vegetable protein-imitation; it is a product derived from culturing real animal muscle tissue cells. Unfortunately we are not talking filet mignon or porter house; the product would be more like hamburger.

The benefits of in vitro meat cultivation include: ease of feeding a larger population, limited land use, more efficient water use, well defined quality, reduced greenhouse gas emissions, and reduced fuel vs. food decision making for food production. During this past summer, a small group of scientists met in Gothenburg, Sweden (organized by Chalmers University of Technology and the European Science Foundation) to review the technology components necessary to reduce this concept to practice. This included discussions on cell lines and culture medium nutrients derived from photosynthetic organisms such as cyanobacteria.

So at the 2025 annual meeting, a company may not simply provide money for the banquet, they may produce the entrée.


About Neal Connors
Dr. Neal Connors is currently the owner/president of Phoenix BioConsulting, LLC (; a company providing consulting services to the fermentation, industrial microbiology, biotechnology, and legal sectors.

Posted 9/20/11 by . Filed under 33rd SBFC, Featured News.

At the 33rd Symposium, banquet speaker, David Baker, Professor of Biochemistry at the University of Washington, discussed his computer game, Foldit. This revolutionary game has been played by tens of thousands and has hit national news for its groundbreaking work. The article, Crystal structure of a monomeric retroviral protease solved by protein folding game players, was recently published in the Nature Structural & Molecular Biology journal.

Many news organizations have picked up the story. Read Cnet’s article on the groundbreaking work of Foldit.

For more info, visit the Visit the Foldit Web site

Posted 9/8/11 by . Filed under Featured News.

Everybody is familiar, at least in passing, with classical strain improvement. You treat cells with a chemical or physical mutagen, kill off most in the process, and screen the survivors for that rare clone which produces more of the product you are interested in. This new strain becomes the starting point for a new round and you repeat the process. It is a bit more involved than that but you get the idea. You never really know why the strain is improved – unless you sequence the thing – but if you are in industry your job is to become rich (because you made more product cheaper) and not famous (because you published a paper).

In the era of metabolic engineering where scientists wanted to be more targeted in the way they improved the productivity of strains, classical strain improvement got the reputation of being too slow and too labor intensive for the improvements that were achieved. That might have been true 20 years ago but with the use of miniaturized cultivation along with automated colony picking and liquid handling; a large number of colonies can be screened regardless of whether their genetic variability was introduced by metabolic engineering or chemical mutagenesis.

Some companies have never forgotten the value of classical strain improvement. A paper given at the 2009 Recent Advances in Fermentation Technology Meeting (RAFT) described how Eli Lilly has used this approach for over fifty years to continually improve strains for in-line natural products. I saw the same thing at Merck for the continual improvement of avermectin and lovastatin producing strains.

It has been pleasantly surprising to see biology companies producing biofuels and renewable chemicals use classical strain improvement as a supplement to synthetic biology or other metabolic engineering approaches. Amyris is one such company to employ this approach as described in a paper given at the 2010 SIM annual meeting (oh, and by the way, didn’t they just have an IPO?). It may not be sexy but it is effective, efficient, and a great tool to have in the tool box.


About Neal Connors
Dr. Neal Connors is currently the owner/president of Phoenix BioConsulting, LLC (; a company providing consulting services to the fermentation, industrial microbiology, biotechnology, and legal sectors.

Posted 8/17/11 by . Filed under News and Updates, Uncategorized.

Bacteria which infect people with cystic fibrosis could help combat other antibiotic-resistant microbes, according to a team from Cardiff and Warwick Universities.

Continuous use of existing antibiotics means that resistant bacteria are now causing major health problems all over the world. New antibiotics are urgently needed to combat the emergence of multidrug-resistant bacteria such as the MRSA superbug.

Now a surprising source of hope has emerged in the form of Burkholderia, a group of bacteria which can cause severe lung infections in people with the genetic disorder cystic fibrosis. However, the Cardiff and Warwick team has now discovered antibiotics from Burkholderia are effective against MRSA and even other cystic fibrosis infecting bacteria.

Dr Eshwar Mahenthiralingam, of Cardiff University’s School of Biosciences, has been studying Burkholderia for the last decade. Using forensic fingerprinting tests to genetically identify the bacteria, Dr Mahenthiralingam’s research group has tracked strains all over the world and helped develop guidelines to prevent it spreading.

By the summer of 2007, Dr Mahenthiralingam had built up a large collection of Burkholderia bacteria. He and his team then decided to screen them for antibiotics active against other bacteria, particularly drugs with the potential to kill other bacteria that infect cystic fibrosis patients. Over the next two years, Dr Mahenthiralingam’s team discovered that around one quarter of Burkholderia bacteria have very strong antibiotic activity on multidrug-resistant pathogens such as MRSA. One particular strain, Burkholderia ambifaria, was found to produce two very potent antibiotics active on resistant bacteria, in particular Acinetobacter baumanii.

The chemical structures of the antibiotics, called enacyloxins, were determined by Professor Gregory Challis and Dr. Lijiang Song at the University of Warwick, demonstrating that they belong to one of the most successful families of natural product drugs, the polyketides. Other examples of polyketides include erythromycin, which is used to cure many bacterial infections, and doxorubicin, used as an anti-cancer drug. Professor Challis commented: “The combination of enzymes used by Burkholderia to make the enacyloxins is very unusual. Our insights into this process should allow us to use cutting edge synthetic biology techniques to produce novel enacyloxin analogues with improved pharmaceutical properties.”

The team’s findings have now been published in the journal Chemistry and Biology. Dr Mahenthiralingam commented: “Burkholderia are soil bacteria like Streptomyces, which are the source of most of our current antibiotics. Our research therefore offers real hope of a completely new source for the identification and engineering of highly potent antibiotics. With antibiotic resistant bacteria causing great suffering around the world, these new sources are urgently needed.”

Greg Challis

Professor of Chemical Biology
Department of Chemistry
University of Warwick