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German Research Consortium Taps Next-Gen Sequencing to Accelerate Industrial Biotech

An industry-academic consortium in Germany has identified next-generation sequencing as one enabling technology to help improve microbial production strains and develop new industrial microbial products, In Sequence has learned.
“The focus is not on sequencing in principle, but sequencing is seen as a tool in order to assist us in developing new production strains, or optimizing genomes to improve production strains,” said Karl-Heinz Maurer, director of enzyme technology at Henkel, a consumer product company based in Düsseldorf. Maurer also serves as chairman of the “Industrieverbund Mikrobielle Genomforschung,” a German industry association for microbial genome research that is spearheading the research consortium.
In addition to Henkel, several industrial, biotechnology, and consumer product companies, including BASF, Bayer Crop Science, BRAIN, Degussa, Milupa, Schering, Südzucker, and Wacker, are contributing a total of approximately €22 million ($28.4 million) to the initiative. The German Ministry for Education and Research is providing an additional €20 million ($25.8 million) under its GenoMik-Plus program. That program also funds three academic centers of excellence, headed by the universities of Bielefeld, Göttingen, and Würzburg, with approximately €12 million.
The microbial genomics research initiative will fund six industry-academic collaborative projects over the next five years, several of which will involve sequencing. All six projects aim to improve biotechnology production of enzymes, peptides, amino acids, or small molecules.
One of the projects, a collaboration between Henkel and the Göttingen Genomics Laboratory at the University of Göttingen, aims to improve enzyme production in Bacillus systems. Henkel uses Bacillus strains to produce enzymes for laundry detergents and automated dishwasher detergents, which constitute the lion’s share of technical enzymes worldwide, according to Maurer.
In order to improve production, the company is working on modifying the genomes of its existing production strains as well as screening alternative Bacillus strains. “In both cases we would like to have information on the genome [sequence] in a very early phase of the research,” Maurer said.
The Göttingen laboratory will help with that. The lab just received a 454 Genome Sequencer FLX last month and initially plans to sequence a number of closely related Bacillus strains for Henkel that seemed promising in initial screens. “We know nothing about them but their ability to be good production strains,” said Maurer.
The 454 platform, which joins the Göttingen lab’s two ABI 3730 sequencers and one GE Healthcare MegaBace 4000 instrument, greatly enhances the lab’s data output and cuts down the time for sequencing genomes of closely related microbes, according to Axel Strittmatter, the laboratory’s manager. “This is why it is important to us, and to our industry partners, to have this technique,” he said.
The Göttingen researchers are also keeping an eye on other new sequencing systems like Solexa’s and ABI/Agencourt’s, he said, but “we have to wait until they can offer a commercial version of these systems”, including technical support.

"The focus is not on sequencing in principle, but sequencing is seen as a tool in order to assist us in developing new production strains, or optimizing genomes to improve production strains.”

Besides the Henkel collaboration, the Göttingen lab is also planning to use the 454 platform to sequence a number of Clostridium strains. While this is an academic research project, Strittmatter said that a number of unnamed companies are interested in those results as well. Clostridium, though it is not a major production strain, possesses several interesting enzymes, for example cellulases, Maurer explained, and might be a good source for genes encoding these enzymes.
The Henkel project is expected to start in March or April, and sequencing will play a role initially as well as at later stages, according to Maurer. “It’s not a situation where all of the sequencing is done within the next 12 months and that’s it,” he said.

What forged the collaboration between competing companies, and with academic researchers? Expectations to improve microbial industrial processes are running high, Maurer said, and “we cannot continue the old style where every company is following its own path.” Joining forces for pre-competitive work, he said, seemed a good idea “in order to get the best out of the technology in a reasonable amount of time and for a reasonable amount of money.”

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