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Chapter 42 : Improving Microbial Robustness Using Systems Biology

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Abstract:

Robustness requires the microbe to be able to rapidly adjust to different stresses derived from temperature and pH changes, nutritional limitations, presence of chemical toxins, and pathogen attacks such as by viruses and phages. This chapter outlines aspects of microbial robustness desirable for specific industries and processes and examines the current status and potential benefits of application of systems biology analysis tools to further improve these processes. Despite the alterations to the central metabolic networks, the organism was able to reroute fluxes and exhibited only minor changes in gene transcription and protein expression. Interestingly, coupled with genomic data, experience has shown that proteins expressed from microorganisms resident in a complex matrix such as soil or biomass can still be identified in the presence of the environmental “contaminating” proteins, making proteomic technology very powerful for dissection of complex biological materials. The application of systems biology tools such as those underway with laboratory strains can be applied to wine and especially lager beer production to build an integrated metabolic model of gene response and metabolite flows as the fermentation process proceeds. The physiological effect of dissolved carbon dioxide has also been examined in continuous cultures of the bacterial ethanol producers, including and , although without the benefit of systems biology tools.

Citation: Mielenz J, Hogsett D. 2010. Improving Microbial Robustness Using Systems Biology, p 605-620. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch42

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Tables

Generic image for table
TABLE 1

Preferred characteristics of a robust microorganism

Citation: Mielenz J, Hogsett D. 2010. Improving Microbial Robustness Using Systems Biology, p 605-620. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch42
Generic image for table
TABLE 2

Examples of industrial organisms with completed genome sequence and potential areas of applied use

Citation: Mielenz J, Hogsett D. 2010. Improving Microbial Robustness Using Systems Biology, p 605-620. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch42
Generic image for table
TABLE 3

Robustness challenges in biomass ethanol production

Citation: Mielenz J, Hogsett D. 2010. Improving Microbial Robustness Using Systems Biology, p 605-620. In Baltz R, Demain A, Davies J, Bull A, Junker B, Katz L, Lynd L, Masurekar P, Reeves C, Zhao H (ed), Manual of Industrial Microbiology and Biotechnology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816827.ch42

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