The influence of cultivation methods on Shewanella oneidensis physiology and proteome expression |
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Authors: | Dwayne A Elias Sandra L Tollaksen David W Kennedy Heather M Mottaz Carol S Giometti Jeffrey S McLean Eric A Hill Grigoriy E Pinchuk Mary S Lipton James K Fredrickson Yuri A Gorby |
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Institution: | (1) Department of Biochemistry, University of Missouri-Columbia, Columbia, MO 65211, USA;(2) Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA;(3) Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99353, USA;(4) J. Craig Venter Institute, 11149 North Torrey Pines Road, Suite 220, La Jolla, CA 92093, USA |
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Abstract: | High-throughput analyses that are central to microbial systems biology and ecophysiology research benefit from highly homogeneous
and physiologically well-defined cell cultures. While attention has focused on the technical variation associated with high-throughput
technologies, biological variation introduced as a function of cell cultivation methods has been largely overlooked. This
study evaluated the impact of cultivation methods, controlled batch or continuous culture in bioreactors versus shake flasks,
on the reproducibility of global proteome measurements in Shewanella
oneidensis MR-1. Variability in dissolved oxygen concentration and consumption rate, metabolite profiles, and proteome was greater in
shake flask than controlled batch or chemostat cultures. Proteins indicative of suboxic and anaerobic growth (e.g., fumarate
reductase and decaheme c-type cytochromes) were more abundant in cells from shake flasks compared to bioreactor cultures, a finding consistent with
data demonstrating that “aerobic” flask cultures were O2 deficient due to poor mass transfer kinetics. The work described herein establishes the necessity of controlled cultivation
for ensuring highly reproducible and homogenous microbial cultures. By decreasing cell to cell variability, higher quality
samples will allow for the interpretive accuracy necessary for drawing conclusions relevant to microbial systems biology research. |
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Keywords: | Controlled cultivation Systems biology Proteomics Shewanella |
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