Plant cell wall polysaccharides can be used as the main feedstock for the production of biofuels. Saccharophagus degradans 2-40 is considered to be a potent system for the production Of Sugars from plant biomass due to its high capability to degrade many complex polysaccharides To understand the degradation metabolism of plant cell wall polysaccharides by S. degradans, the cell growth, enzyme activity profiles, and the metabolite profiles were analyzed by gas chromatography-time of flight mass spectrometry using different carbon Sources including cellulose, xylan, glucose and xylose. The specific activity of cellulose was only found to be significantly higher when cellulose was used as the sole carbon Source, but the xylanase activity increased when xylan, xylose, or cellulose was used as the carbon source, In addition, principal component analysis of 98 identified metabolites in S. degradans revealed four distinct groups that differed based oil the carbon source used. Furthermore. metabolite profiling showed that the use of cellulose 01 xylan as polysaccharides led to increased, abundances of fatty acids, nucleotides and glucuronic acid compared to the use of glucose or xylose. Finally, intermediates in the pentose phosphate pathway seemed to be up-regulated on xylose or xylan when compared to those on glucose or cellulose. Such metabolic responses of S. degradans under plant cell wall polysaccharides simply that its metabolic system is transformed to more efficiently degrade polysaccharides and conserve energy. This study demonstrates that the gas chromatography-time of flight mass spectrometry based global metabolomics are useful for understanding microbial metabolism and evaluating its fermentation characteristics Biotechnol. Bioeng. 2010;105: 477-488. (C) 2009 Wiley Periodicals, Inc.