Glycan foraging in vivo by an intestine-adapted bacterial symbiont

Justin L. Sonnenburg^1,2, Jian Xu^1,2, Douglas G. Leip^1,2, Chien-Huan Chen^1,2, Benjamin P. Westover^1,3, Jeremy Weatherford³, Jeremy D. Buhler^1,3, and Jeffrey I. Gordon^1,2

1. Center for Genome Sciences, 2. Departments of Molecular Biology and Pharmacology, 3. Department of Computer Science and Engineering, Washington University, St. Louis, MO 63108

Supplementary Data:

Transcriptional profiling of Bacteroides thetaiotaomicron was performed on samples taken from (i) chemostat cultures (in vitro) and (ii) from the ceca of gnotobiotic monoassociated NMRI mice (in vivo). In vitro whole genome transcriptional profiles were obtained from biological duplicate cultures. Aliquots were taken from each culture at five timepoints during growth from log to stationary phase in three types of media: (i) minimal media glucose (MM-G), (ii) minimal media maltotriose (MM-M), and (iii) rich media (TYG). In vivo profiling was performed on 12 mice, each colonized with B. thetaiotaomicron for ten days. The in vivo profiling was conducted in two separate experiments: (i) 6 male NMRI mice fed standard polysaccharide rich mouse chow (cecum-1, -2, -3, -4, -5, -6); and (ii) 3 male NMRI mice fed standard polysaccharide rich mouse chow (cecum-7, -8, -9) plus 3 male NMRI mice fed a simple sugar diet containing glucose and sucrose but deficient in polysaccharides (cecum-10, -11, -12).