Glycan foraging in vivo by an intestine-adapted bacterial symbiont

Justin L. Sonnenburg1,2, Jian Xu1,2, Douglas G. Leip1,2, Chien-Huan Chen1,2, Benjamin P. Westover1,3, Jeremy Weatherford3, Jeremy D. Buhler1,3, and Jeffrey I. Gordon1,2

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).

Science Supporting Online Material (SOM.pdf)

View DataSets on Metabolic Pathways - B. thetaiotaomicron
 
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 MetaView B. thetaiotaomicron Gene-To-Enzyme Assignment
  
 In Vitro Time Course Data Sets: five time-points from log to stationary phase.
 
Minimal Media + Glucose (MM-G)
Minimal Media + Maltotriose (MM-M)
Rich Media (TYG)
 
In Vivo Data Set: 
B. thetaiotaomicron in Cecum
experiment 1: 6 mice on standard polysaccharide-rich chow;
experiment 2: 3 mice on standard polysaccharide-rich chow and 3 mice on glucose/sucrose simple sugar diet
  
 Comparisons:
 
Genes up/down-regulated in Cecum experiment 1 (standard chow)
(standard chow - polysaccharide rich) compared to all time-points in MM-G
Genes up-regulated in Cecum experiment 2 (standard chow)
(standard chow - polysaccharide rich) compared to all time-points in MM-G
Genes up-regulated in Cecum experiment 2 (glucose/sucrose chow)
(glucose/sucrose chow) compared to all time-points in MM-G
  
Additional Data Files
 Raw MicroArray Data Files (.CEL)
 Raw MicroArray Data Files (.EXP)
 
 
B. thetaiotaomicron - Genes up-regulated in vivo
 Standard, polysaccharide rich chow (experiment 1)
1237 B. thetaiotaomicron genes up-regulated in cecum experiment 1 (standard chow) compared to all time-points of MM-G.
 Standard, polysaccharide rich chow (experiment 2)
1169 B. thetaiotaomicron genes up-regulated in cecum experiment 2 (standard chow) compared to all time-points of MM-G.
 Simple sugar (glucose/sucrose) chow (experiment 2)
709 B. thetaiotaomicron genes up-regulated in cecum experiment 2 (glucose/sucrose chow) compared to all time-points of MM-G.
B. thetaiotaomicron - Genes down-regulated in vivo
 Standard, polysaccharide rich chow (experiment 1)
519 B. thetaiotaomicron genes down-regulated in cecum experiment 1 (standard chow) compared to all time-points of MM-G.
  
  B. thetaiotaomicron GeneChip Probe Sets
  B. thetaiotaomicron GeneChip library file