Data from: Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome
Data files
Aug 22, 2013 version files 18.86 GB
-
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_01.raw
81.96 MB
-
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_02.raw
212.24 MB
-
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_03.raw
222.69 MB
-
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_04.raw
222.30 MB
-
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_05.raw
220.72 MB
-
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_06.raw
219.63 MB
-
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_07.raw
218.57 MB
-
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_08.raw
218.05 MB
-
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_09.raw
216.77 MB
-
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_10.raw
214.26 MB
-
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_11.raw
213.30 MB
-
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_12.raw
186.20 MB
-
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_01.raw
89.68 MB
-
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_02.raw
219.17 MB
-
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_03.raw
225.32 MB
-
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_04.raw
223.83 MB
-
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_05.raw
222.70 MB
-
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_06.raw
221.67 MB
-
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_07.raw
220.47 MB
-
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_08.raw
219.23 MB
-
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_09.raw
216.91 MB
-
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_10.raw
214.26 MB
-
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_11.raw
212.66 MB
-
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_12.raw
183.41 MB
-
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_01.raw
84.20 MB
-
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_02.raw
215.61 MB
-
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_03.raw
210.78 MB
-
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_04.raw
205.80 MB
-
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_05.raw
205.55 MB
-
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_06.raw
205 MB
-
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_07.raw
202.15 MB
-
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_08.raw
201.85 MB
-
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_09.raw
200.42 MB
-
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_10.raw
200.85 MB
-
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_11.raw
199.25 MB
-
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_12.raw
171.41 MB
-
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_01.raw
78.40 MB
-
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_02.raw
202.83 MB
-
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_03.raw
198.27 MB
-
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_04.raw
195.08 MB
-
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_05.raw
196.98 MB
-
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_06.raw
198.41 MB
-
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_07.raw
199.82 MB
-
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_08.raw
197.61 MB
-
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_09.raw
196.04 MB
-
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_10.raw
196.54 MB
-
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_11.raw
200.13 MB
-
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_12.raw
170.08 MB
-
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_01.raw
76.22 MB
-
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_02.raw
206.16 MB
-
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_03.raw
212.50 MB
-
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_04.raw
211.58 MB
-
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_05.raw
211.27 MB
-
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_06.raw
210.52 MB
-
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_07.raw
210.39 MB
-
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_08.raw
206.86 MB
-
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_09.raw
205.01 MB
-
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_10.raw
202.75 MB
-
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_11.raw
201.22 MB
-
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_12.raw
178.43 MB
-
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_01.raw
83.94 MB
-
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_02.raw
208.30 MB
-
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_03.raw
213.68 MB
-
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_04.raw
212.07 MB
-
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_05.raw
211.72 MB
-
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_06.raw
210.71 MB
-
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_07.raw
209.48 MB
-
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_08.raw
205.61 MB
-
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_09.raw
203.02 MB
-
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_10.raw
199.87 MB
-
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_11.raw
197.91 MB
-
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_12.raw
175.04 MB
-
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_01.raw
82.31 MB
-
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_02.raw
212.92 MB
-
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_03.raw
221.58 MB
-
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_04.raw
217.79 MB
-
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_05.raw
213.21 MB
-
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_06.raw
213.65 MB
-
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_07.raw
211.98 MB
-
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_08.raw
209.49 MB
-
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_09.raw
206.61 MB
-
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_10.raw
206.92 MB
-
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_11.raw
206.58 MB
-
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_12.raw
181.20 MB
-
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_01.raw
82.14 MB
-
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_02.raw
211.20 MB
-
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_03.raw
218.43 MB
-
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_04.raw
216.36 MB
-
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_05.raw
210.74 MB
-
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_06.raw
212.09 MB
-
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_07.raw
211.22 MB
-
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_08.raw
207.99 MB
-
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_09.raw
205.04 MB
-
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_10.raw
202.65 MB
-
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_11.raw
202.70 MB
-
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_12.raw
178.68 MB
Abstract
The human gut microbiota is an important metabolic organ. However, little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In the current study, gnotobiotic mice colonized with a simplified model microbiota composed of 12 sequenced human gut bacterial species were fed oscillating diets of disparate composition. Rapid, reproducible and reversible changes in community structure were observed. Time series microbial RNA-Seq analyses revealed staggered functional responses to diet shifts throughout the community that were heavily focused on carbohydrate and amino acid metabolism. High-resolution shotgun metaproteomics confirmed many of these responses at a protein level. One member, Bacteroides cellulosilyticus WH2, proved exceptionally fit regardless of diet. Its genome encoded more carbohydrate active enzymes than any known Bacteroidetes. Transcriptional profiling indicated that B. cellulosilyticus WH2 is an adaptive forager that tailors its versatile carbohydrate utilization strategy to available dietary polysaccharides, with a strong emphasis on plant-derived xylans abundant in dietary staples like cereal grains. Two highly expressed, diet-specific polysaccharide utilization loci (PULs) in B. cellulosilyticus WH2 were identified, one with characteristics of xylan utilization systems. Introduction of a B. cellulosilyticus WH2 library comprising 26,750 isogenic transposon mutants into gnotobiotic mice along with other model community members confirmed that these loci represent critical diet-specific fitness determinants. The specific carbohydrates that trigger overexpression of these two loci and many of the organism's 111 other predicted PULs were identified by RNA-Seq during in vitro growth on 31 distinct carbohydrate substrates, allowing us to better interpret in vivo RNA-Seq and proteomics data. These results offer insight into how gut microbes adapt to dietary perturbations, both at a community level and from the perspective of a well-adapted symbiont with exceptional saccharolytic capabilities, and illustrate the value of studying defined models of the human gut microbiota.
- McNulty, Nathan P. et al. (2013), Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome, PLoS Biology, Article-journal, https://doi.org/10.1371/journal.pbio.1001637
