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.
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_01
First salt pulse for Ceca 1, run 3
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_02
Second salt pulse for ceca 1, run 3
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_03
Third salt pulse for ceca 1, run 3
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Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_06
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_07
Seventh salt pulse for ceca 1, run 3
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_08
Eight salt pulse for ceca 1, run 3
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Ninth salt pulse for ceca 1, run 3
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Tenth salt pulse for ceca 1, run 3
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Eleventh salt pulse for ceca 1, run 3
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Last salt pulse for ceca 1, run 3
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_01
First salt pulse for ceca 1, run 4
Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_02
Second salt pulse for ceca 1, run 4
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Third salt pulse for ceca 1, run 4
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Fourth salt pulse for ceca 1, run 4
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Fifth salt pulse for ceca 1, run 4
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Sixth salt pulse for ceca 1, run 4
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Seventh salt pulse for ceca 1, run 4
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Eighth salt pulse for ceca 1, run 4
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Ninth salt pulse for ceca 1, run 4
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Tenth salt pulse for ceca 1, run 4
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Eleventh salt pulse for ceca 1, run 4
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Last salt pulse for ceca 1, run 4
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_01
First salt pulse for ceca 2, run 3
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_02
Second salt pulse for ceca 2, run 3
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_03
Third salt pulse for ceca 2, run 3
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_04
Fourth salt pulse for ceca 2, run 3
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_05
Fifth salt pulse for ceca 2, run 3
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_06
Sixth salt pulse for ceca 2, run 3
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_07
Seventh salt pulse for ceca 2, run 3
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_08
Eighth salt pulse for ceca 2, run 3
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_09
Ninth salt pulse for ceca 2, run 3
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_10
Tenth salt pulse for ceca 2, run 3
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_11
Eleventh salt pulse for ceca 2, run 3
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_12
Final salt pulse for ceca 2, run 3
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_01
First salt pulse for ceca 2, run 4
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_02
Second salt pulse for ceca 2, run 4
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_03
Third salt pulse for ceca 2, run 4
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_04
Fourth salt pulse for ceca 2, run 4
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_05
Fifth salt pulse for ceca 2, run 4
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_06
Sixth salt pulse for ceca 2, run 4
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_07
Seventh salt pulse for ceca 2, run 4
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_08
Eighth salt pulse for ceca 2, run 4
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_09
Ninth salt pulse for ceca 2, run 4
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_10
Tenth salt pulse for ceca 2, run 4
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_11
Eleventh salt pulse for ceca 2, run 4
Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_12
Final salt pulse for ceca 2, run 4
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_01
First salt pulse for ceca 9, run 4
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_02
Second salt pulse for ceca 9, run 4
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_03
Third salt pulse for ceca 9, run 4
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_04
Fourth salt pulse for ceca 9, run 4
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_05
Fifth salt pulse for ceca 9, run 4
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_06
Sixth salt pulse for ceca 9, run 4
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_07
Seventh salt pulse for ceca 9, run 4
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_08
Eighth salt pulse for ceca 9, run 4
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_09
Ninth salt pulse for ceca 9, run 4
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_10
Tenth salt pulse for ceca 9, run 4
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_11
Eleventh salt pulse for ceca 9, run 4
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_12
Final salt pulse for ceca 9, run 4
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_01
First salt pulse for ceca 9, run 5
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_02
Second salt pulse for ceca 9, run 5
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_03
Third salt pulse for ceca 9, run 5
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_04
Fourth salt pulse for ceca 9, run 5
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_05
Fifth salt pulse for ceca 9, run 5
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_06
Sixth salt pulse for ceca 9, run 5
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_07
Seventh salt pulse for ceca 9, run 5
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_08
Eighth salt pulse for ceca 9, run 5
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_09
Ninth salt pulse for ceca 9, run 5
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_10
Tenth salt pulse for ceca 9, run 5
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_11
Eleventh salt pulse for ceca 9, run 5
Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_12
Final salt pulse for ceca 9, run 5
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_01
First salt pulse for ceca 12, run 4
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_02
Second salt pulse for ceca 12, run 4
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_03
Third salt pulse for ceca 12, run 4
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_04
Fourth salt pulse for ceca 12, run 4
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_05
Fifth salt pulse for ceca 12, run 4
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_06
Sixth salt pulse for ceca 12, run 4
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_07
Seventh salt pulse for ceca 12, run 4
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_08
Eighth salt pulse for ceca 12, run 4
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_09
Ninth salt pulse for ceca 12, run 4
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_10
Tenth salt pulse for ceca 12, run 4
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_11
Eleventh salt pulse for ceca 12, run 4
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_12
Final salt pulse for ceca 12, run 4
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_01
First salt pulse for ceca 12, run 5
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_02
Second salt pulse for ceca 12, run 5
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_03
Third salt pulse for ceca 12, run 5
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_04
Fourth salt pulse for ceca 12, run 5
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_05
Fifth salt pulse for ceca 12, run 5
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_06
Sixth salt pulse for ceca 12, run 5
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_07
Seventh salt pulse for ceca 12, run 5
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_08
Eighth salt pulse for ceca 12, run 5
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_09
Ninth salt pulse for ceca 12, run 5
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_10
Tenth salt pulse for ceca 12, run 5
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_11
Eleventh salt pulse for ceca 12, run 5
Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_12
Final salt pulse for ceca 12, run 5