DOI: 10.5061/dryad.7fj1k
title: Data from: Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome

description: 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.
description: Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_01First salt pulse for Ceca 1, run 3Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_02Second salt pulse for ceca 1, run 3Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_03Third salt pulse for ceca 1, run 3Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_04Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_05Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_06Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_07Seventh salt pulse for ceca 1, run 3Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_08Eight salt pulse for ceca 1, run 3Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_09Ninth salt pulse for ceca 1, run 3Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_10Tenth salt pulse for ceca 1, run 3Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_11Eleventh salt pulse for ceca 1, run 3Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032310_12Last salt pulse for ceca 1, run 3Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_01First salt pulse for ceca 1, run 4Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_02Second salt pulse for ceca 1, run 4Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_03Third salt pulse for ceca 1, run 4Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_04Fourth salt pulse for ceca 1, run 4Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_05Fifth salt pulse for ceca 1, run 4Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_06Sixth salt pulse for ceca 1, run 4Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_07Seventh salt pulse for ceca 1, run 4Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_08Eighth salt pulse for ceca 1, run 4Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_09Ninth salt pulse for ceca 1, run 4Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_10Tenth salt pulse for ceca 1, run 4Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_11Eleventh salt pulse for ceca 1, run 4Cecal_1_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032410_12Last salt pulse for ceca 1, run 4Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_01First salt pulse for ceca 2, run 3Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_02Second salt pulse for ceca 2, run 3Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_03Third salt pulse for ceca 2, run 3Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_04Fourth salt pulse for ceca 2, run 3Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_05Fifth salt pulse for ceca 2, run 3Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_06Sixth salt pulse for ceca 2, run 3Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_07Seventh salt pulse for ceca 2, run 3Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_08Eighth salt pulse for ceca 2, run 3Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_09Ninth salt pulse for ceca 2, run 3Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_10Tenth salt pulse for ceca 2, run 3Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_11Eleventh salt pulse for ceca 2, run 3Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run3_032910_12Final salt pulse for ceca 2, run 3Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_01First salt pulse for ceca 2, run 4Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_02Second salt pulse for ceca 2, run 4Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_03Third salt pulse for ceca 2, run 4Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_04Fourth salt pulse for ceca 2, run 4Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_05Fifth salt pulse for ceca 2, run 4Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_06Sixth salt pulse for ceca 2, run 4Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_07Seventh salt pulse for ceca 2, run 4Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_08Eighth salt pulse for ceca 2, run 4Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_09Ninth salt pulse for ceca 2, run 4Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_10Tenth salt pulse for ceca 2, run 4Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_11Eleventh salt pulse for ceca 2, run 4Cecal_2_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_033010_12Final salt pulse for ceca 2, run 4Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_01First salt pulse for ceca 9, run 4Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_02Second salt pulse for ceca 9, run 4Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_03Third salt pulse for ceca 9, run 4Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_04Fourth salt pulse for ceca 9, run 4Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_05Fifth salt pulse for ceca 9, run 4Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_06Sixth salt pulse for ceca 9, run 4Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_07Seventh salt pulse for ceca 9, run 4Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_08Eighth salt pulse for ceca 9, run 4Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_09Ninth salt pulse for ceca 9, run 4Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_10Tenth salt pulse for ceca 9, run 4Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_11Eleventh salt pulse for ceca 9, run 4Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032510_12Final salt pulse for ceca 9, run 4Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_01First salt pulse for ceca 9, run 5Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_02Second salt pulse for ceca 9, run 5Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_03Third salt pulse for ceca 9, run 5Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_04Fourth salt pulse for ceca 9, run 5Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_05Fifth salt pulse for ceca 9, run 5Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_06Sixth salt pulse for ceca 9, run 5Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_07Seventh salt pulse for ceca 9, run 5Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_08Eighth salt pulse for ceca 9, run 5Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_09Ninth salt pulse for ceca 9, run 5Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_10Tenth salt pulse for ceca 9, run 5Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_11Eleventh salt pulse for ceca 9, run 5Cecal_9_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032610_12Final salt pulse for ceca 9, run 5Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_01First salt pulse for ceca 12, run 4Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_02Second salt pulse for ceca 12, run 4Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_03Third salt pulse for ceca 12, run 4Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_04Fourth salt pulse for ceca 12, run 4Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_05Fifth salt pulse for ceca 12, run 4Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_06Sixth salt pulse for ceca 12, run 4Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_07Seventh salt pulse for ceca 12, run 4Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_08Eighth salt pulse for ceca 12, run 4Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_09Ninth salt pulse for ceca 12, run 4Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_10Tenth salt pulse for ceca 12, run 4Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_11Eleventh salt pulse for ceca 12, run 4Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run4_032710_12Final salt pulse for ceca 12, run 4Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_01First salt pulse for ceca 12, run 5Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_02Second salt pulse for ceca 12, run 5Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_03Third salt pulse for ceca 12, run 5Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_04Fourth salt pulse for ceca 12, run 5Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_05Fifth salt pulse for ceca 12, run 5Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_06Sixth salt pulse for ceca 12, run 5Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_07Seventh salt pulse for ceca 12, run 5Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_08Eighth salt pulse for ceca 12, run 5Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_09Ninth salt pulse for ceca 12, run 5Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_10Tenth salt pulse for ceca 12, run 5Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_11Eleventh salt pulse for ceca 12, run 5Cecal_12_100uL_SDSTCAUrea_2d_24hr_OrbiVelos_Run5_032810_12Final salt pulse for ceca 12, run 5