Extended Data Fig. 8: Asparagine and glutamine can be used as sole nitrogen sources by most tested Bacteroidetes.
From: A metabolomics pipeline for the mechanistic interrogation of the gut microbiome
a, Top, an example decision tree from a forest that can differentiate Bacteroidetes versus bacteria from the other four represented phyla with >97% accuracy. For each decision node, phylum-level increases and decreases based on metabolite levels are shown (relative fold change compared to the bacterial medium controls, log2-transformed). Actinobacteria (n = 20), Bacteroidetes (n = 57), Firmicutes (n = 83), Fusobacteria (n = 3) and Proteobacteria (n = 10). Dashed line, metabolite threshold. Box, median, 25th and 75th percentiles; whiskers: Tukey’s method. Bottom, the 10 most important features differentiating the five tested phyla. Data are shown as median metabolite log2-fold-change values for each phylum; metabolites and phyla are ordered by Ward linkage distance. b, Representative growth curves from two independent experiments, each with n = 3 biological replicates for a subset of Bacteroides spp. using modified SMM with the indicated nitrogen source. Legend colours for the sole nitrogen source are the same in b–d. c, Representative growth curves of one experiment with n = 5 biological replicates for 60 Bacteroidetes using modified SMM with the indicated nitrogen sources. d, Growth curves of wild-type and mutant B. thetaiotaomicron (Bt) grown in defined minimal media with either cysteine (top) (one experiment, n = 3 biological replicates) or sodium sulfide (Na2S, bottom) as sole reduced sulfur sources (one experiment, n = 3 biological replicates). e, Amino acid production and consumption levels in gnotobiotic mice mono-colonized with B. thetaiotaomicron (one experiment, n = 5 mice). Box, median, 25th and 75th percentiles; whiskers, Tukey’s method. Numeric labels in b and c correspond to the following: 1, B. acidifaciens DSMZ 15896; 2, B. caccae ATCC 43185; 3, B. caccae BEI HM-728; 4, B. cellulosilyticus BEI HM-726; 5, B. cellulosilyticus DSMZ 14838; 6, B. coprophilus DSMZ 18228; 7, B. dorei BEI HM-29; 8, B. dorei BEI HM-717; 9, B. dorei BEI HM-718; 10, B. dorei BEI HM-719; 11, B. dorei DSMZ 17855; 12, B. eggerthii ATCC 27754; 13, B. eggerthii DSMZ 20697; 14, B. finegoldii BEI HM-727; 15, B. finegoldii DSMZ 17565; 16, B. fragilis BEI HM-20; 17, B. fragilis BEI HM-710; 18, B. fragilis BEI HM-711; 19, B. fragilis BEI HM-714; 20, B. fragilis NCTC 9343; 21, B. intestinalis DSMZ 17393; 22, B. ovatus ATCC 8483; 23, B. ovatus BEI HM-222; 24, B. pectinophilus ATCC 43243; 25, B. plebeius DSMZ 17135; 26, B. salyersiae BEI HM-725; 27, Bacteroides sp. BEI HM-18; 28, Bacteroides sp. BEI HM-189; 29, Bacteroides sp. BEI HM-19; 30, Bacteroides sp. BEI HM-22; 31, Bacteroides sp. BEI HM-23; 32, Bacteroides sp. BEI HM-258; 33, Bacteroides sp. BEI HM-27; 34, Bacteroides sp. BEI HM-28; 35, Bacteroides sp. BEI HM-58; 36, B. stercoris ATCC 43183; 37, B. stercoris BEI HM-1036; 38, B. thetaiotaomicron 3730; 39, B. thetaiotaomicron 3731; 40, B. thetaiotaomicron 633; 41, B. thetaiotaomicron 7330; 42, B. thetaiotaomicron 7853; 43, B. thetaiotaomicron 8702; 44, B. thetaiotaomicron 8713; 45, B. thetaiotaomicron 8736; 46, B. thetaiotaomicron 940; 47, B. thetaiotaomicron VPI 5482; 48, B. thetaiotaomicron WH302; 49, B. thetaiotaomicron WH305; 50, B. uniformis ATCC 8492; 51, B. vulgatus ATCC 8482; 52, B. vulgatus BEI HM-720; 53, B. xylanisolvens DSMZ 18836; 54, P. distasonis ATCC 8503; 55, P. distasonis BEI HM-169; 56, P. johnsonii BEI HM-731; 57, P. johnsonii DSMZ 18315; 58, P. merdae ATCC 43184; 59, P. merdae BEI HM-729; 60, P. merdae BEI HM-730.
