Bindloss et al ATP measurements For determination of intracellular ATP measurements, primary colonocytes were isolated as described above. ATP measurement in colonocyte lysates was performed by using a ATP Colorimetry Assay Kit (Biovision), according to manufacturer's instructions Statistical Analysis Fold changes of ratios(bacterial competitive index, mRNA levels and protein levels), percentages(flow cytometry )and bacterial numbers were transformed logarithmically prior to statistical analysis. An unpaired Student's t test was used on the transformed data to determine whether differences between groups were statistically significant(p<0.05) When more than two treatments were used, statistically significant differences between groups were determined by one-way ANOVA followed by Tukey's HSD test(between >2 groups). Significance of differences in hypoxia scores was determined by a one-tailed non- parametric test(Kruskal Wallis) Supplementary Material Refer to Web version on PubMed Central for supplementary material. Acknowledgments We acknowledge the Host-Microbe Systems Biology Core(HMSB Core)at the UC Davis School of Medicine for expert technical assistance with microbiota sequence analysis. The data reported in the manuscript are tabulated the main paper and in the supplementary materials. M.X. B. and A.J. B. filed invention report number 0577501-16-0038 at iEdison. gov for a treatment to prevent post-antibiotic expansion of Enterobacteriaceae. This work was supported by Public Health Service Grants Al060555(SA C ) TROO1861(EEO ) All12241(CA L ) DKO87307(C G), All09799(R. M.T), All12258(R. M.T), All12949(AJ B andR. M.T), Al096528(A. B ) AI112445(A.J.B.), and Alll4922(A.JB.) References and notes 1. Shin NR, Whon TW, Bae JW. Proteobacteria: microbial signature of dysbiosis in gut microbiota Trends Biotechnol. 2015; 33: 496-503. [PubMed: 26210164 2. Spees AM, et al. Streptomycin-induced inflammation enhances Escherichia coli gut colonization through nitrate respiration. MBio. 2013: 4: e00430-00413 Rivera-Chavez F, et al. Depletion of Butyrate- Producing Clostridia from the Gut Microbiota Drives an Aerobic Luminal Expansion of Salmonella Cell Host Microbe 2016: 19: 443-454.[ PubMed 27078066] 4. Winter SE, et al. Host-derived nitrate boosts growth of E. coli in the inflamed gut. Science. 2013: 339:708-711. pUbmEd:23393266] 5. Donohoe DR, et al. The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon Cell Metab. 2011; 13: 517-526[PubMed: 21531334] 6. Marion-Letellier R, Butler M, Dechelotte P, Playford R, Ghosh S. Comparison of cytokine modulation by natural peroxisome proliferator-activated receptor gamma ligands with synthetic ligands in intestinal-like Caco-2 cells and human dendritic cells- potential for dietary modulation of peroxisome proliferator-activated receptor gamma in intestinal inflammation. Am J Clin Nutr. 2008 87:939-948 7. Lefebvre M, et al. Peroxisome proliferator-activated receptor gamma is induced during differentiation of colon epithelium cells. J Endocrinol. 1999; 162: 331-340. [PubMed: 10467224] Science Author manuscript; available in PMC 2017 October 1ATP measurements For determination of intracellular ATP measurements, primary colonocytes were isolated as described above. ATP measurement in colonocyte lysates was performed by using a ATP Colorimetry Assay Kit (Biovision), according to manufacturer’s instructions. Statistical Analysis Fold changes of ratios (bacterial competitive index, mRNA levels and protein levels), percentages (flow cytometry) and bacterial numbers were transformed logarithmically prior to statistical analysis. An unpaired Student’s t test was used on the transformed data to determine whether differences between groups were statistically significant (p < 0.05). When more than two treatments were used, statistically significant differences between groups were determined by one-way ANOVA followed by Tukey’s HSD test (between > 2 groups). Significance of differences in hypoxia scores was determined by a one-tailed non￾parametric test (Kruskal Wallis). Supplementary Material Refer to Web version on PubMed Central for supplementary material. Acknowledgments We acknowledge the Host-Microbe Systems Biology Core (HMSB Core) at the UC Davis School of Medicine for expert technical assistance with microbiota sequence analysis. The data reported in the manuscript are tabulated in the main paper and in the supplementary materials. M.X.B. and A.J.B. filed invention report number 0577501-16-0038 at iEdison.gov for a treatment to prevent post-antibiotic expansion of Enterobacteriaceae. This work was supported by Public Health Service Grants AI060555 (S.A.C.), TR001861 (E.E.O.), AI112241 (C.A.L.), DK087307 (C.G.), AI109799 (R.M.T), AI112258 (R.M.T), AI112949 (A.J.B. and R.M.T.), AI096528 (A.J.B.), AI112445 (A.J.B.), and AI114922 (A.J.B.). References and Notes 1. Shin NR, Whon TW, Bae JW. Proteobacteria: microbial signature of dysbiosis in gut microbiota. Trends Biotechnol. 2015; 33:496–503. [PubMed: 26210164] 2. Spees AM, et al. Streptomycin-induced inflammation enhances Escherichia coli gut colonization through nitrate respiration. MBio. 2013; 4:e00430–00413. 3. Rivera-Chavez F, et al. Depletion of Butyrate-Producing Clostridia from the Gut Microbiota Drives an Aerobic Luminal Expansion of Salmonella. Cell Host Microbe. 2016; 19:443–454. [PubMed: 27078066] 4. Winter SE, et al. Host-derived nitrate boosts growth of E. coli in the inflamed gut. Science. 2013; 339:708–711. [PubMed: 23393266] 5. Donohoe DR, et al. The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon. Cell Metab. 2011; 13:517–526. [PubMed: 21531334] 6. Marion-Letellier R, Butler M, Dechelotte P, Playford RJ, Ghosh S. Comparison of cytokine modulation by natural peroxisome proliferator-activated receptor gamma ligands with synthetic ligands in intestinal-like Caco-2 cells and human dendritic cells– potential for dietary modulation of peroxisome proliferator-activated receptor gamma in intestinal inflammation. Am J Clin Nutr. 2008; 87:939–948. [PubMed: 18400717] 7. Lefebvre M, et al. Peroxisome proliferator-activated receptor gamma is induced during differentiation of colon epithelium cells. J Endocrinol. 1999; 162:331–340. [PubMed: 10467224] Byndloss et al. Page 14 Science. Author manuscript; available in PMC 2017 October 16. Author Manuscript Author Manuscript Author Manuscript Author Manuscript