Microbial Respiration and Formate Oxidation as Metabolic Signatures of Inflammation-Associated Dysbiosis

Abaibou, 1995, Expression and characterization of the Escherichia coli fdo locus and a possible physiological role for aerobic formate dehydrogenase, J. Bacteriol., 177, 7141, 10.1128/jb.177.24.7141-7149.1995 Ahmed, 2012, Critical roles of Notch and Wnt/β-catenin pathways in the regulation of hyperplasia and/or colitis in response to bacterial infection, Infect. Immun., 80, 3107, 10.1128/IAI.00236-12 Baumgart, 2012, Crohn’s disease, Lancet, 380, 1590, 10.1016/S0140-6736(12)60026-9 Baumgart, 2007, Culture independent analysis of ileal mucosa reveals a selective increase in invasive Escherichia coli of novel phylogeny relative to depletion of Clostridiales in Crohn’s disease involving the ileum, ISME J., 1, 403, 10.1038/ismej.2007.52 Berg, 1990, Structural genes for nitrate-inducible formate dehydrogenase in Escherichia coli K-12, Genetics, 125, 691, 10.1093/genetics/125.4.691 Berg, 2002, Rapid development of colitis in NSAID-treated IL-10-deficient mice, Gastroenterology, 123, 1527, 10.1053/gast.2002.1231527 Berry, 2012, Phylotype-level 16S rRNA analysis reveals new bacterial indicators of health state in acute murine colitis, ISME J., 6, 2091, 10.1038/ismej.2012.39 Blattner, 1997, The complete genome sequence of Escherichia coli K-12, Science, 277, 1453, 10.1126/science.277.5331.1453 Buchfink, 2015, Fast and sensitive protein alignment using DIAMOND, Nat. Methods, 12, 59, 10.1038/nmeth.3176 Cheng, 2007, S- and N-Oxide Reductases, Ecosal Plus, 2, 2, 10.1128/ecosalplus.3.2.8 Cockburn, 2016, Polysaccharide Degradation by the Intestinal Microbiota and Its Influence on Human Health and Disease, J. Mol. Biol., 428, 3230, 10.1016/j.jmb.2016.06.021 Cole, 2008, Respiration of Nitrate and Nitrite, Ecosal Plus, 3, 3, 10.1128/ecosal.3.2.5 Eaves-Pyles, 2008, Escherichia coli isolated from a Crohn’s disease patient adheres, invades, and induces inflammatory responses in polarized intestinal epithelial cells, Int. J. Med. Microbiol., 298, 397, 10.1016/j.ijmm.2007.05.011 Eilam, 2014, Glycan degradation (GlyDeR) analysis predicts mammalian gut microbiota abundance and host diet-specific adaptations, MBio, 5, 5, 10.1128/mBio.01526-14 Faith, 2011, Predicting a human gut microbiota’s response to diet in gnotobiotic mice, Science, 333, 101, 10.1126/science.1206025 Fischbach, 2011, Eating for two: how metabolism establishes interspecies interactions in the gut, Cell Host Microbe, 10, 336, 10.1016/j.chom.2011.10.002 Flint, 2012, Microbial degradation of complex carbohydrates in the gut, Gut Microbes, 3, 289, 10.4161/gmic.19897 Frank, 2007, Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases, Proc. Natl. Acad. Sci. USA, 104, 13780, 10.1073/pnas.0706625104 Giaffer, 1991, The assessment of faecal flora in patients with inflammatory bowel disease by a simplified bacteriological technique, J. Med. Microbiol., 35, 238, 10.1099/00222615-35-4-238 Gutnick, 1969, Compounds which serve as the sole source of carbon or nitrogen for Salmonella typhimurium LT-2, J. Bacteriol., 100, 215, 10.1128/JB.100.1.215-219.1969 Hou, 2008, Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia, Biol. Direct, 3, 26, 10.1186/1745-6150-3-26 Huson, 2007, MEGAN analysis of metagenomic data, Genome Res., 17, 377, 10.1101/gr.5969107 Kelly, 2015, Crosstalk between Microbiota-Derived Short-Chain Fatty Acids and Intestinal Epithelial HIF Augments Tissue Barrier Function, Cell Host Microbe, 17, 662, 10.1016/j.chom.2015.03.005 Koropatkin, 2012, How glycan metabolism shapes the human gut microbiota, Nat. Rev. Microbiol., 10, 323, 10.1038/nrmicro2746 Lehtiö, 2004, The pyruvate formate lyase family: sequences, structures and activation, Protein Eng. Des. Sel., 17, 545, 10.1093/protein/gzh059 Leimkühler, 2016, Bacterial molybdoenzymes: old enzymes for new purposes, FEMS Microbiol. Rev., 40, 1, 10.1093/femsre/fuv043 Lopez, 2016, Virulence factors enhance Citrobacter rodentium expansion through aerobic respiration, Science, 353, 1249, 10.1126/science.aag3042 Lupp, 2007, Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae, Cell Host Microbe, 2, 119, 10.1016/j.chom.2007.06.010 Magalon, 2008, Biosynthesis and Insertion of the Molybdenum Cofactor, Ecosal Plus, 3, 3, 10.1128/ecosalplus.3.6.3.13 Martens, 2014, The devil lies in the details: how variations in polysaccharide fine-structure impact the physiology and evolution of gut microbes, J. Mol. Biol., 426, 3851, 10.1016/j.jmb.2014.06.022 Nagalingam, 2011, Microbial ecology of the murine gut associated with the development of dextran sodium sulfate-induced colitis, Inflamm. Bowel Dis., 17, 917, 10.1002/ibd.21462 Patel, 2014, The pyruvate dehydrogenase complexes: structure-based function and regulation, J. Biol. Chem., 289, 16615, 10.1074/jbc.R114.563148 Raetz, 2013, Parasite-induced TH1 cells and intestinal dysbiosis cooperate in IFN-γ-dependent elimination of Paneth cells, Nat. Immunol., 14, 136, 10.1038/ni.2508 Ragsdale, 2003, Pyruvate ferredoxin oxidoreductase and its radical intermediate, Chem. Rev., 103, 2333, 10.1021/cr020423e Rigottier-Gois, 2013, Dysbiosis in inflammatory bowel diseases: the oxygen hypothesis, ISME J., 7, 1256, 10.1038/ismej.2013.80 Rivera-Chávez, 2016, Depletion of Butyrate-Producing Clostridia from the Gut Microbiota Drives an Aerobic Luminal Expansion of Salmonella, Cell Host Microbe, 19, 443, 10.1016/j.chom.2016.03.004 Ruiz-Herrera, 1969, Nitrate reductase complex of Escherichia coli K-12: isolation and characterization of mutants unable to reduce nitrate, J. Bacteriol., 97, 1291, 10.1128/JB.97.3.1291-1297.1969 Samuel, 2006, A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism, Proc. Natl. Acad. Sci. USA, 103, 10011, 10.1073/pnas.0602187103 Sawers, 2004, Fermentative Pyruvate and Acetyl-Coenzyme A Metabolism, Ecosal Plus, 1, 1, 10.1128/ecosalplus.3.5.3 Sawers, 2004, Anaerobic Formate and Hydrogen Metabolism, Ecosal Plus, 1, 1, 10.1128/ecosalplus.3.5.4 Scott, 1976, Formation of the formate-nitrate electron transport pathway from inactive components in Escherichia coli, J. Bacteriol., 126, 478, 10.1128/JB.126.1.478-486.1976 Seksik, 2003, Alterations of the dominant faecal bacterial groups in patients with Crohn’s disease of the colon, Gut, 52, 237, 10.1136/gut.52.2.237 Shin, 2015, Proteobacteria: microbial signature of dysbiosis in gut microbiota, Trends Biotechnol., 33, 496, 10.1016/j.tibtech.2015.06.011 Sonnenburg, 2016, Diet-microbiota interactions as moderators of human metabolism, Nature, 535, 56, 10.1038/nature18846 Sonnenburg, 2010, Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations, Cell, 141, 1241, 10.1016/j.cell.2010.05.005 Stecher, 2007, Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota, PLoS Biol., 5, 2177, 10.1371/journal.pbio.0050244 Tasman, 1935, The formation of hydrogen from glucose and formic acid by the so-called “resting” B. coli. I, Biochem. J., 29, 1749, 10.1042/bj0291749 Thauer, 1972, Properties and function of the pyruvate-formate-lyase reaction in clostridiae, Eur. J. Biochem., 27, 282, 10.1111/j.1432-1033.1972.tb01837.x Unden, 2014, The Aerobic and Anaerobic Respiratory Chain of Escherichia coli and Salmonella enterica: Enzymes and Energetics, Ecosal Plus, 6, 10.1128/ecosalplus.ESP-0005-2013 Vujkovic-Cvijin, 2013, Dysbiosis of the gut microbiota is associated with HIV disease progression and tryptophan catabolism, Sci. Transl. Med., 5, 193ra91, 10.1126/scitranslmed.3006438 Wang, 2003, Coordinate regulation of the Escherichia coli formate dehydrogenase fdnGHI and fdhF genes in response to nitrate, nitrite, and formate: roles for NarL and NarP, J. Bacteriol., 185, 5076, 10.1128/JB.185.17.5076-5085.2003 Winter, 2013, The dynamics of gut-associated microbial communities during inflammation, EMBO Rep., 14, 319, 10.1038/embor.2013.27 Winter, 2013, Host-derived nitrate boosts growth of E. coli in the inflamed gut, Science, 339, 708, 10.1126/science.1232467 Wrigley, 1961, Formic acid dehydrogenasecytochrome b1 complex from Escherichia coli, Biochem. Biophys. Res. Commun., 4, 66, 10.1016/0006-291X(61)90257-1 Wu, 2011, Linking long-term dietary patterns with gut microbial enterotypes, Science, 334, 105, 10.1126/science.1208344