Microbiome and metabolome data integration provides insight into health and disease
Tài liệu tham khảo
Rumsfeld D, Myers R. DoD News Briefing. Available at: http://archive.defense.gov/Transcripts/Transcript.aspx?TranscriptID52636 2002. Accessed April 20, 2017.
Stahl, 1985, Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences, Appl Environ Microbiol, 49, 1379, 10.1128/AEM.49.6.1379-1384.1985
Pace, 1997, A molecular view of microbial diversity and the biosphere, Science, 276, 734, 10.1126/science.276.5313.734
Pace, 2009, Mapping the tree of life: progress and prospects, Microbiol Mol Biol Rev, 73, 565, 10.1128/MMBR.00033-09
Rappé, 2002, Cultivation of the ubiquitous SAR11 marine bacterioplankton clade, Nature, 418, 630, 10.1038/nature00917
Huse, 2008, Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing, PLoS Genet, 4, e1000255, 10.1371/journal.pgen.1000255
Tsementzi, 2016, SAR11 bacteria linked to ocean anoxia and nitrogen loss, Nature, 536, 179, 10.1038/nature19068
Dethlefsen, 2008, The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing, PLoS Biol, 6, e280, 10.1371/journal.pbio.0060280
McKenna, 2008, The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis, PLoS Pathog, 4, e20, 10.1371/journal.ppat.0040020
Caporaso, 2011, Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample, Proc Natl Acad Sci U S A, 108, 4516, 10.1073/pnas.1000080107
Caporaso, 2010, QIIME allows analysis of high-throughput community sequencing data, Nat Methods, 7, 335, 10.1038/nmeth.f.303
Quast, 2013, The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Res, 41, D590, 10.1093/nar/gks1219
DeSantis, 2006, Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB, Appl Environ Microbiol, 72, 5069, 10.1128/AEM.03006-05
Raman, 2013, Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease, Clin Gastroenterol Hepatol, 11, 868, 10.1016/j.cgh.2013.02.015
Martinez, 2017, Western diets, and metabolic diseases: are they linked?, Gut Microbes, 8, 130, 10.1080/19490976.2016.1270811
Evrensel, 2015, The gut-brain Axis: the missing link in depression, Clin Psychopharmacol Neurosci, 13, 239, 10.9758/cpn.2015.13.3.239
Halfvarson, 2017, Dynamics of the human gut microbiome in inflammatory bowel disease, Nat Microbiol, 2, 17004, 10.1038/nmicrobiol.2017.4
Dickson, 2017, Gut microbiota: diagnosing IBD with the gut microbiome, Nat Rev Gastroenterol Hepatol, 14, 195, 10.1038/nrgastro.2017.25
Kitai, 2016, Exploring the microbiome in heart failure, Curr Heart Fail Rep, 13, 103, 10.1007/s11897-016-0285-9
Wang, 2011, Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease, Nature, 472, 57, 10.1038/nature09922
Haiser, 2013, Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta, Science, 341, 295, 10.1126/science.1235872
Clayton, 2012, Metabolic differences underlying two distinct rat urinary phenotypes, a suggested role for gut microbial metabolism of phenylalanine and a possible connection to autism, FEBS Lett, 586, 956, 10.1016/j.febslet.2012.01.049
Buie, 2015, Potential etiologic factors of microbiome disruption in autism, Clin Ther, 37, 976, 10.1016/j.clinthera.2015.04.001
Rosenfeld, 2015, Microbiome disturbances and autism spectrum Disorders, Drug Metab Dispos, 43, 1557, 10.1124/dmd.115.063826
Kanehisa, 2017, KEGG: new perspectives on genomes, pathways, diseases and drugs, Nucleic Acids Res, 45, D353, 10.1093/nar/gkw1092
Caspi, 2014, The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases, Nucleic Acids Res, 42, D459, 10.1093/nar/gkt1103
Guo, 2017, Discovery of reactive microbiota-derived metabolites that inhibit host proteases, Cell, 168, 517, 10.1016/j.cell.2016.12.021
Wishart, 2016, Emerging applications of metabolomics in drug discovery and precision medicine, Nat Rev Drug Discov, 15, 473, 10.1038/nrd.2016.32
Sethi, 2017, Recent advances in lipidomics: analytical and clinical perspectives, Prostaglandins Other Lipid Mediat, 128, 8, 10.1016/j.prostaglandins.2016.12.002
Armstrong, 2009, Leukotriene-E4 in human urine: comparison of on-line purification and liquid chromatography–tandem mass spectrometry to affinity purification followed by enzyme immunoassay, J Chromatogr B Analyt Technol Biomed Life Sci, 877, 3169, 10.1016/j.jchromb.2009.08.011
Armstrong, 2007, Analysis of 25 underivatized amino acids in human plasma using ion-pairing reversed-phase liquid chromatography/time-of-flight mass spectrometry, Rapid Commun Mass Spectrom, 21, 2717, 10.1002/rcm.3124
Spratlin, 2009, Clinical applications of metabolomics in oncology: a review, Clin Cancer Res, 15, 431, 10.1158/1078-0432.CCR-08-1059
Markley, 2017, The future of NMR-based metabolomics, Curr Opin Biotechnol, 43, 34, 10.1016/j.copbio.2016.08.001
Kohler, 2016, Analytical pitfalls and challenges in clinical metabolomics, Bioanalysis, 8, 1509, 10.4155/bio-2016-0090
Persicke, 2012, MSEA: metabolite set enrichment analysis in the MeltDB metabolomics software platform: metabolic profiling of Corynebacterium glutamicum as an example, Metabolomics, 8, 310, 10.1007/s11306-011-0311-6
Xia, 2016, Using MetaboAnalyst 3.0 for comprehensive metabolomics data analysis, Curr Protoc Bioinformatics, 55, 10.1002/cpbi.11
Garg, 2017, Natural products as mediators of disease, Nat Prod Rep, 34, 194, 10.1039/C6NP00063K
Donia, 2015, Small molecules from the human microbiota, Science, 349, 1254766, 10.1126/science.1254766
Wikoff, 2009, Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites, Proc Natl Acad Sci U S A, 106, 3698, 10.1073/pnas.0812874106
Marcobal, 2013, A metabolomic view of how the human gut microbiota impacts the host metabolome using humanized and gnotobiotic mice, ISME J, 7, 1933, 10.1038/ismej.2013.89
Martin, 2007, A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model, Mol Syst Biol, 3, 112, 10.1038/msb4100153
Martin, 2008, Probiotic modulation of symbiotic gut microbial-host metabolic interactions in a humanized microbiome mouse model, Mol Syst Biol, 4, 157, 10.1038/msb4100190
Gilbert, 2016, Microbiome-wide association studies link dynamic microbial consortia to disease, Nature, 535, 94, 10.1038/nature18850
Clarke, 2014, Minireview: gut microbiota: the neglected endocrine organ, Mol Endocrinol, 28, 1221, 10.1210/me.2014-1108
Sridharan, 2014, Prediction and quantification of bioactive microbiota metabolites in the mouse gut, Nat Commun, 5, 5492, 10.1038/ncomms6492
Ursell, 2014, The intestinal metabolome: an Intersection between microbiota and host, Gastroenterology, 146, 1470, 10.1053/j.gastro.2014.03.001
Li, 2014, An integrated catalog of reference genes in the human gut microbiome, Nat Biotechnol, 32, 834, 10.1038/nbt.2942
Theriot, 2014, Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection, Nat Commun, 5, 781, 10.1038/ncomms4114
Donia, 2014, A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics, Cell, 158, 1402, 10.1016/j.cell.2014.08.032
Theriot, 2016, Antibiotic-induced alterations of the gut microbiota alter secondary bile acid production and allow for Clostridium difficile spore germination and outgrowth in the large intestine, mSphere, 1, 10.1128/mSphere.00045-15
Antunes, 2011, Effect of antibiotic treatment on the intestinal metabolome, Antimicrobial Agents Chemother, 55, 1494, 10.1128/AAC.01664-10
Swann, 2011, Variation in antibiotic-induced microbial recolonization impacts on the host metabolic phenotypes of rats, J Proteome Res, 10, 3590, 10.1021/pr200243t
Romick-Rosendale, 2009, NMR-based metabonomics analysis of mouse urine and fecal extracts following oral treatment with the broad-spectrum antibiotic enrofloxacin (Baytril), Magn Reson Chem, 47, S36, 10.1002/mrc.2511
David, 2013, Diet rapidly and reproducibly alters the human gut microbiome, Nature, 505, 559, 10.1038/nature12820
Ruengsomwong, 2014, Senior thai fecal microbiota comparison between vegetarians and non-vegetarians using PCR-DGGE and real-time PCR, J Microbiol Biotechnol, 24, 1026, 10.4014/jmb.1310.10043
Turnbaugh, 2009, A core gut microbiome in obese and lean twins, Nature, 457, 480, 10.1038/nature07540
Wu, 2016, Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production, Gut, 65, 63, 10.1136/gutjnl-2014-308209
Scalbert, 2014, The food metabolome: a window over dietary exposure, Am J Clin Nutr, 99, 1286, 10.3945/ajcn.113.076133
Edmands, 2015, Polyphenol metabolome in human urine and its association with intake of polyphenol-rich foods across European countries, Am J Clin Nutr, 102, 905, 10.3945/ajcn.114.101881
De Angelis, 2015, Effect of whole-grain barley on the human fecal microbiota and metabolome, Appl Environ Microbiol, 81, 7945, 10.1128/AEM.02507-15
Heinritz, 2016, Intestinal microbiota and microbial metabolites are changed in a pig model fed a high-fat/low-fiber or a low-fat/high-fiber diet, PLoS One, 11, e0154329, 10.1371/journal.pone.0154329
Russell, 2011, High-protein, reduced-carbohydrate weight-loss diets promote metabolite profiles likely to be detrimental to colonic health, Am J Clin Nutr, 93, 1062, 10.3945/ajcn.110.002188
Trompette, 2014, Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis, Nat Med, 20, 159, 10.1038/nm.3444
Montoliu, 2016, Modeling longitudinal metabonomics and microbiota interactions in C57BL/6 mice fed a high fat diet, Anal Chem, 88, 7617, 10.1021/acs.analchem.6b01343
Grice, 2009, Topographical and temporal diversity of the human skin microbiome, Science, 324, 1190, 10.1126/science.1171700
Bouslimani, 2015, Molecular cartography of the human skin surface in 3D, Proc Natl Acad Sci U S A, 112, E2120, 10.1073/pnas.1424409112
Claus, 2016, The gut microbiota: a major player in the toxicity of environmental pollutants?, NPJ Biofilms Microbiomes, 2, 16003, 10.1038/npjbiofilms.2016.3
Sowada, 2014, Degradation of benzo[a]pyrene by bacterial isolates from human skin, FEMS Microbiol Ecol, 88, 129, 10.1111/1574-6941.12276
Spanogiannopoulos, 2016, The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism, Nat Rev Micro, 14, 273, 10.1038/nrmicro.2016.17
Lee, 2014, Gut microbiota-generated metabolites in animal health and disease, Nat Chem Biol, 10, 416, 10.1038/nchembio.1535
Wilson, 2017, Natural product discovery from the human microbiome, J Biol Chem, 292, 8546, 10.1074/jbc.R116.762906
Cohen, 2015, Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist, Proc Natl Acad Sci U S A, 112, E4825, 10.1073/pnas.1508737112
Zipperer, 2016, Human commensals producing a novel antibiotic impair pathogen colonization, Nature, 535, 511, 10.1038/nature18634
Hsiao, 2013, Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental Disorders, Cell, 155, 1451, 10.1016/j.cell.2013.11.024
Neis, 2015, The role of microbial amino acid metabolism in host metabolism, Nutrients, 7, 2930, 10.3390/nu7042930
Koeth, 2013, Intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis, Nat Med, 19, 576, 10.1038/nm.3145
Harvey, 2015, The re-emergence of natural products for drug discovery in the genomics era, Nat Rev Drug Discov, 14, 111, 10.1038/nrd4510
Moree, 2012, Interkingdom metabolic transformations captured by microbial imaging mass spectrometry, Proc Natl Acad Sci U S A, 109, 13811, 10.1073/pnas.1206855109
Blin, 2013, antiSMASH 2.0–a versatile platform for genome mining of secondary metabolite producers, Nucleic Acids Res, 41, W204, 10.1093/nar/gkt449
Medema, 2011, antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences, Nucleic Acids Res, 39, W339, 10.1093/nar/gkr466
Weber, 2015, antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters, Nucleic Acids Res, 43, W237, 10.1093/nar/gkv437
Blin, 2017, antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification, Nucleic Acids Res, 45, W36, 10.1093/nar/gkx319
Zierep, 2017, SeMPI: a genome-based secondary metabolite prediction and identification web server, Nucleic Acids Res, 45, W64, 10.1093/nar/gkx289
Khater, 2017, SBSPKSv2: structure-based sequence analysis of polyketide synthases and non-ribosomal peptide synthetases, Nucleic Acids Res, 45, W72, 10.1093/nar/gkx344
Balskus, 2015, Colibactin: understanding an elusive gut bacterial genotoxin, Nat Prod Rep, 32, 1534, 10.1039/C5NP00091B
Chu, 2016, Discovery of MRSA active antibiotics using primary sequence from the human microbiome, Nat Chem Biol, 12, 1004, 10.1038/nchembio.2207
Kersten, 2013, Glycogenomics as a mass spectrometry-guided genome-mining method for microbial glycosylated molecules, Proc Natl Acad Sci U S A, 110, E4407, 10.1073/pnas.1315492110
Kersten, 2011, A mass spectrometry–guided genome mining approach for natural product peptidogenomics, Nat Chem Biol, 7, 794, 10.1038/nchembio.684
Pedersen, 2016, Human gut microbes impact host serum metabolome and insulin sensitivity, Nature, 535, 376, 10.1038/nature18646
Faust, 2012, Microbial interactions: from networks to models, Nat Rev Microbiol, 10, 538, 10.1038/nrmicro2832
Faust, 2012, Microbial Co-occurrence relationships in the human microbiome, PLoS Comput Biol, 8, e1002606, 10.1371/journal.pcbi.1002606
Kelder, 2014, Correlation network analysis reveals relationships between diet-induced changes in human gut microbiota and metabolic health, Nutr Diabetes, 4, e122, 10.1038/nutd.2014.18
Lozupone, 2012, Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts, Genome Res, 22, 1974, 10.1101/gr.138198.112
Weiss, 2016, Correlation detection strategies in microbial data sets vary widely in sensitivity and precision, ISME J, 10, 1669, 10.1038/ismej.2015.235
Derewacz, 2015, Mapping microbial response metabolomes for induced natural product discovery, ACS Chem Biol, 10, 1998, 10.1021/acschembio.5b00001
Goodwin, 2015, Structuring microbial metabolic responses to multiplexed stimuli via self-organizing metabolomics maps, Chem Biol, 22, 661, 10.1016/j.chembiol.2015.03.020
Goodwin, 2014, Phenotypic mapping of metabolic profiles using self-organizing maps of high-dimensional mass spectrometry data, Anal Chem, 86, 6563, 10.1021/ac5010794
Quinn, 2016, Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome, ISME J, 10, 1483, 10.1038/ismej.2015.207
Wang, 2016, Sharing and community curation of mass spectrometry data with global natural products social molecular networking, Nat Biotech, 34, 828, 10.1038/nbt.3597
Yang, 2013, Molecular networking as a dereplication strategy, J Nat Prod, 76, 1686, 10.1021/np400413s
Watrous, 2012, Mass spectral molecular networking of living microbial colonies, Proc Natl Acad Sci U S A, 109, E1743, 10.1073/pnas.1203689109
Rutledge, 2015, Discovery of microbial natural products by activation of silent biosynthetic gene clusters, Nat Rev Microbiol, 13, 509, 10.1038/nrmicro3496
Browne, 2016, Culturing of “unculturable” human microbiota reveals novel taxa and extensive sporulation, Nature, 533, 543, 10.1038/nature17645
Stewart, 2002, Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov, Int J Syst Evol Microbiol, 52, 2141
Goodman, 2011, Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice, Proc Natl Acad Sci U S A, 108, 6252, 10.1073/pnas.1102938108
Oberhardt, 2015, Harnessing the landscape of microbial culture media to predict new organism–media pairings, Nat Commun, 6, 8493, 10.1038/ncomms9493
Bertrand, 2014, Metabolite induction via microorganism co-culture: a potential way to enhance chemical diversity for drug discovery, Biotechnol Adv, 32, 1180, 10.1016/j.biotechadv.2014.03.001
D’Onofrio, 2010, Siderophores from neighboring organisms promote the growth of uncultured bacteria, Chem Biol, 17, 254, 10.1016/j.chembiol.2010.02.010
Barkal, 2016, Microbial metabolomics in open microscale platforms, Nat Commun, 7, 10610, 10.1038/ncomms10610
Lagier, 2012, Microbial culturomics: paradigm shift in the human gut microbiome study, Clin Microbiol Infect, 18, 1185, 10.1111/1469-0691.12023
Ling, 2015, A new antibiotic kills pathogens without detectable resistance, Nature, 517, 455, 10.1038/nature14098
Zengler, 2002, Cultivating the uncultured, Proc Natl Acad Sci U S A, 99, 15681, 10.1073/pnas.252630999
Fritz, 2013, From meta-omics to causality: experimental models for human microbiome research, Microbiome, 1, 14, 10.1186/2049-2618-1-14
Shah, 2016, A microfluidics-based in vitro model of the gastrointestinal human–microbe interface, Nat Commun, 7, 11535, 10.1038/ncomms11535
Rooks, 2016, Gut microbiota, metabolites and host immunity, Nat Rev Immunol, 16, 341, 10.1038/nri.2016.42
Lundberg, 2016, Antibiotic-treated versus germ-free rodents for microbiota transplantation studies, Gut Microbes, 7, 68, 10.1080/19490976.2015.1127463
Winston, 2016, Impact of microbial derived secondary bile acids on colonization resistance against Clostridium difficile in the gastrointestinal tract, Anaerobe, 41, 44, 10.1016/j.anaerobe.2016.05.003
Wang, 2015, Non-lethal inhibition of gut microbial trimethylamine production for the treatment of atherosclerosis, Cell, 163, 1585, 10.1016/j.cell.2015.11.055
Sassone-Corsi, 2016, Microcins mediate competition among Enterobacteriaceae in the inflamed gut, Nature, 540, 280, 10.1038/nature20557
Tan, 2015, Unraveling interactions in microbial communities - from co-cultures to microbiomes, J Microbiol, 53, 295, 10.1007/s12275-015-5060-1
Edlund, 2013, An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome, Microbiome, 1, 25, 10.1186/2049-2618-1-25
Auchtung, 2015, Cultivation of stable, reproducible microbial communities from different fecal donors using minibioreactor arrays (MBRAs), Microbiome, 3, 42, 10.1186/s40168-015-0106-5
Robinson, 2014, Epidemic Clostridium difficile strains demonstrate increased competitive fitness compared to nonepidemic isolates, Infect Immun, 82, 2815, 10.1128/IAI.01524-14
von Martels, 2017, The role of gut microbiota in health and disease: in vitro modeling of host-microbe interactions at the aerobe-anaerobe interphase of the human gut, Anaerobe, 44, 3, 10.1016/j.anaerobe.2017.01.001
Rao, 2015, Fecal microbiota transplantation for the management of Clostridium difficile infection, Infect Dis Clin North Am, 29, 109, 10.1016/j.idc.2014.11.009
Buffie, 2015, Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile, Nature, 517, 205, 10.1038/nature13828
Paramsothy, 2017, Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial, Lancet, 389, 1218, 10.1016/S0140-6736(17)30182-4
Moayyedi, 2015, Fecal microbiota transplantation induces remission in patients with active ulcerative colitis in a randomized controlled trial, Gastroenterology, 149, 102, 10.1053/j.gastro.2015.04.001
Bajaj, 2014, Randomised clinical trial: Lactobacillus GG modulates gut microbiome, metabolome and endotoxemia in patients with cirrhosis, Aliment Pharmacol Ther, 39, 1113, 10.1111/apt.12695
Floch, 2015, Recommendations for probiotic use–2015 update: proceedings and consensus opinion, J Clin Gastroenterol, 49 Suppl 1, S69, 10.1097/MCG.0000000000000420
Gauffin Cano, 2012, Bacteroides uniformis CECT 7771 ameliorates metabolic and immunological dysfunction in mice with high-fat-diet induced obesity, PLoS One, 7, e41079, 10.1371/journal.pone.0041079
Everard, 2013, Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity, Proc Natl Acad Sci U S A, 110, 9066, 10.1073/pnas.1219451110
Neff, 2016, Diverse intestinal bacteria contain putative zwitterionic capsular polysaccharides with anti-inflammatory properties, Cell Host Microbe, 20, 535, 10.1016/j.chom.2016.09.002
Mazmanian, 2008, A microbial symbiosis factor prevents intestinal inflammatory disease, Nature, 453, 620, 10.1038/nature07008
Atarashi, 2013, Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota, Nature, 500, 232, 10.1038/nature12331
Bindels, 2015, Towards a more comprehensive concept for prebiotics, Nat Rev Gastroenterol Hepatol, 12, 303, 10.1038/nrgastro.2015.47
Tzortzis, 2005, Synthesis of prebiotic galactooligosaccharides using whole cells of a novel strain, bifidobacterium bifidum NCIMB 41171, Appl Microbiol Biotechnol, 68, 412, 10.1007/s00253-005-1919-0
Depeint, 2008, Prebiotic evaluation of a novel galactooligosaccharide mixture produced by the enzymatic activity of Bifidobacterium bifidum NCIMB 41171, in healthy humans: a randomized, double-blind, crossover, placebo-controlled intervention study, Am J Clin Nutr, 87, 785, 10.1093/ajcn/87.3.785
O’Mahony, 2005, Lactobacillus and bifidobacterium in irritable bowel syndrome: symptom responses and relationship to cytokine profiles, Gastroenterology, 128, 541, 10.1053/j.gastro.2004.11.050
Whorwell, 2006, Efficacy of an encapsulated probiotic bifidobacterium infantis 35624 in women with irritable bowel syndrome, Am J Gastroenterol, 101, 1581, 10.1111/j.1572-0241.2006.00734.x
Guyonnet, 2007, Effect of a fermented milk containing Bifidobacterium animalis DN-173 010 on the health-related quality of life and symptoms in irritable bowel syndrome in adults in primary care: a multicentre, randomized, double-blind, controlled trial, Aliment Pharmacol Ther, 26, 475, 10.1111/j.1365-2036.2007.03362.x
Silk, 2009, Clinical trial: the effects of a trans-galactooligosaccharide prebiotic on faecal microbiota and symptoms in irritable bowel syndrome, Aliment Pharmacol Ther, 29, 508, 10.1111/j.1365-2036.2008.03911.x
Suez, 2017, The path towards microbiome-based metabolite treatment, Nat Microbiol, 2, 17075, 10.1038/nmicrobiol.2017.75
Canani, 2011, Potential beneficial effects of butyrate in intestinal and extraintestinal diseases, World J Gastroenterol, 17, 1519, 10.3748/wjg.v17.i12.1519
Zimmerman, 2012, Butyrate suppresses colonic inflammation through HDAC1-dependent Fas upregulation and Fas-mediated apoptosis of T cells, Am J Physiol Gastrointest Liver Physiol, 302, G1405, 10.1152/ajpgi.00543.2011
Hamer, 2010, Effect of butyrate enemas on inflammation and antioxidant status in the colonic mucosa of patients with ulcerative colitis in remission, Clin Nutr, 29, 738, 10.1016/j.clnu.2010.04.002
Zeevi, 2015, Personalized nutrition by prediction of glycemic responses, Cell, 163, 1079, 10.1016/j.cell.2015.11.001
Haiser, 2014, Mechanistic insight into digoxin inactivation by Eggerthella lenta augments our understanding of its pharmacokinetics, Gut Microbes, 5, 233, 10.4161/gmic.27915
Clayton, 2009, Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism, Proc Natl Acad Sci U S A, 106, 14728, 10.1073/pnas.0904489106
Turnbaugh, 2008, An invitation to the marriage of metagenomics and metabolomics, Cell, 134, 708, 10.1016/j.cell.2008.08.025