Johnson AJ, Vangay P, Al-Ghalith GA, Hillmann BM, Ward TL, Shields-Cutler RR, et al. Daily sampling reveals personalized diet-microbiome associations in humans. Cell Host Microbe. 2019;25:789–802.
Article CAS PubMed Google Scholar
Maldonado-Gómez MX, Martínez I, Bottacini F, O’Callaghan A, Ventura M, van Sinderen D, et al. Stable engraftment of Bifidobacterium longum AH1206 in the human gut depends on individualized features of the resident microbiome. Cell Host Microbe. 2016;20:515–26.
David LA, Materna AC, Friedman J, Campos-Baptista MI, Blackburn MC, Perrotta A et al. Host lifestyle affects human microbiota on daily timescales. Genome Biol. 2015;15.
Kovatcheva-Datchary P, Nilsson A, Akrami R, Lee YS, de Vadder F, Arora T, et al. Dietary fiber-induced improvement in glucose metabolism is associated with increased abundance of Prevotella. Cell Metab. 2015;22:971–82.
Article CAS PubMed Google Scholar
Rodriguez J, Hiel S, Neyrinck AM, Le Roy T, Pötgens SA, Leyrolle Q, et al. Discovery of the gut microbial signature driving the efficacy of prebiotic intervention in obese patients. Gut. 2020;69:1975–87.
Article CAS PubMed Google Scholar
Nguyen NK, Deehan EC, Zhang Z, Jin M, Baskota N, Perez-Muñoz ME et al. Gut microbiota modulation with long-chain corn bran arabinoxylan in adults with overweight and obesity is linked to an individualized temporal increase in fecal propionate. Microbiome. 2020;8.
Zeevi D, Korem T, Zmora N, Halpern Z, Elinav E, Correspondence ES, et al. Personalized nutrition by prediction of glycemic responses. Cell. 2015;163:1079–94.
Article CAS PubMed Google Scholar
Berry SE, Valdes AM, Drew DA, Asnicar F, Mazidi M, Wolf J, et al. Human postprandial responses to food and potential for precision nutrition. Nat Med. 2020;26:964–73.
Article CAS PubMed PubMed Central Google Scholar
Gibson R, Hutkins R, Sanders M, Al E. Expert consensus document: the International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics. Nat Rev Gastroenterol Hepatol. 2017;14:491–502.
Clayton TA, Baker D, Lindon JC, Everett JR, Nicholson JK. Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism. Proc Natl Acad Sci USA. 2009;106:14728–33.
Article CAS PubMed PubMed Central Google Scholar
Volokh O, Klimenko N, Berezhnaya Y, Tyakht A, Nesterova P, Popenko A et al. Human gut microbiome response induced by fermented dairy product intake in healthy volunteers. Nutrients. 2019;11.
Martínez I, Kim J, Duffy PR, Schlegel VL, Walter J. Resistant starches types 2 and 4 have differential effects on the composition of the fecal microbiota in human subjects. PLoS ONE. 2010;5:e15046.
Article PubMed PubMed Central Google Scholar
Krumbeck JA, Rasmussen HE, Hutkins RW, Clarke J, Shawron K, Keshavarzian A et al. Probiotic Bifidobacterium strains and galactooligosaccharides improve intestinal barrier function in obese adults but show no synergism when used together as synbiotics. Microbiome. 2018;6.
Davis L, Martínez I, Walter J, Goin C, Hutkins RW. Barcoded pyrosequencing reveals that consumption of galactooligosaccharides results in a highly specific bifidogenic response in humans. PLoS ONE. 2011;6:e25200.
Article CAS PubMed PubMed Central Google Scholar
Ramos-Romero S, Léniz A, Martínez-Maqueda D, Amézqueta S, Fernández-Quintela A, Hereu M et al. Inter-individual variability in insulin response after grape pomace supplementation in subjects at high cardiometabolic risk: role of microbiota and miRNA. Mol Nutr Food Res. 2021;65.
Cantu-Jungles TM, Hamaker BR. New view on dietary fiber selection for predictable shifts in gut microbiota. mBio. 2020;11:e02179–19.
CAS PubMed PubMed Central Google Scholar
Ryu G, Kim H, Koh A. Approaching precision medicine by tailoring the microbiota. Mamm Genome. 2021;1:3.
Loomba R, Seguritan V, Li W, Long T, Klitgord N, Bhatt A, et al. Gut microbiome-based metagenomic signature for non-invasive detection of advanced fibrosis in human nonalcoholic fatty liver disease. Cell Metab. 2017;25:1054–62.
Article CAS PubMed PubMed Central Google Scholar
Gupta VK, Kim M, Bakshi U, Cunningham KY, Davis JM, Lazaridis KN et al. A predictive index for health status using species-level gut microbiome profiling. Nat Commun. 2020;11.
Leeming ER, Louca P, Gibson R, Menni C, Spector TD, Le Roy CI. The complexities of the diet-microbiome relationship: advances and perspectives. Genome Med. 2021;13.
Korpela K, Flint HJ, Johnstone AM, Lappi J, Poutanen K, Dewulf E, et al. Gut microbiota signatures predict host and microbiota responses to dietary interventions in obese individuals. PLoS ONE. 2014;9:e90702.
Article PubMed PubMed Central Google Scholar
Selak M, Rivière A, Moens F, Van den Abbeele P, Geirnaert A, Rogelj I, et al. Inulin-type fructan fermentation by bifidobacteria depends on the strain rather than the species and region in the human intestine. Appl Microbiol Biotechnol. 2016;100:4097–107.
Article CAS PubMed Google Scholar
Zhu A, Sunagawa S, Mende DR, Bork P. Inter-individual differences in the gene content of human gut bacterial species. Genome Biol. 2015;16:1–13.
Johnson JS, Spakowicz DJ, Hong BY, Petersen LM, Demkowicz P, Chen L et al. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat Commun. 2019;10.
Deehan EC, Yang C, Perez-Muñoz ME, Nguyen NK, Cheng CC, Triador L et al. Precision microbiome modulation with discrete dietary fiber structures directs short-chain fatty acid production. Cell Host Microbe. 2020;27.
Filippis F, De, Pasolli E, Tett A, Tarallo S, Naccarati A, Angelis M, De, et al. Distinct genetic and functional traits of human intestinal Prevotella copri strains are associated with different habitual diets. Cell Host Microbe. 2019;25:444–53.
Flint HJ, Scott KP, Duncan SH, Louis P, Forano E. Microbial degradation of complex carbohydrates in the gut. Gut Microbes. 2012;3:289–306.
Article PubMed PubMed Central Google Scholar
Ndeh D, Gilbert HJ. Biochemistry of complex glycan depolymerisation by the human gut microbiota. FEMS Microbiol Rev. 2018;42:146–64.
Article CAS PubMed Google Scholar
Sheridan PO, Martin JC, Lawley TD, Browne HP, Harris HMB, Bernalier-Donadille A, et al. Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes. Microb Genom. 2015;2:e000043.
Wexler AG, Goodman AL. An insider’s perspective: Bacteroides as a window into the microbiome. Nat Microbiol. 2017;2.
Kundi ZM, Lee JC-Y, Pihlajamäki J, Chan CB, Leung KS, So SSY et al. Dietary fiber from oat and rye brans ameliorate western diet–induced body weight gain and hepatic inflammation by the modulation of short-chain fatty acids, bile acids, and tryptophan metabolism. Mol Nutr Food Res. 2021;65.
Tanes C, Bittinger K, Gao Y, Friedman ES, Nessel L, Paladhi UR, et al. Role of dietary fiber in the recovery of the human gut microbiome and its metabolome. Cell Host Microbe. 2021;29:394–407.
Article CAS PubMed PubMed Central Google Scholar
Yoshida K, Hirano R, Sakai Y, Choi M, Sakanaka M, Kurihara S et al. Bifidobacterium response to lactulose ingestion in the gut relies on a solute-binding protein-dependent ABC transporter. Commun Biol. 2021;4.
Holmes ZC, Silverman JD, Dressman HK, Wei Z, Dallow EP, Armstrong SC, et al. Short-chain fatty acid production by gut microbiota from children with obesity differs according to prebiotic choice and bacterial community composition. mBio. 2020;11:1–15.
Algera JP, Magnusson MK, Öhman L, Störsrud S, Simrén M, Törnblom H. Randomised controlled trial: effects of gluten-free diet on symptoms and the gut microenvironment in irritable bowel syndrome. Aliment Pharmacol Ther. 2022;56:1318–27.
Article PubMed PubMed Central Google Scholar
Cheng R, Wang L, Le S, Yang Y, Zhao C, Zhang X, et al. A randomized controlled trial for response of microbiome network to exercise and diet intervention in patients with nonalcoholic fatty liver disease. Nat Commun 2022. 2022;13:1.
Rej A, Sanders DS, Shaw CC, Buckle R, Trott N, Agrawal A, et al. Efficacy and acceptability of Dietary therapies in Non-constipated irritable bowel syndrome: a Randomized Trial of Traditional Dietary advice, the low FODMAP Diet, and the Gluten-Free Diet. Clinl Gastroenterol Hepatol. 2022;20:2876–e288715.
Reid G, Gaudier E, Guarner F, Huffnagle GB, Macklaim JM, Munoz AM et al. Responders and non-responders to probiotic interventions: how can we improve the odds? Gut Microbes. 2010;1.
Ojima MN, Yoshida K, Sakanaka M, Jiang L, Odamaki T, Katayama T. Ecological and molecular perspectives on responders and non-responders to probiotics and prebiotics. Curr Opin Biotechnol. 2022;73:108–20.
Article CAS PubMed Google Scholar
Blaak EE, Canfora EE, Theis S, Frost G, Groen AK, Mithieux G, et al. Short chain fatty acids in human gut and metabolic health. Benef Microbes. 2020;11:411–55.
Article CAS PubMed Google Scholar
Davis L, Martínez I, Walter J, Hutkins R. A dose dependent impact of prebiotic galactooligosaccharides on the intestinal microbiota of healthy adults. Int J Food Microbiol. 2010;144:285–92.
Article CAS PubMed Google Scholar
Topping DL, Clifton PM. Short-chain fatty acids and human colonic function: roles of resistant starch and nonstarch polysaccharides. Physiol Rev. 2001;81:1031–64.
Article CAS PubMed Google Scholar
Oliver A, Chase AB, Weihe C, Orchanian SB, Riedel SF, Hendrickson CL, et al. High-fiber, whole-food dietary intervention alters the human gut microbiome but notgecal short-chain fatty acids. mSystems. 2021;6:e00115–21.
Article CAS PubMed PubMed Central Google Scholar
Rahman MN, Diantini A, Fattah M, Barliana MI, Wijaya A. A highly sensitive, simple, and fast gas chromatography–mass spectrometry method for the quantification of serum short-chain fatty acids and their potential features in central obesity. Anal Bioanal Chem. 2021;413:6837–44.
Article CAS PubMed Google Scholar
Neyrinck AM, Rodriguez J, Zhang Z, Nazare JA, Bindels LB, Cani PD, et al. Breath volatile metabolome reveals the impact of dietary fibres on the gut microbiota: Proof of concept in healthy volunteers. EBioMedicine. 2022;80:104051.
Article CAS PubMed PubMed Central Google Scholar
Lee JHJ, Zhu J. Analyses of short-chain fatty acids and exhaled breath volatiles in dietary intervention trials for metabolic diseases. Exp Biol Med. 2021;246:778.
Dalile B, Vervliet B, Bergonzelli G, Verbeke K, van Oudenhove L. Colon-delivered short-chain fatty acids attenuate the cortisol response to psychosocial stress in healthy men: a randomized, placebo-controlled trial. Neuropsychopharmacol 2020. 2020;45:13.
Comments (0)