- 1. Sender R, Fuchs S, Milo R. Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans. Cell. 2016;164(3):337-340. doi:10.1016/j.cell.2016.01.013
- 2. Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J. 2017;474(11):1823-1836. Published 2017 May 16. doi:10.1042/BCJ20160510
- 3. Almeida A, Mitchell AL, Boland M, et al. A new genomic blueprint of the human gut microbiota. Nature. 2019;568(7753):499-504. doi:10.1038/s41586-019-0965-1.
- 4. Gilbert JA. Our unique microbial identity. Genome Biol. 2015;16(1):97. Published 2015 May 14. doi:10.1186/s13059-015-0664-7
- 5. Eisenstein M. The hunt for a healthy microbiome. Nature. 2020;577(7792):S6-S8. doi:10.1038/d41586-020-00193-3
- 6. Macfarlane GT, Macfarlane S. Bacteria, colonic fermentation, and gastrointestinal health. J AOAC Int. 2012;95(1):50-60. doi:10.5740/jaoacint.sge_macfarlane
- 7. Rowland I, Gibson G, Heinken A, et al. Gut microbiota functions: metabolism of nutrients and other food components. Eur J Nutr. 2018;57(1):1-24. doi:10.1007/s00394-017-1445-8
- 8. LeBlanc JG, Milani C, de Giori GS, Sesma F, van Sinderen D, Ventura M. Bacteria as vitamin suppliers to their host: a gut microbiota perspective. Curr Opin Biotechnol. 2013;24(2):160-168. doi:10.1016/j.copbio.2012.08.005
- 9. Belkaid Y, Hand TW. Role of the microbiota in immunity and inflammation. Cell. 2014;157(1):121-141. doi:10.1016/j.cell.2014.03.011
- 10. Wong SY, Cadwell K. There was collusion: Microbes in inflammatory bowel disease. PLoS Pathog. 2018;14(9):e1007215. Published 2018 Sep 20. doi:10.1371/journal.ppat.1007215
- 12. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature. 2006;444(7122):1022-1023. doi:10.1038/4441022a
- 11. Crohn's & Colitis UK. Which ‘bad’ bacteria in the gut can lead to inflammation? 2014; https://www.crohnsandcolitis.org.uk/research/research-projects/projects/which-bad-bacteria-in-the-gut-can-lead-to-inflammation
- 13. Turnbaugh PJ, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins. Nature. 2009;457(7228):480-484. doi:10.1038/nature07540 13. Turnbaugh PJ, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins. Nature. 2009;457(7228):480-484. doi:10.1038/nature07540
- 14. Canfora EE, Meex RCR, Venema K, Blaak EE. Gut microbial metabolites in obesity, NAFLD and T2DM. Nat Rev Endocrinol. 2019;15(5):261-273. doi:10.1038/s41574-019-0156-z
- 15. Zhao L, Zhang F, Ding X, et al. Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes. Science. 2018;359(6380):1151-1156. doi:10.1126/science.aao5774
- 16. Wilson NG, Hernandez-Leyva A, Kau AL. The ABCs of wheeze: Asthma and bacterial communities. PLoS Pathog. 2019;15(4):e1007645. Published 2019 Apr 25. doi:10.1371/journal.ppat.1007645
- 17. Tang WH, Wang Z, Levison BS, et al. Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk. N Engl J Med. 2013;368(17):1575-1584. doi:10.1056/NEJMoa1109400
- 18. Wang Z, Roberts AB, Buffa JA, et al. Non-lethal Inhibition of Gut Microbial Trimethylamine Production for the Treatment of Atherosclerosis. Cell. 2015;163(7):1585-1595. doi:10.1016/j.cell.2015.11.055
- 19. den Besten G, van Eunen K, Groen AK, Venema K, Reijngoud DJ, Bakker BM. The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. J Lipid Res. 2013;54(9):2325-2340. doi:10.1194/jlr.R036012
- 20. James SL, Muir JG, Curtis SL, Gibson PR. Dietary fibre: a roughage guide. Intern Med J. 2003;33(7):291-296. doi:10.1046/j.1445-5994.2003.00404.x
- 21. Wong JM, de Souza R, Kendall CW, Emam A, Jenkins DJ. Colonic health: fermentation and short chain fatty acids. J Clin Gastroenterol. 2006;40(3):235-243. doi:10.1097/00004836-200603000-00015
- 22. Cummings JH, Pomare EW, Branch WJ, Naylor CP, Macfarlane GT. Short chain fatty acids in human large intestine, portal, hepatic and venous blood. Gut. 1987;28(10):1221-1227. doi:10.1136/gut.28.10.1221
- 23. McNeil NI, Cummings JH, James WP. Short chain fatty acid absorption by the human large intestine. Gut. 1978;19(9):819-822. doi:10.1136/gut.19.9.819
- 24. Ruppin H, Bar-Meir S, Soergel KH, Wood CM, Schmitt MG Jr. Absorption of short-chain fatty acids by the colon. Gastroenterology. 1980;78(6):1500-1507.
- 25. Rey FE, Faith JJ, Bain J, et al. Dissecting the in vivo metabolic potential of two human gut acetogens. J Biol Chem. 2010;285(29):22082-22090. doi:10.1074/jbc.M110.117713.
- 26. Scott KP, Martin JC, Campbell G, Mayer CD, Flint HJ. Whole-genome transcription profiling reveals genes up-regulated by growth on fucose in the human gut bacterium "Roseburia inulinivorans". J Bacteriol. 2006;188(12):4340-4349. doi:10.1128/JB.00137-06
- 27. Duncan SH, Barcenilla A, Stewart CS, Pryde SE, Flint HJ. Acetate utilization and butyryl coenzyme A (CoA):acetate-CoA transferase in butyrate-producing bacteria from the human large intestine. Appl Environ Microbiol. 2002;68(10):5186-5190. doi:10.1128/aem.68.10.5186-5190.2002
- 28. Baxter NT, Schmidt AW, Venkataraman A, Kim KS, Waldron C, Schmidt TM. Dynamics of Human Gut Microbiota and Short-Chain Fatty Acids in Response to Dietary Interventions with Three Fermentable Fibers. mBio. 2019;10(1):e02566-18. Published 2019 Jan 29. doi:10.1128/mBio.02566-18
- 29. Zmora N, Suez J, Elinav E. You are what you eat: diet, health and the gut microbiota. Nat Rev Gastroenterol Hepatol. 2019;16(1):35-56. doi:10.1038/s41575-018-0061-2
- 30. Schönfeld P, Wojtczak L. Short- and medium-chain fatty acids in energy metabolism: the cellular perspective. J Lipid Res. 2016;57(6):943-954. doi:10.1194/jlr.R067629
- 31. Boets E, Gomand SV, Deroover L, et al. Systemic availability and metabolism of colonic-derived short-chain fatty acids in healthy subjects: a stable isotope study. J Physiol. 2017;595(2):541-555. doi:10.1113/JP272613
- 32. Dalile B, Van Oudenhove L, Vervliet B, Verbeke K. The role of short-chain fatty acids in microbiota-gut-brain communication. Nat Rev Gastroenterol Hepatol. 2019;16(8):461-478. doi:10.1038/s41575-019-0157-3
- 33. Tarini J, Wolever TM. The fermentable fibre inulin increases postprandial serum short-chain fatty acids and reduces free-fatty acids and ghrelin in healthy subjects. Appl Physiol Nutr Metab. 2010;35(1):9-16. doi:10.1139/H09-119
- 34. Byrne CS, Chambers ES, Morrison DJ, Frost G. The role of short chain fatty acids in appetite regulation and energy homeostasis. Int J Obes (Lond). 2015;39(9):1331-1338. doi:10.1038/ijo.2015.84
- 35. Katsurada K, Yada T. Neural effects of gut- and brain-derived glucagon-like peptide-1 and its receptor agonist. J Diabetes Investig. 2016;7 Suppl 1(Suppl 1):64-69. doi:10.1111/jdi.12464
- 36. Anderberg RH, Richard JE, Hansson C, Nissbrandt H, Bergquist F, Skibicka KP. GLP-1 is both anxiogenic and antidepressant; divergent effects of acute and chronic GLP-1 on emotionality. Psychoneuroendocrinology. 2016;65:54-66. doi:10.1016/j.psyneuen.2015.11.021
- 37. Painsipp E, Herzog H, Holzer P. The gut-mood axis: a novel role of the gut hormone peptide YY on emotional-affective behaviour in mice. BMC Pharmacol. 2009;9(Suppl 2):A13. Published 2009 Nov 12. doi:10.1186/1471-2210-9-S2-A13
- 38. Morrison CD. Leptin signaling in brain: A link between nutrition and cognition?. Biochim Biophys Acta. 2009;1792(5):401-408. doi:10.1016/j.bbadis.2008.12.004
- 39. Farr OM, Tsoukas MA, Mantzoros CS. Leptin and the brain: influences on brain development, cognitive functioning and psychiatric disorders. Metabolism. 2015;64(1):114-130. doi:10.1016/j.metabol.2014.07.004
- 40. Bali A, Jaggi AS. An Integrative Review on Role and Mechanisms of Ghrelin in Stress, Anxiety and Depression. Curr Drug Targets. 2016;17(5):495-507. doi:10.2174/1389450116666150518095650
- 41. Craft S, Baker LD, Montine TJ, et al. Intranasal insulin therapy for Alzheimer disease and amnestic mild cognitive impairment: a pilot clinical trial. Arch Neurol. 2012;69(1):29-38. doi:10.1001/archneurol.2011.233
- 42. Reger MA, Watson GS, Green PS, et al. Intranasal insulin improves cognition and modulates beta-amyloid in early AD [published correction appears in Neurology. 2008 Sep 9;71(11):866]. Neurology. 2008;70(6):440-448. doi:10.1212/01.WNL.0000265401.62434.36
- 43. Chambers ES, Viardot A, Psichas A, et al. Effects of targeted delivery of propionate to the human colon on appetite regulation, body weight maintenance and adiposity in overweight adults. Gut. 2015;64(11):1744-1754. doi:10.1136/gutjnl-2014-307913
- 44. Frost G, Sleeth ML, Sahuri-Arisoylu M, et al. The short-chain fatty acid acetate reduces appetite via a central homeostatic mechanism. Nat Commun. 2014;5:3611. Published 2014 Apr 29. doi:10.1038/ncomms4611
- 45. DeFronzo, R., Ferrannini, E., Groop, L. et al. Type 2 diabetes mellitus. Nat Rev Dis Primers 1, 15019 (2015). https://doi.org/10.1038/nrdp.2015.19
- 46. Trikkalinou A, Papazafiropoulou AK, Melidonis A. Type 2 diabetes and quality of life. World J Diabetes. 2017;8(4):120-129. doi:10.4239/wjd.v8.i4.120
- 47. Qin J, Li Y, Cai Z, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 2012;490(7418):55-60. doi:10.1038/nature11450
- 48. Larsen N, Vogensen FK, van den Berg FW, et al. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One. 2010;5(2):e9085. Published 2010 Feb 5. doi:10.1371/journal.pone.0009085
- 49. Yadav H, Lee JH, Lloyd J, Walter P, Rane SG. Beneficial metabolic effects of a probiotic via butyrate-induced GLP-1 hormone secretion. J Biol Chem. 2013;288(35):25088-25097. doi:10.1074/jbc.M113.452516
- 50. Freeland KR, Wolever TM. Acute effects of intravenous and rectal acetate on glucagon-like peptide-1, peptide YY, ghrelin, adiponectin and tumour necrosis factor-alpha. Br J Nutr. 2010;103(3):460-466. doi:10.1017/S0007114509991863
- 51. Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome [published correction appears in Gastroenterology. 2013 Jan;144(1):250]. Gastroenterology. 2012;143(4):913-6.e7. doi:10.1053/j.gastro.2012.06.031
- 52. Whitlock G, Lewington S, et al. Body-mass index and cause-specific mortality in 900 000 adults: collaborative analyses of 57 prospective studies. Lancet. 2009;373(9669):1083-1096. doi:10.1016/S0140-6736(09)60318-4
- 52. Shah AD, Langenberg C, Rapsomaniki E, et al. Type 2 diabetes and incidence of cardiovascular diseases: a cohort study in 1·9 million people. Lancet Diabetes Endocrinol. 2015;3(2):105-113. doi:10.1016/S2213-8587(14)70219-0
- 54. Huda-Faujan N, Abdulamir AS, Fatimah AB, et al. The impact of the level of the intestinal short chain Fatty acids in inflammatory bowel disease patients versus healthy subjects. Open Biochem J. 2010;4:53-58. Published 2010 May 13. doi:10.2174/1874091X01004010053
- 55. Steinhart AH, Brzezinski A, Baker JP. Treatment of refractory ulcerative proctosigmoiditis with butyrate enemas. Am J Gastroenterol. 1994;89(2):179-183.
- 56. Patz J, Jacobsohn WZ, Gottschalk-Sabag S, Zeides S, Braverman DZ. Treatment of refractory distal ulcerative colitis with short chain fatty acid enemas. Am J Gastroenterol. 1996;91(4):731-734.
- 57. Di Sabatino A, Morera R, Ciccocioppo R, et al. Oral butyrate for mildly to moderately active Crohn's disease. Aliment Pharmacol Ther. 2005;22(9):789-794. doi:10.1111/j.1365-2036.2005.02639.x
- 58. Rutter M, Saunders B, Wilkinson K, et al. Severity of inflammation is a risk factor for colorectal neoplasia in ulcerative colitis. Gastroenterology. 2004;126(2):451-459. doi:10.1053/j.gastro.2003.11.010
- 59. O'Keefe SJ, Chung D, Mahmoud N, et al. Why do African Americans get more colon cancer than Native Africans?. J Nutr. 2007;137(1 Suppl):175S-182S. doi:10.1093/jn/137.1.175S
- 60. Ou J, Carbonero F, Zoetendal EG, et al. Diet, microbiota, and microbial metabolites in colon cancer risk in rural Africans and African Americans. Am J Clin Nutr. 2013;98(1):111-120. doi:10.3945/ajcn.112.056689
- 61. Clausen MR, Bonnén H, Mortensen PB. Colonic fermentation of dietary fibre to short chain fatty acids in patients with adenomatous polyps and colonic cancer. Gut. 1991;32(8):923-928. doi:10.1136/gut.32.8.923
- 62. Weir TL, Manter DK, Sheflin AM, Barnett BA, Heuberger AL, Ryan EP. Stool microbiome and metabolome differences between colorectal cancer patients and healthy adults. PLoS One. 2013;8(8):e70803. Published 2013 Aug 6. doi:10.1371/journal.pone.0070803
- 63. Weaver GA, Krause JA, Miller TL, Wolin MJ. Short chain fatty acid distributions of enema samples from a sigmoidoscopy population: an association of high acetate and low butyrate ratios with adenomatous polyps and colon cancer. Gut. 1988;29(11):1539-1543. doi:10.1136/gut.29.11.1539
- 64. Thorburn AN, McKenzie CI, Shen S, et al. Evidence that asthma is a developmental origin disease influenced by maternal diet and bacterial metabolites. Nat Commun. 2015;6:7320. Published 2015 Jun 23. doi:10.1038/ncomms8320
- 65. Theiler A, Bärnthaler T, Platzer W, et al. Butyrate ameliorates allergic airway inflammation by limiting eosinophil trafficking and survival. J Allergy Clin Immunol. 2019;144(3):764‐776. doi:10.1016/j.jaci.2019.05.002
- 67. Koh A, De Vadder F, Kovatcheva-Datchary P, Bäckhed F. From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites. Cell. 2016;165(6):1332‐1345. doi:10.1016/j.cell.2016.05.041
- 66. Dalile B, Van Oudenhove L, Vervliet B, Verbeke K. The role of short-chain fatty acids in microbiota-gut-brain communication. Nat Rev Gastroenterol Hepatol. 2019;16(8):461-478. doi:10.1038/s41575-019-0157-3
- 68. Meyer D, Stasse-Wolthuis M. The bifidogenic effect of inulin and oligofructose and its consequences for gut health. Eur J Clin Nutr. 2009;63(11):1277‐1289. doi:10.1038/ejcn.2009.64
- 69. Niness KR. Inulin and oligofructose: what are they?. J Nutr. 1999;129(7 Suppl):1402S‐6S. doi:10.1093/jn/129.7.1402S
- 70. van Dokkum W, Wezendonk B, Srikumar TS, van den Heuvel EG. Effect of nondigestible oligosaccharides on large-bowel functions, blood lipid concentrations and glucose absorption in young healthy male subjects. Eur J Clin Nutr. 1999;53(1):1‐7. doi:10.1038/sj.ejcn.1600668
- 71. Gråsten, S., Liukkonen, K-H., Chrevatidis, A., El-Nezami, H., Poutanen, K., & Mykkänen, H. (2003). Effects of wheat pentosan and inulin on the metabolic activity of fecal microbiota and on bowel function in healthy humans. Nutrition Research, 23(11), 1503-1514. https://doi.org/10.1016/S0271-5317(03)00164-7
- 72. Bridges SR, Anderson JW, Deakins DA, Dillon DW, Wood CL. Oat bran increases serum acetate of hypercholesterolemic men. Am J Clin Nutr. 1992;56(2):455‐459. doi:10.1093/ajcn/56.2.455
- 73. H.N. Englyst, S. Hay, G.T. Macfarlane, Polysaccharide breakdown by mixed populations of human faecal bacteria, FEMS Microbiology Ecology, Volume 3, Issue 3, June 1987, Pages 163–171, https://doi.org/10.1111/j.1574-6968.1987.tb02352.x
- 74. Bang SJ, Kim G, Lim MY, et al. The influence of in vitro pectin fermentation on the human fecal microbiome. AMB Express. 2018;8(1):98. Published 2018 Jun 16. doi:10.1186/s13568-018-0629-9
- 75. Remely M, Hippe B, Geretschlaeger I, Stegmayer S, Hoefinger I, Haslberger A. Increased gut microbiota diversity and abundance of Faecalibacterium prausnitzii and Akkermansia after fasting: a pilot study. Wien Klin Wochenschr. 2015;127(9-10):394‐398.
- 76. Dao MC, Everard A, Aron-Wisnewsky J, et al. Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology. Gut. 2016;65(3):426‐436. doi:10.1136/gutjnl-2014-308778
- 77. Vogt JA, Pencharz PB, Wolever TM. L-Rhamnose increases serum propionate in humans. Am J Clin Nutr. 2004;80(1):89‐94. doi:10.1093/ajcn/80.1.89
- 78. Fredstrom SB, Lampe JW, Jung HJ, Slavin JL. Apparent fiber digestibility and fecal short-chain fatty acid concentrations with ingestion of two types of dietary fiber [published correction appears in JPEN J Parenter Enteral Nutr 1994 Mar-Apr;18(2):197]. JPEN J Parenter Enteral Nutr. 1994;18(1):14‐19. doi:10.1177/014860719401800114
- 79. Strobel HJ. Vitamin B12-dependent propionate production by the ruminal bacterium Prevotella ruminicola 23. Appl Environ Microbiol. 1992;58(7):2331‐2333.
- 80. Englyst HN, Kingman SM, Cummings JH. Classification and measurement of nutritionally important starch fractions. Eur J Clin Nutr. 1992;46 Suppl 2:S33‐S50.
- 81. Topping DL, Clifton PM. Short-chain fatty acids and human colonic function: roles of resistant starch and nonstarch polysaccharides. Physiol Rev. 2001;81(3):1031‐1064. doi:10.1152/physrev.2001.81.3.1031
- 82. Murphy MM, Douglass JS, Birkett A. Resistant starch intakes in the United States [published correction appears in J Am Diet Assoc. 2008 May;108(5):890]. J Am Diet Assoc. 2008;108(1):67‐78. doi:10.1016/j.jada.2007.10.012
- 83. Louis P, Flint HJ. Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine. FEMS Microbiol Lett. 2009;294(1):1‐8. doi:10.1111/j.1574-6968.2009.01514.x
- 84. Dostal A, Lacroix C, Bircher L, et al. Iron Modulates Butyrate Production by a Child Gut Microbiota In Vitro. mBio. 2015;6(6):e01453-15. Published 2015 Nov 17. doi:10.1128/mBio.01453-15
- 85. Zmora N, Suez J, Elinav E. You are what you eat: diet, health and the gut microbiota. Nat Rev Gastroenterol Hepatol. 2019;16(1):35-56. doi:10.1038/s41575-018-0061-2
- 86. Flint HJ, Scott KP, Louis P, Duncan SH. The role of the gut microbiota in nutrition and health. Nat Rev Gastroenterol Hepatol. 2012;9(10):577‐589. Published 2012 Sep 4. doi:10.1038/nrgastro.2012.156
- 87. Lin CS, Chang CJ, Lu CC, et al. Impact of the gut microbiota, prebiotics, and probiotics on human health and disease. Biomed J. 2014;37(5):259‐268. doi:10.4103/2319-4170.138314
- 88. Engen PA, Green SJ, Voigt RM, Forsyth CB, Keshavarzian A. The Gastrointestinal Microbiome: Alcohol Effects on the Composition of Intestinal Microbiota. Alcohol Res. 2015;37(2):223‐236.
- 89. Nash V, Ranadheera CS, Georgousopoulou EN, et al. The effects of grape and red wine polyphenols on gut microbiota - A systematic review. Food Res Int. 2018;113:277‐287. doi:10.1016/j.foodres.2018.07.019
- 90. Marinac CR, Nelson SH, Breen CI, et al. Prolonged Nightly Fasting and Breast Cancer Prognosis. JAMA Oncol. 2016;2(8):1049‐1055. doi:10.1001/jamaoncol.2016.0164
- 91. Parkar SG, Kalsbeek A, Cheeseman JF. Potential Role for the Gut Microbiota in Modulating Host Circadian Rhythms and Metabolic Health. Microorganisms. 2019;7(2):41. Published 2019 Jan 31. doi:10.3390/microorganisms7020041
- 92. De Palma G, Collins SM, Bercik P, Verdu EF. The microbiota-gut-brain axis in gastrointestinal disorders: stressed bugs, stressed brain or both? J Physiol. 2014;592(14):2989‐2997. doi:10.1113/jphysiol.2014.273995
- 93. Colgan SP. Swimming through the gut: implications of fluid transport on the microbiome. Dig Dis Sci. 2013;58(3):602‐603. doi:10.1007/s10620-013-2575-3
- 94. Monda V, Villano I, Messina A, et al. Exercise Modifies the Gut Microbiota with Positive Health Effects. Oxid Med Cell Longev. 2017;2017:3831972. doi:10.1155/2017/3831972
- 95. Savin Z, Kivity S, Yonath H, Yehuda S. Smoking and the intestinal microbiome. Arch Microbiol. 2018;200(5):677‐684. doi:10.1007/s00203-018-1506-2
- 96. Jaquet M, Rochat I, Moulin J, Cavin C, Bibiloni R. Impact of coffee consumption on the gut microbiota: a human volunteer study. Int J Food Microbiol. 2009;130(2):117‐121. doi:10.1016/j.ijfoodmicro.2009.01.011
- 97. Bond T, Derbyshire E. Tea Compounds and the Gut Microbiome: Findings from Trials and Mechanistic Studies. Nutrients. 2019;11(10):2364. Published 2019 Oct 3. doi:10.3390/nu11102364
- 98. Qin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464(7285):59‐65. doi:10.1038/nature08821
- 99. Kaur H, Bose C, Mande SS. Tryptophan Metabolism by Gut Microbiome and Gut-Brain-Axis: An in silico Analysis. Front Neurosci. 2019;13:1365. Published 2019 Dec 18. doi:10.3389/fnins.2019.01365
- 100. Parker A, Fonseca S, Carding SR. Gut microbes and metabolites as modulators of blood-brain barrier integrity and brain health. Gut Microbes. 2020;11(2):135‐157. doi:10.1080/19490976.2019.1638722
- 101. Siddik MAB, Shin AC. Recent Progress on Branched-Chain Amino Acids in Obesity, Diabetes, and Beyond. Endocrinol Metab (Seoul). 2019;34(3):234-246. doi:10.3803/EnM.2019.34.3.234
- 102. Cryan JF, Dinan TG. Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour. Nat Rev Neurosci. 2012;13(10):701‐712. doi:10.1038/nrn3346
- 103. Furman D, Campisi J, Verdin E, et al. Chronic inflammation in the etiology of disease across the life span. Nat Med. 2019;25(12):1822-1832. doi:10.1038/s41591-019-0675-0
- 104.Dantzer R, Heijnen CJ, Kavelaars A, Laye S, Capuron L. The neuroimmune basis of fatigue. Trends Neurosci. 2014;37(1):39-46. doi:10.1016/j.tins.2013.10.003
- 105. Draper A, Koch RM, van der Meer JW, et al. Effort but not Reward Sensitivity is Altered by Acute Sickness Induced by Experimental Endotoxemia in Humans. Neuropsychopharmacology. 2018;43(5):1107-1118. doi:10.1038/npp.2017.231
- 106. Valles-Colomer M, Falony G, Darzi Y, et al. The neuroactive potential of the human gut microbiota in quality of life and depression. Nat Microbiol. 2019;4(4):623‐632. doi:10.1038/s41564-018-0337-x
- 107. Cowen PJ, Browning M. What has serotonin to do with depression?. World Psychiatry. 2015;14(2):158-160. doi:10.1002/wps.20229
- 108. Meltzer CC, Smith G, DeKosky ST, et al. Serotonin in aging, late-life depression, and Alzheimer's disease: the emerging role of functional imaging. Neuropsychopharmacology. 1998;18(6):407-430. doi:10.1016/S0893-133X(97)00194-2
- 109. Yano JM, Yu K, Donaldson GP, et al. Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis [published correction appears in Cell. 2015 Sep 24;163:258]. Cell. 2015;161(2):264‐276. doi:10.1016/j.cell.2015.02.047
- 110. Reigstad CS, Salmonson CE, Rainey JF 3rd, et al. Gut microbes promote colonic serotonin production through an effect of short-chain fatty acids on enterochromaffin cells. FASEB J. 2015;29(4):1395‐1403. doi:10.1096/fj.14-259598
- 111. Desbonnet L, Clarke G, Shanahan F, Dinan TG, Cryan JF. Microbiota is essential for social development in the mouse. Mol Psychiatry. 2014;19(2):146‐148. doi:10.1038/mp.2013.65
- 112. Ohland CL, Kish L, Bell H, et al. Effects of Lactobacillus helveticus on murine behavior are dependent on diet and genotype and correlate with alterations in the gut microbiome. Psychoneuroendocrinology. 2013;38(9):1738‐1747. doi:10.1016/j.psyneuen.2013.02.008
- 113. Bravo JA, Forsythe P, Chew MV, et al. Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve. Proc Natl Acad Sci U S A. 2011;108(38):16050‐16055. doi:10.1073/pnas.1102999108
- 114. Sofi F, Abbate R, Gensini GF, Casini A. Accruing evidence on benefits of adherence to the Mediterranean diet on health: an updated systematic review and meta-analysis. Am J Clin Nutr. 2010;92(5):1189‐1196. doi:10.3945/ajcn.2010.29673
- 115. Pahwa R, Goyal A, Bansal P, et al. Chronic Inflammation, viewed 28 October 2020, https://www.ncbi.nlm.nih.gov/books/NBK493173/
- 116. NHS, Inflammatory bowel disease (IBD), viewed 26 August 2020, https://www.nhs.uk/conditions/inflammatory-bowel-disease/
- 117. Khor B, Gardet A, Xavier RJ. Genetics and pathogenesis of inflammatory bowel disease. Nature. 2011;474(7351):307-317. Published 2011 Jun 15. doi:10.1038/nature10209
- 118. Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A. 2007;104(34):13780-13785. doi:10.1073/pnas.0706625104
- 119. Albenberg LG, Lewis JD, Wu GD. Food and the gut microbiota in inflammatory bowel diseases: a critical connection. Curr Opin Gastroenterol. 2012;28(4):314-320. doi:10.1097/MOG.0b013e328354586f
- 120. Parada Venegas D, De la Fuente MK, Landskron G, et al. Short Chain Fatty Acids (SCFAs)-Mediated Gut Epithelial and Immune Regulation and Its Relevance for Inflammatory Bowel Diseases [published correction appears in Front Immunol. 2019 Jun 28;10:1486]. Front Immunol. 2019;10:277. Published 2019 Mar 11. doi:10.3389/fimmu.2019.00277
- 121. Porter CK, Cash BD, Pimentel M, Akinseye A, Riddle MS. Risk of inflammatory bowel disease following a diagnosis of irritable bowel syndrome. BMC Gastroenterol. 2012;12:55. Published 2012 May 28. doi:10.1186/1471-230X-12-55
- 122. Rodino-Janeiro BK, Vicario M, Alonso-Cotoner C, Pascua-Garcia R, Santos J. A Review of Microbiota and Irritable Bowel Syndrome: Future in Therapies. Adv Ther. 2018;35(3):289-310. doi:10.1007/s12325-018-0673-5
- 123. Rajilić-Stojanović M, Biagi E, Heilig HG, et al. Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome. Gastroenterology. 2011;141(5):1792-1801. doi:10.1053/j.gastro.2011.07.043
- 124. Pozuelo M, Panda S, Santiago A, et al. Reduction of butyrate- and methane-producing microorganisms in patients with Irritable Bowel Syndrome. Sci Rep. 2015;5:12693. Published 2015 Aug 4. doi:10.1038/srep12693
- 125. NHS, Diverticular disease and diverticulitis, viewed 27 October 2020, https://www.nhs.uk/conditions/diverticular-disease-and-diverticulitis/
- 126. Barbara G, Scaioli E, Barbaro MR, et al. Gut microbiota, metabolome and immune signatures in patients with uncomplicated diverticular disease. Gut. 2017;66(7):1252-1261. doi:10.1136/gutjnl-2016-312377
- 127. Maeda Y, Takeda K. Host-microbiota interactions in rheumatoid arthritis. Exp Mol Med. 2019;51(12):1-6. Published 2019 Dec 11. doi:10.1038/s12276-019-0283-6
- 128. Alpizar-Rodriguez D, Lesker TR, Gronow A, et al. Prevotella copri in individuals at risk for rheumatoid arthritis. Ann Rheum Dis. 2019;78(5):590-593. doi:10.1136/annrheumdis-2018-214514
- 129. De Filippo C, Cavalieri D, Di Paola M, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A. 2010;107(33):14691-14696. doi:10.1073/pnas.1005963107
- 130. Mikuls TR, Payne JB, Yu F, et al. Periodontitis and Porphyromonas gingivalis in patients with rheumatoid arthritis. Arthritis Rheumatol. 2014;66(5):1090-1100. doi:10.1002/art.38348
- 131. Konig MF, Abusleme L, Reinholdt J, et al. Aggregatibacter actinomycetemcomitans-induced hypercitrullination links periodontal infection to autoimmunity in rheumatoid arthritis. Sci Transl Med. 2016;8(369):369ra176. doi:10.1126/scitranslmed.aaj1921
- 132. Wilson NG, Hernandez-Leyva A, Kau AL. The ABCs of wheeze: Asthma and bacterial communities. PLoS Pathog. 2019;15(4):e1007645. Published 2019 Apr 25. doi:10.1371/journal.ppat.1007645
- 133. Fujimura KE, Sitarik AR, Havstad S, et al. Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation. Nat Med. 2016;22(10):1187-1191. doi:10.1038/nm.4176
- 134. Arrieta MC, Stiemsma LT, Dimitriu PA, et al. Early infancy microbial and metabolic alterations affect risk of childhood asthma. Sci Transl Med. 2015;7(307):307ra152. doi:10.1126/scitranslmed.aab2271
- 135. Trompette A, Gollwitzer ES, Yadava K, et al. Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med. 2014;20(2):159-166. doi:10.1038/nm.3444
- 136. McLoughlin R, Berthon BS, Rogers GB, et al. Soluble fibre supplementation with and without a probiotic in adults with asthma: A 7-day randomised, double blind, three way cross-over trial. EBioMedicine. 2019;46:473-485. doi:10.1016/j.ebiom.2019.07.048
- 137. Turnbaugh PJ, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins. Nature. 2009;457(7228):480-484. doi:10.1038/nature07540
- 138. Goodrich JK, Waters JL, Poole AC, et al. Human genetics shape the gut microbiome. Cell. 2014;159(4):789-799. doi:10.1016/j.cell.2014.09.053
- 139. Beaumont M, Goodrich JK, Jackson MA, et al. Heritable components of the human fecal microbiome are associated with visceral fat. Genome Biol. 2016;17(1):189. Published 2016 Sep 26. doi:10.1186/s13059-016-1052-7
- 140. Tang WH, Wang Z, Levison BS, et al. Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk. N Engl J Med. 2013;368(17):1575-1584. doi:10.1056/NEJMoa1109400
- 141. Jie Z, Xia H, Zhong SL, et al. The gut microbiome in atherosclerotic cardiovascular disease. Nat Commun. 2017;8(1):845. Published 2017 Oct 10. doi:10.1038/s41467-017-00900-1
- 142. Zhu Q, Gao R, Zhang Y, et al. Dysbiosis signatures of gut microbiota in coronary artery disease. Physiol Genomics. 2018;50(10):893-903. doi:10.1152/physiolgenomics.00070.2018
- 143. Karlsson FH, Fåk F, Nookaew I, et al. Symptomatic atherosclerosis is associated with an altered gut metagenome. Nat Commun. 2012;3:1245. doi:10.1038/ncomms2266
- 144. Qin J, Li Y, Cai Z, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 2012;490(7418):55-60. doi:10.1038/nature11450
- 145. Karlsson FH, Tremaroli V, Nookaew I, et al. Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature. 2013;498(7452):99-103. doi:10.1038/nature12198
- 146. Shin NR, Lee JC, Lee HY, et al. An increase in the Akkermansia spp. population induced by metformin treatment improves glucose homeostasis in diet-induced obese mice. Gut. 2014;63(5):727-735. doi:10.1136/gutjnl-2012-303839
- 147. Karlsson CL, Onnerfält J, Xu J, Molin G, Ahrné S, Thorngren-Jerneck K. The microbiota of the gut in preschool children with normal and excessive body weight. Obesity (Silver Spring). 2012;20(11):2257-2261. doi:10.1038/oby.2012.110
- 148. Santacruz A, Collado MC, García-Valdés L, et al. Gut microbiota composition is associated with body weight, weight gain and biochemical parameters in pregnant women. Br J Nutr. 2010;104(1):83-92. doi:10.1017/S0007114510000176
- 149. Baxter NT, Zackular JP, Chen GY, Schloss PD. Structure of the gut microbiome following colonization with human feces determines colonic tumor burden. Microbiome. 2014;2:20. Published 2014 Jun 17. doi:10.1186/2049-2618-2-20
- 150. Dejea CM, Wick EC, Hechenbleikner EM, et al. Microbiota organization is a distinct feature of proximal colorectal cancers. Proc Natl Acad Sci U S A. 2014;111(51):18321-18326. doi:10.1073/pnas.1406199111
- 151. Drewes JL, White JR, Dejea CM, et al. High-resolution bacterial 16S rRNA gene profile meta-analysis and biofilm status reveal common colorectal cancer consortia [published correction appears in NPJ Biofilms Microbiomes. 2019 Jan 9;5:2]. NPJ Biofilms Microbiomes. 2017;3:34. Published 2017 Nov 29. doi:10.1038/s41522-017-0040-3
- 152. Chen J, Domingue JC, Sears CL. Microbiota dysbiosis in select human cancers: Evidence of association and causality. Semin Immunol. 2017;32:25-34. doi:10.1016/j.smim.2017.08.001
- 153. Weaver GA, Krause JA, Miller TL, Wolin MJ. Short chain fatty acid distributions of enema samples from a sigmoidoscopy population: an association of high acetate and low butyrate ratios with adenomatous polyps and colon cancer. Gut. 1988;29(11):1539-1543. doi:10.1136/gut.29.11.1539
- 154. Weir TL, Manter DK, Sheflin AM, Barnett BA, Heuberger AL, Ryan EP. Stool microbiome and metabolome differences between colorectal cancer patients and healthy adults. PLoS One. 2013;8(8):e70803. Published 2013 Aug 6. doi:10.1371/journal.pone.0070803
- 155. Wang X, Wang J, Rao B, Deng L. Gut flora profiling and fecal metabolite composition of colorectal cancer patients and healthy individuals. Exp Ther Med. 2017;13(6):2848-2854. doi:10.3892/etm.2017.4367
- 156. Gensollen T, Iyer SS, Kasper DL, Blumberg RS. How colonization by microbiota in early life shapes the immune system. Science. 2016;352(6285):539-544. doi:10.1126/science.aad9378
- 157. Gensollen T, Iyer SS, Kasper DL, Blumberg RS. How colonization by microbiota in early life shapes the immune system. Science. 2016;352(6285):539-544. doi:10.1126/science.aad9378
- 158. Reyman M, van Houten MA, van Baarle D, et al. Author Correction: Impact of delivery mode-associated gut microbiota dynamics on health in the first year of life. Nat Commun. 2019;10(1):5352. Published 2019 Nov 25. doi:10.1038/s41467-019-13373-1
- 159. Dominguez-Bello MG, Costello EK, Contreras M, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A. 2010;107(26):11971-11975. doi:10.1073/pnas.1002601107
- 160. Sevelsted A, Stokholm J, Bønnelykke K, Bisgaard H. Cesarean section and chronic immune disorders. Pediatrics. 2015;135(1):e92-e98. doi:10.1542/peds.2014-0596
- 161. Mueller NT, Whyatt R, Hoepner L, et al. Prenatal exposure to antibiotics, cesarean section and risk of childhood obesity. Int J Obes (Lond). 2015;39(4):665-670. doi:10.1038/ijo.2014.180
- 162. Krautkramer KA, Fan J, Bäckhed F. Gut microbial metabolites as multi-kingdom intermediates [published online ahead of print, 2020 Sep 23]. Nat Rev Microbiol. 2020;10.1038/s41579-020-0438-4. doi:10.1038/s41579-020-0438-4
- 163. NHS, Gout, viewed 4 November 2020, https://www.nhs.uk/conditions/gout/
- 164. Crane JK, Naeher TM, Broome JE, Boedeker EC. Role of host xanthine oxidase in infection due to enteropathogenic and Shiga-toxigenic Escherichia coli. Infect Immun. 2013;81(4):1129-1139. doi:10.1128/IAI.01124-12
- 165. Guo Z, Zhang J, Wang Z, et al. Intestinal Microbiota Distinguish Gout Patients from Healthy Humans. Sci Rep. 2016;6:20602. Published 2016 Feb 8. doi:10.1038/srep20602
- 166. Richette P, Bardin T. Gout. Lancet. 2010;375(9711):318-328. doi:10.1016/S0140-6736(09)60883-7
- 167. Kamada, N., Seo, S., Chen, G. et al. Role of the gut microbiota in immunity and inflammatory disease. Nat Rev Immunol 13, 321–335 (2013). https://doi.org/10.1038/nri3430
- 168. Zhou X, Li J, Guo J, et al. Gut-dependent microbial translocation induces inflammation and cardiovascular events after ST-elevation myocardial infarction. Microbiome. 2018;6(1):66. Published 2018 Apr 3. doi:10.1186/s40168-018-0441-4
- 169. Marques FZ, Nelson E, Chu PY, et al. High-Fiber Diet and Acetate Supplementation Change the Gut Microbiota and Prevent the Development of Hypertension and Heart Failure in Hypertensive Mice. Circulation. 2017;135(10):964-977. doi:10.1161/CIRCULATIONAHA.116.024545
- 170. NHS, Cardiovascular disease, viewed 11 November 2020, https://www.nhs.uk/conditions/cardiovascular-disease/
- 171. NHS, Bowel cancer, viewed 11 November 2020, https://www.nhs.uk/conditions/bowel-cancer/
- 172. NHS, Type 2 diabetis, viewed 12 November 2020, https://www.nhs.uk/conditions/type-2-diabetes/