The Relation Between Diet and Microbiota

Aslıhan Özdemir; Zehra Büyüktuncer Demirel

Review

The Relation Between Diet and Microbiota

Year 2017, - Mikrobiyota, 25 - 33, 15.11.2017

Aslıhan Özdemir Zehra Büyüktuncer Demirel

Abstract

The composition and functions of gut microbiota that composed of microorganisms including bacteria, viruses, fungi, and protozoa are effected by various factors such as mode of delivery, breastmilk, age, antibiotic use, and diet. Among these, diet is a manageable factor, therefore, it takes great attention. The fi rst dietary factor effects microbiota is breastfeeding, because it is well known that human milk oligosaccharides, lysosomes, lactoferrin, antibodies, and cytokines increase Bifi dobacterium counts. Following breastfeeding, foods chosen in weaning period and dietary pattern shapes microbiota. It is shown that microbiota reaches adult composition at about 2-3 years old and can change with short and long term regulations. The fi rst dietary factors that affect microbiota in adulthood are dietary carbohydrate (especially fi bre), protein and lipid content. It is shown that diets high in animal protein and saturated fats; low in fi bre and carbohydrates decrease gut microbiota richness and diversity and increase Firmicutes and Proteobacteria colonisation. High-fi bre and plant-based diets increase gut bacterial diversity as well as Prevotella and Xylanibacter species. Short chain fatty acids occur after fermentation of indigestible carbohydrates that also present prebiotic properties, are energy sources for gut bacteria as well as enhance health through anti-infl ammatory, anticarcinogenic and immune-modulatory impacts. Dietary alive probiotic microorganisms are as important as prebiotic content of diets for modulation of microbiota. At this point, potential benefi ts of fermented foods attract attention. Even if effects of diet on microbiota has begun to be understood, further research is needed to refl ect our knowledge to advice.

Keywords

Diet, Microbiota, Prebiotics, Probiotics

References

1. Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host-bacterial mutualism in the human intestine. Science. 2005;307(5717):1915-20.
2. Neish AS. Microbes in gastrointestinal health and disease. Gastroenterology. 2009;136(1):65-80.
3. Morgan XC, Segata N, Huttenhower C. Biodiversity and functional genomics in the human microbiome. Trends in genetics. 2013;29(1):51-8.
4. Ursell LK, Clemente JC, Rideout JR, Gevers D, Caporaso JG, Knight R. The interpersonal and intrapersonal diversity of humanassociated microbiota in key body sites. Journal of Allergy and Clinical Immunology. 2012;129(5):1204-8.
5. Tilg H, Kaser A. Gut microbiome, obesity, and metabolic dysfunction. The Journal of clinical investigation. 2011;121(6):2126-32.
6. Gill SR, Pop M, DeBoy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, et al. Metagenomic analysis of the human distal gut microbiome. Science. 2006;312(5778):1355-9.
7. Flint HJ, Duncan SH, Scott KP, Louis P. Interactions and competition within the microbial community of the human colon: links between diet and health. Environmental microbiology. 2007;9(5):1101-11.
8. Walker AW, Ince J, Duncan SH, Webster LM, Holtrop G, Ze X, et al. Dominant and diet-responsive groups of bacteria within the human colonic microbiota. The ISME journal. 2011;5(2):220-30.
9. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota. PLoS biology. 2007;5(7):e177. doi: 10.1371/journal.pbio.0050177. PubMed PMID: 17594176; PubMed Central PMCID: PMC1896187.
10. Fouhy F, Ross RP, Fitzgerald GF, Stanton C, Cotter PD. Composition of the early intestinal microbiota: knowledge, knowledge gaps and the use of high-throughput sequencing to address these gaps. Gut microbes. 2012;3(3):203-20. doi: 10.4161/gmic.20169. PubMed PMID: 22572829; PubMed Central PMCID: PMC3427213.
11. Marchesi JR. Human distal gut microbiome. Environmental microbiology. 2011;13(12):3088-102. Epub 2011/09/13. doi: 10.1111/j.1462-2920.2011.02574.x. PubMed PMID: 21906225.
12. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486(7402):222-7. doi: 10.1038/ nature11053. PubMed PMID: 22699611; PubMed Central PMCID: PMC3376388.
13. Koleva PT, Kim JS, Scott JA, Kozyrskyj AL. Microbial programming of health and disease starts during fetal life. Birth defects research Part C, Embryo today : reviews. 2015;105(4):265-77. Epub 2015/12/15. doi: 10.1002/bdrc.21117. PubMed PMID: 26663884.
14. Penders J, Thijs C, Vink C, Stelma FF, Snijders B, Kummeling I, et al. Factors infl uencing the composition of the intestinal microbiota in early infancy. Pediatrics. 2006;118(2):511-21. Epub 2006/08/03. doi: 10.1542/peds.2005-2824. PubMed PMID: 16882802.
15. Rodríguez JM, Murphy K, Stanton C, Ross RP, Kober OI, Juge N, et al. The composition of the gut microbiota throughout life, with an emphasis on early life. Microbial ecology in health and disease. 2015;26(1):26050.
16. Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, et al. Succession of microbial consortia in the developing infant gut microbiome. Proceedings of the National Academy of Sciences. 2011;108(Supplement 1):4578-85.
17. Peterson J, Garges S, Giovanni M, McInnes P, Wang L, Schloss JA, et al. The NIH human microbiome project. Genome research. 2009;19(12):2317-23
18. Coppa GV, Bruni S, Morelli L, Soldi S, Gabrielli O. The fi rst prebiotics in humans: human milk oligosaccharides. Journal of clinical gastroenterology. 2004;38(6 Suppl):S80-3. Epub 2004/06/29. PubMed PMID: 15220665.
19. Ballard O, Morrow AL. Human milk composition: nutrients and bioactive factors. Pediatric clinics of North America. 2013;60(1):49- 74. Epub 2012/11/28. doi: 10.1016/j.pcl.2012.10.002. PubMed PMID: 23178060; PubMed Central PMCID: PMCPmc3586783.
20. Madan JC, Hoen AG, Lundgren SN, Farzan SF, Cottingham KL, Morrison HG, et al. Association of Cesarean Delivery and Formula Supplementation With the Intestinal Microbiome of 6-Week-Old Infants. JAMA pediatrics. 2016;170(3):212-9. Epub 2016/01/12. doi: 10.1001/jamapediatrics.2015.3732. PubMed PMID: 26752321; PubMed Central PMCID: PMCPmc4783194.
21. Laursen MF, Bahl MI, Michaelsen KF, Licht TR. First Foods and Gut Microbes. Frontiers in microbiology. 2017;8:356. Epub 2017/03/23. doi: 10.3389/fmicb.2017.00356. PubMed PMID: 28321211; PubMed Central PMCID: PMCPmc5337510.
22. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486(7402):222-7.
23. Schnorr SL, Candela M, Rampelli S, Centanni M, Consolandi C, Basaglia G, et al. Gut microbiome of the Hadza hunter-gatherers. Nature communications. 2014;5.
24. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proceedings of the National Academy of Sciences. 2010;107(33):14691-6.
25. Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, et al. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science. 2016;352(6285):565-9.
26. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen Y-Y, Keilbaugh SA, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011;334(6052):105-8.
27. De Filippis F, Pellegrini N, Vannini L, Jeffery IB, La Storia A, Laghi L, et al. High-level adherence to a Mediterranean diet benefi cially impacts the gut microbiota and associated metabolome. Gut. 2015:gutjnl-2015-309957.
28. Zimmer J, Lange B, Frick J, Sauer H, Zimmermann K, Schwiertz A, et al. A vegan or vegetarian diet substantially alters the human colonic faecal microbiota. European journal of clinical nutrition. 2012;66(1):53.
29. Wu GD, Compher C, Chen EZ, Smith SA, Shah RD, Bittinger K, et al. Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. Gut. 2016;65(1):63-72.
30. Kabeerdoss J, Devi RS, Mary RR, Ramakrishna BS. Faecal microbiota composition in vegetarians: comparison with omnivores in a cohort of young women in southern India. British Journal of Nutrition. 2012;108(6):953-7.
31. Bonder MJ, Tigchelaar EF, Cai X, Trynka G, Cenit MC, Hrdlickova B, et al. The infl uence of a short-term gluten-free diet on the human gut microbiome. Genome medicine. 2016;8(1):45.
32. Sanz Y. Effects of a gluten-free diet on gut microbiota and immune function in healthy adult humans. Gut Microbes. 2010;1(3):135-7.
33. Zivkovic AM, German JB, Lebrilla CB, Mills DA. Human milk glycobiome and its impact on the infant gastrointestinal microbiota. Proceedings of the National Academy of Sciences. 2011;108(Supplement 1):4653-8
34. Rowland I, Gibson G, Heinken A, Scott K, Swann J, Thiele I, et al. Gut microbiota functions: metabolism of nutrients and other food components. European Journal of Nutrition. 2017:1-24.
35. Macfarlane G, Gibson G, Cummings J. Comparison of fermentation reactions in different regions of the human colon. Journal of applied microbiology. 1992;72(1):57-64.
36. Steliou K, Boosalis MS, Perrine SP, Sangerman J, Faller DV. Butyrate histone deacetylase inhibitors. BioResearch open access. 2012;1(4):192-8.
37. De Vadder F, Kovatcheva-Datchary P, Goncalves D, Vinera J, Zitoun C, Duchampt A, et al. Microbiota-generated metabolites promote metabolic benefi ts via gut-brain neural circuits. Cell. 2014;156(1):84-96.
38. Chambers ES, Viardot A, Psichas A, Morrison DJ, Murphy KG, ZacVarghese SE, et al. Effects of targeted delivery of propionate to the human colon on appetite regulation, body weight maintenance and adiposity in overweight adults. Gut. 2014:gutjnl-2014-307913.
39. Duncan SH, Holtrop G, Lobley GE, Calder AG, Stewart CS, Flint HJ. Contribution of acetate to butyrate formation by human faecal bacteria. British Journal of Nutrition. 2004;91(6):915-23.
40. Frost G, Sleeth ML, Sahuri-Arisoylu M, Lizarbe B, Cerdan S, Brody L, et al. The short-chain fatty acid acetate reduces appetite via a central homeostatic mechanism. Nature communications. 2014;5:3611.
41. Sonnenburg ED, Smits SA, Tikhonov M, Higginbottom SK, Wingreen NS, Sonnenburg JL. Diet-induced extinctions in the gut microbiota compound over generations. Nature. 2016;529(7585):212-5.
42. Cummings JH, Branch WJ. Fermentation and the production of short-chain fatty acids in the human large intestine. Dietary fi ber: Springer; 1986. p. 131-49.
43. Halmos EP, Christophersen CT, Bird AR, Shepherd SJ, Gibson PR, Muir JG. Diets that differ in their FODMAP content alter the colonic luminal microenvironment. Gut. 2014:gutjnl-2014-307264.
44. Macfarlane G, Cummings J, Allison C. Protein degradation by human intestinal bacteria. Microbiology. 1986;132(6):1647-56.
45. Hentges DJ, Maier BR, Burton GC, Flynn MA, Tsutakawa RK. Effect of a high-beef diet on the fecal bacterial fl ora of humans. Cancer research. 1977;37(2):568-71.
46. Russell WR, Gratz SW, Duncan SH, Holtrop G, Ince J, Scobbie L, et al. High-protein, reduced-carbohydrate weight-loss diets promote metabolite profi les likely to be detrimental to colonic health. The American journal of clinical nutrition. 2011;93(5):1062-72.
47. Drasar B, Crowther J, Goddard P, Hawksworth G, Hill M, Peach S, et al. The relation between diet and the gut microfl ora in man. Proc Nutr Soc. 1973;32(2):49-52.
48. Fava F, Gitau R, Griffi n B, Gibson G, Tuohy K, Lovegrove J. The type and quantity of dietary fat and carbohydrate alter faecal microbiome and short-chain fatty acid excretion in a metabolic syndrome'atrisk'population. International journal of obesity. 2013;37(2):216.
49. Cani PD, Possemiers S, Van de Wiele T, Guiot Y, Everard A, Rottier O, et al. Changes in gut microbiota control infl ammation in obese mice through a mechanism involving GLP-2-driven improvement of gut permeability. Gut. 2009;58(8):1091-103.
50. Manach C, Scalbert A, Morand C, Rémésy C, Jiménez L. Polyphenols: food sources and bioavailability. The American journal of clinical nutrition. 2004;79(5):727-47.
51. Marín L, Miguélez EM, Villar CJ, Lombó F. Bioavailability of dietary polyphenols and gut microbiota metabolism: antimicrobial properties. BioMed research international. 2015;2015.
52. Braune A, Engst W, Blaut M. Identifi cation and functional expression of genes encoding fl avonoid Oβand Cβglycosidases in intestinal bacteria. Environmental microbiology. 2016;18(7):2117-29.
53. Eid N, Enani S, Walton G, Corona G, Costabile A, Gibson G, et al. The impact of date palm fruits and their component polyphenols, on gut microbial ecology, bacterial metabolites and colon cancer cell proliferation. Journal of nutritional science. 2014;3.
54. Jin JS, Touyama M, Hisada T, Benno Y. Effects of green tea consumption on human fecal microbiota with special reference to Bifi dobacterium species. Microbiology and immunology. 2012;56(11):729-39.
55. Ankolekar C, Johnson D, Pinto MdS, Johnson K, Labbe R, Shetty K. Inhibitory potential of tea polyphenolics and infl uence of extraction time against Helicobacter pylori and lack of inhibition of benefi cial lactic acid bacteria. Journal of medicinal food. 2011;14(11):1321-9.
56. Nakayama M, Shigemune N, Tsugukuni T, Jun H, Matsushita T, Mekada Y, et al. Mechanism of the combined anti-bacterial effect of green tea extract and NaCl against Staphylococcus aureus and Escherichia coli O157: H7. Food control. 2012;25(1):225-32.
57. Hill M. Intestinal fl ora and endogenous vitamin synthesis. European Journal of Cancer Prevention. 1997;6(2):S43-S5.
58. Gustafsson BE, Daft FS, Mc DE, Smith JC, Fitzgerald RJ. Effects of vitamin K-active compounds and intestinal microorganisms in vitamin K-defi cient germfree rats. The Journal of nutrition. 1962;78:461-8. Epub 1962/12/01. PubMed PMID: 13951405.
59. Frick PG, Riedler G, Brogli H. Dose response and minimal daily requirement for vitamin K in man. J Appl Physiol. 1967;23(3):387- 9. Epub 1967/09/01. PubMed PMID: 6047959.
60. Guarner F, Khan AG, Garisch J, Eliakim R, Gangl A, Thomson A, et al. World Gastroenterology Organisation Global Guidelines: probiotics and prebiotics October 2011. Journal of clinical gastroenterology. 2012;46(6):468-81. doi: 10.1097/MCG.0b013e3182549092. PubMed PMID: 22688142.
61. Hidaka H, Eida T, Takizawa T, Tokunaga T, Tashiro Y. Effects of fructooligosaccharides on intestinal fl ora and human health. Bifi dobacteria and microfl ora. 1986;5(1):37-50.
62. Meyer D. Health benefi ts of prebiotic fi bers. Advances in food and nutrition research. 2015;74:47-91. Epub 2015/01/28. doi: 10.1016/bs.afnr.2014.11.002. PubMed PMID: 25624035.
63. Schley P, Field C. The immune-enhancing effects of dietary fi bres and prebiotics. British Journal of Nutrition. 2002;87(S2):S221-S30.
64. Joint FAO/WHO Working Group: Guidelines for the evaluation of probiotics in food: report of a joint FAO/WHO working group on drafting guidelines for the evaluation of probiotics in food. London, ON, Canada. 2002.
65. Goossens D, Jonkers D, Stobberingh E, Bogaard Avd, Russel M, Stockbrugger R. Probiotics in gastroenterology: indications and future perspectives. Scandinavian Journal of GastroenterologySupplements. 2003;38(239):15-6.
66. Tannock G, Munro K, Harmsen H, Welling G, Smart J, Gopal P. Analysis of the fecal microfl ora of human subjects consuming a probiotic product containing Lactobacillus rhamnosusDR20. Applied and environmental microbiology. 2000;66(6):2578-88.
67. Johansson M-L, Nobaek S, Berggren A, Nyman M, Björck I, Ahrne S, et al. Survival of Lactobacillus plantarum DSM 9843 (299v), and effect on the short-chain fatty acid content of faeces after ingestion of a rose-hip drink with fermented oats. International journal of food microbiology. 1998;42(1):29-38.
68. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al. Diet rapidly and reproducibly alters the human gut

Beslenme ve Mikrobiyota İlişkisi

Year 2017, - Mikrobiyota, 25 - 33, 15.11.2017

Aslıhan Özdemir Zehra Büyüktuncer Demirel

Abstract

Bakteri, virüs, mantar ve protozoa gibi çok sayıda mikroorganizmadan oluşan bağırsak mikrobiyotasının kompozisyonu ve fonksiyonu, doğum şekli, anne sütü alımı, antibiyotik kullanımı ve beslenme gibi çeşitli faktörlerden etkilenmektedir. Bu faktörler arasında beslenme düzenlenebilir bir etmen olması nedeniyle büyük ilgi çekmektedir. Mikrobiyotayı etkileyen ilk diyetsel etmen anne sütü alma durumudur çünkü anne sütünde bulunan oligosakkarit, lizozom, laktoferrin, antikor ve sitokinlerin bağırsaktaki Bifi dobacterium sayısını arttırdığı iyi bilinmektedir. Anne sütünden sonra, ek besinlere geçiş sürecinde seçilen besinler ve beslenme modeli mikrobiyotayı şekillendirmektedir. Ortalama 2-3 yaşta yetişkin kompozisyonuna ulaşan mikrobiyotanın, beslenmede yapılan kısa ve uzun dönem düzenlemeler ile değişebildiği gösterilmiştir. Yetişkin dönemde mikrobiyotayı etkileyen diyetsel etmenlerin başında, diyetin karbonhidrat (özellikle posa), protein ve yağ içeriğinin geldiği görülmektedir. Yüksek hayvansal protein ve doymuş yağ; düşük posa ve karbonhidrat içeren diyetlerin bağırsak mikrobiyotasının zenginliğini ve çeşitliliğini azalttığı, Firmicutes ve Proteobacteria kolonizasyonunu artırdığı gösterilmiştir. Yüksek posalı ve bitkisel bazlı diyetlerin ise bağırsaktaki bakteri çeşitlilik ile Prevotella ve Xylanibacter türlerini artırdığı saptanmıştır. Prebiyotik özellik de gösteren sindirilmeyen karbonhidrat bileşenlerinin mikrobiyotadaki bakteriler tarafından fermantasyonu sonucunda oluşan kısa zincirli yağ asitleri hem kolonositler için enerji kaynağı olmakta, hem de antiinfl amatuvar, antikarsinojenik ve immünomodülatör etkiler göstererek sağlığı geliştirebilmektedirler. Mikrobiyotanın düzenlenmesinde diyetin prebiyotik içeriği kadar önemli olan bir konu, diyetle alınan canlı probiyotik mikroorganizmalardır. Bu noktada, fermente besinlerin potansiyel yararları dikkat çekmektedir. Beslenmenin mikrobiyota üzerine etkileri anlaşılmaya başlanmış olsa da, bunların öneriye dönüştürülebilmesi için ileri araştırmalara gereksinim bulunmaktadır.

Keywords

Beslenme, Mikrobiyota, Prebiyotik, Probiyotik

References

1. Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host-bacterial mutualism in the human intestine. Science. 2005;307(5717):1915-20.
2. Neish AS. Microbes in gastrointestinal health and disease. Gastroenterology. 2009;136(1):65-80.
3. Morgan XC, Segata N, Huttenhower C. Biodiversity and functional genomics in the human microbiome. Trends in genetics. 2013;29(1):51-8.
4. Ursell LK, Clemente JC, Rideout JR, Gevers D, Caporaso JG, Knight R. The interpersonal and intrapersonal diversity of humanassociated microbiota in key body sites. Journal of Allergy and Clinical Immunology. 2012;129(5):1204-8.
5. Tilg H, Kaser A. Gut microbiome, obesity, and metabolic dysfunction. The Journal of clinical investigation. 2011;121(6):2126-32.
6. Gill SR, Pop M, DeBoy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, et al. Metagenomic analysis of the human distal gut microbiome. Science. 2006;312(5778):1355-9.
7. Flint HJ, Duncan SH, Scott KP, Louis P. Interactions and competition within the microbial community of the human colon: links between diet and health. Environmental microbiology. 2007;9(5):1101-11.
8. Walker AW, Ince J, Duncan SH, Webster LM, Holtrop G, Ze X, et al. Dominant and diet-responsive groups of bacteria within the human colonic microbiota. The ISME journal. 2011;5(2):220-30.
9. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota. PLoS biology. 2007;5(7):e177. doi: 10.1371/journal.pbio.0050177. PubMed PMID: 17594176; PubMed Central PMCID: PMC1896187.
10. Fouhy F, Ross RP, Fitzgerald GF, Stanton C, Cotter PD. Composition of the early intestinal microbiota: knowledge, knowledge gaps and the use of high-throughput sequencing to address these gaps. Gut microbes. 2012;3(3):203-20. doi: 10.4161/gmic.20169. PubMed PMID: 22572829; PubMed Central PMCID: PMC3427213.
11. Marchesi JR. Human distal gut microbiome. Environmental microbiology. 2011;13(12):3088-102. Epub 2011/09/13. doi: 10.1111/j.1462-2920.2011.02574.x. PubMed PMID: 21906225.
12. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486(7402):222-7. doi: 10.1038/ nature11053. PubMed PMID: 22699611; PubMed Central PMCID: PMC3376388.
13. Koleva PT, Kim JS, Scott JA, Kozyrskyj AL. Microbial programming of health and disease starts during fetal life. Birth defects research Part C, Embryo today : reviews. 2015;105(4):265-77. Epub 2015/12/15. doi: 10.1002/bdrc.21117. PubMed PMID: 26663884.
14. Penders J, Thijs C, Vink C, Stelma FF, Snijders B, Kummeling I, et al. Factors infl uencing the composition of the intestinal microbiota in early infancy. Pediatrics. 2006;118(2):511-21. Epub 2006/08/03. doi: 10.1542/peds.2005-2824. PubMed PMID: 16882802.
15. Rodríguez JM, Murphy K, Stanton C, Ross RP, Kober OI, Juge N, et al. The composition of the gut microbiota throughout life, with an emphasis on early life. Microbial ecology in health and disease. 2015;26(1):26050.
16. Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, et al. Succession of microbial consortia in the developing infant gut microbiome. Proceedings of the National Academy of Sciences. 2011;108(Supplement 1):4578-85.
17. Peterson J, Garges S, Giovanni M, McInnes P, Wang L, Schloss JA, et al. The NIH human microbiome project. Genome research. 2009;19(12):2317-23
18. Coppa GV, Bruni S, Morelli L, Soldi S, Gabrielli O. The fi rst prebiotics in humans: human milk oligosaccharides. Journal of clinical gastroenterology. 2004;38(6 Suppl):S80-3. Epub 2004/06/29. PubMed PMID: 15220665.
19. Ballard O, Morrow AL. Human milk composition: nutrients and bioactive factors. Pediatric clinics of North America. 2013;60(1):49- 74. Epub 2012/11/28. doi: 10.1016/j.pcl.2012.10.002. PubMed PMID: 23178060; PubMed Central PMCID: PMCPmc3586783.
20. Madan JC, Hoen AG, Lundgren SN, Farzan SF, Cottingham KL, Morrison HG, et al. Association of Cesarean Delivery and Formula Supplementation With the Intestinal Microbiome of 6-Week-Old Infants. JAMA pediatrics. 2016;170(3):212-9. Epub 2016/01/12. doi: 10.1001/jamapediatrics.2015.3732. PubMed PMID: 26752321; PubMed Central PMCID: PMCPmc4783194.
21. Laursen MF, Bahl MI, Michaelsen KF, Licht TR. First Foods and Gut Microbes. Frontiers in microbiology. 2017;8:356. Epub 2017/03/23. doi: 10.3389/fmicb.2017.00356. PubMed PMID: 28321211; PubMed Central PMCID: PMCPmc5337510.
22. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486(7402):222-7.
23. Schnorr SL, Candela M, Rampelli S, Centanni M, Consolandi C, Basaglia G, et al. Gut microbiome of the Hadza hunter-gatherers. Nature communications. 2014;5.
24. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proceedings of the National Academy of Sciences. 2010;107(33):14691-6.
25. Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, et al. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science. 2016;352(6285):565-9.
26. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen Y-Y, Keilbaugh SA, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011;334(6052):105-8.
27. De Filippis F, Pellegrini N, Vannini L, Jeffery IB, La Storia A, Laghi L, et al. High-level adherence to a Mediterranean diet benefi cially impacts the gut microbiota and associated metabolome. Gut. 2015:gutjnl-2015-309957.
28. Zimmer J, Lange B, Frick J, Sauer H, Zimmermann K, Schwiertz A, et al. A vegan or vegetarian diet substantially alters the human colonic faecal microbiota. European journal of clinical nutrition. 2012;66(1):53.
29. Wu GD, Compher C, Chen EZ, Smith SA, Shah RD, Bittinger K, et al. Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. Gut. 2016;65(1):63-72.
30. Kabeerdoss J, Devi RS, Mary RR, Ramakrishna BS. Faecal microbiota composition in vegetarians: comparison with omnivores in a cohort of young women in southern India. British Journal of Nutrition. 2012;108(6):953-7.
31. Bonder MJ, Tigchelaar EF, Cai X, Trynka G, Cenit MC, Hrdlickova B, et al. The infl uence of a short-term gluten-free diet on the human gut microbiome. Genome medicine. 2016;8(1):45.
32. Sanz Y. Effects of a gluten-free diet on gut microbiota and immune function in healthy adult humans. Gut Microbes. 2010;1(3):135-7.
33. Zivkovic AM, German JB, Lebrilla CB, Mills DA. Human milk glycobiome and its impact on the infant gastrointestinal microbiota. Proceedings of the National Academy of Sciences. 2011;108(Supplement 1):4653-8
34. Rowland I, Gibson G, Heinken A, Scott K, Swann J, Thiele I, et al. Gut microbiota functions: metabolism of nutrients and other food components. European Journal of Nutrition. 2017:1-24.
35. Macfarlane G, Gibson G, Cummings J. Comparison of fermentation reactions in different regions of the human colon. Journal of applied microbiology. 1992;72(1):57-64.
36. Steliou K, Boosalis MS, Perrine SP, Sangerman J, Faller DV. Butyrate histone deacetylase inhibitors. BioResearch open access. 2012;1(4):192-8.
37. De Vadder F, Kovatcheva-Datchary P, Goncalves D, Vinera J, Zitoun C, Duchampt A, et al. Microbiota-generated metabolites promote metabolic benefi ts via gut-brain neural circuits. Cell. 2014;156(1):84-96.
38. Chambers ES, Viardot A, Psichas A, Morrison DJ, Murphy KG, ZacVarghese SE, et al. Effects of targeted delivery of propionate to the human colon on appetite regulation, body weight maintenance and adiposity in overweight adults. Gut. 2014:gutjnl-2014-307913.
39. Duncan SH, Holtrop G, Lobley GE, Calder AG, Stewart CS, Flint HJ. Contribution of acetate to butyrate formation by human faecal bacteria. British Journal of Nutrition. 2004;91(6):915-23.
40. Frost G, Sleeth ML, Sahuri-Arisoylu M, Lizarbe B, Cerdan S, Brody L, et al. The short-chain fatty acid acetate reduces appetite via a central homeostatic mechanism. Nature communications. 2014;5:3611.
41. Sonnenburg ED, Smits SA, Tikhonov M, Higginbottom SK, Wingreen NS, Sonnenburg JL. Diet-induced extinctions in the gut microbiota compound over generations. Nature. 2016;529(7585):212-5.
42. Cummings JH, Branch WJ. Fermentation and the production of short-chain fatty acids in the human large intestine. Dietary fi ber: Springer; 1986. p. 131-49.
43. Halmos EP, Christophersen CT, Bird AR, Shepherd SJ, Gibson PR, Muir JG. Diets that differ in their FODMAP content alter the colonic luminal microenvironment. Gut. 2014:gutjnl-2014-307264.
44. Macfarlane G, Cummings J, Allison C. Protein degradation by human intestinal bacteria. Microbiology. 1986;132(6):1647-56.
45. Hentges DJ, Maier BR, Burton GC, Flynn MA, Tsutakawa RK. Effect of a high-beef diet on the fecal bacterial fl ora of humans. Cancer research. 1977;37(2):568-71.
46. Russell WR, Gratz SW, Duncan SH, Holtrop G, Ince J, Scobbie L, et al. High-protein, reduced-carbohydrate weight-loss diets promote metabolite profi les likely to be detrimental to colonic health. The American journal of clinical nutrition. 2011;93(5):1062-72.
47. Drasar B, Crowther J, Goddard P, Hawksworth G, Hill M, Peach S, et al. The relation between diet and the gut microfl ora in man. Proc Nutr Soc. 1973;32(2):49-52.
48. Fava F, Gitau R, Griffi n B, Gibson G, Tuohy K, Lovegrove J. The type and quantity of dietary fat and carbohydrate alter faecal microbiome and short-chain fatty acid excretion in a metabolic syndrome'atrisk'population. International journal of obesity. 2013;37(2):216.
49. Cani PD, Possemiers S, Van de Wiele T, Guiot Y, Everard A, Rottier O, et al. Changes in gut microbiota control infl ammation in obese mice through a mechanism involving GLP-2-driven improvement of gut permeability. Gut. 2009;58(8):1091-103.
50. Manach C, Scalbert A, Morand C, Rémésy C, Jiménez L. Polyphenols: food sources and bioavailability. The American journal of clinical nutrition. 2004;79(5):727-47.
51. Marín L, Miguélez EM, Villar CJ, Lombó F. Bioavailability of dietary polyphenols and gut microbiota metabolism: antimicrobial properties. BioMed research international. 2015;2015.
52. Braune A, Engst W, Blaut M. Identifi cation and functional expression of genes encoding fl avonoid Oβand Cβglycosidases in intestinal bacteria. Environmental microbiology. 2016;18(7):2117-29.
53. Eid N, Enani S, Walton G, Corona G, Costabile A, Gibson G, et al. The impact of date palm fruits and their component polyphenols, on gut microbial ecology, bacterial metabolites and colon cancer cell proliferation. Journal of nutritional science. 2014;3.
54. Jin JS, Touyama M, Hisada T, Benno Y. Effects of green tea consumption on human fecal microbiota with special reference to Bifi dobacterium species. Microbiology and immunology. 2012;56(11):729-39.
55. Ankolekar C, Johnson D, Pinto MdS, Johnson K, Labbe R, Shetty K. Inhibitory potential of tea polyphenolics and infl uence of extraction time against Helicobacter pylori and lack of inhibition of benefi cial lactic acid bacteria. Journal of medicinal food. 2011;14(11):1321-9.
56. Nakayama M, Shigemune N, Tsugukuni T, Jun H, Matsushita T, Mekada Y, et al. Mechanism of the combined anti-bacterial effect of green tea extract and NaCl against Staphylococcus aureus and Escherichia coli O157: H7. Food control. 2012;25(1):225-32.
57. Hill M. Intestinal fl ora and endogenous vitamin synthesis. European Journal of Cancer Prevention. 1997;6(2):S43-S5.
58. Gustafsson BE, Daft FS, Mc DE, Smith JC, Fitzgerald RJ. Effects of vitamin K-active compounds and intestinal microorganisms in vitamin K-defi cient germfree rats. The Journal of nutrition. 1962;78:461-8. Epub 1962/12/01. PubMed PMID: 13951405.
59. Frick PG, Riedler G, Brogli H. Dose response and minimal daily requirement for vitamin K in man. J Appl Physiol. 1967;23(3):387- 9. Epub 1967/09/01. PubMed PMID: 6047959.
60. Guarner F, Khan AG, Garisch J, Eliakim R, Gangl A, Thomson A, et al. World Gastroenterology Organisation Global Guidelines: probiotics and prebiotics October 2011. Journal of clinical gastroenterology. 2012;46(6):468-81. doi: 10.1097/MCG.0b013e3182549092. PubMed PMID: 22688142.
61. Hidaka H, Eida T, Takizawa T, Tokunaga T, Tashiro Y. Effects of fructooligosaccharides on intestinal fl ora and human health. Bifi dobacteria and microfl ora. 1986;5(1):37-50.
62. Meyer D. Health benefi ts of prebiotic fi bers. Advances in food and nutrition research. 2015;74:47-91. Epub 2015/01/28. doi: 10.1016/bs.afnr.2014.11.002. PubMed PMID: 25624035.
63. Schley P, Field C. The immune-enhancing effects of dietary fi bres and prebiotics. British Journal of Nutrition. 2002;87(S2):S221-S30.
64. Joint FAO/WHO Working Group: Guidelines for the evaluation of probiotics in food: report of a joint FAO/WHO working group on drafting guidelines for the evaluation of probiotics in food. London, ON, Canada. 2002.
65. Goossens D, Jonkers D, Stobberingh E, Bogaard Avd, Russel M, Stockbrugger R. Probiotics in gastroenterology: indications and future perspectives. Scandinavian Journal of GastroenterologySupplements. 2003;38(239):15-6.
66. Tannock G, Munro K, Harmsen H, Welling G, Smart J, Gopal P. Analysis of the fecal microfl ora of human subjects consuming a probiotic product containing Lactobacillus rhamnosusDR20. Applied and environmental microbiology. 2000;66(6):2578-88.
67. Johansson M-L, Nobaek S, Berggren A, Nyman M, Björck I, Ahrne S, et al. Survival of Lactobacillus plantarum DSM 9843 (299v), and effect on the short-chain fatty acid content of faeces after ingestion of a rose-hip drink with fermented oats. International journal of food microbiology. 1998;42(1):29-38.
68. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al. Diet rapidly and reproducibly alters the human gut

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Subjects	Health Care Administration
Journal Section	Review
Authors	Aslıhan Özdemir This is me Zehra Büyüktuncer Demirel
Publication Date	November 15, 2017
Acceptance Date	August 25, 2017
Published in Issue	Year 2017 - Mikrobiyota

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AMA	Özdemir A, Büyüktuncer Demirel Z. The Relation Between Diet and Microbiota. J Biotechnol and Strategic Health Res. November 2017;1:25-33.

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Journal of Biotechnology and Strategic Health Research