Healthy and Unhealthy Aging and the Human Microbiome

Literature Cited

1. 1.

   O'Toole PW, Claesson MJ. 2010.. Gut microbiota: changes throughout the lifespan from infancy to elderly. . Int. Dairy J. 20::281–91
   [Google Scholar]
2. 2.

   Claesson MJ, Clooney AG, O'Toole PW. 2017.. A clinician's guide to microbiome analysis. . Nat. Rev. Gastroenterol. Hepatol. 14::585–95
   [Google Scholar]
3. 3.

   Claesson MJ, Jeffery IB, Conde S, et al. 2012.. Gut microbiota composition correlates with diet and health in the elderly. . Nature 488::178–85
   [Google Scholar]
4. 4.

   Ryan FJ, Ahern AM, Fitzgerald RS, et al. 2020.. Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease. . Nat. Commun. 11::1512
   [Google Scholar]
5. 5.

   Li JV, Swann J, Marchesi JR. 2017.. Biology of the microbiome 2: metabolic role. . Gastroenterol. Clin. N. Am. 46::37–47
   [Google Scholar]
6. 6.

   Durack J, Lynch SV. 2019.. The gut microbiome: relationships with disease and opportunities for therapy. . J. Exp. Med. 216::20–40
   [Google Scholar]
7. 7.

   Lynch SV, Pedersen O. 2016.. The human intestinal microbiome in health and disease. . N. Engl. J. Med. 375::2369–79
   [Google Scholar]
8. 8.

   Ley RE, Backhed F, Turnbaugh P, et al. 2005.. Obesity alters gut microbial ecology. . PNAS 102::11070–75
   [Google Scholar]
9. 9.

   Caruso R, Lo BC, Nunez G. 2020.. Host–microbiota interactions in inflammatory bowel disease. . Nat. Rev. Immunol. 20::411–26
   [Google Scholar]
10. 10.

    Collins SM. 2014.. A role for the gut microbiota in IBS. . Nat. Rev. Gastroenterol. Hepatol. 11::497–505
    [Google Scholar]
11. 11.

    Jeffery IB, Das A, O'Herlihy E, et al. 2020.. Differences in fecal microbiomes and metabolomes of people with versus without irritable bowel syndrome and bile acid malabsorption. . Gastroenterology 158::1016–28.e8
    [Google Scholar]
12. 12.

    Forslund K, Hildebrand F, Nielsen T, et al. 2015.. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. . Nature 528::262–66
    [Google Scholar]
13. 13.

    Shanahan F, van Sinderen D, O'Toole PW, Stanton C. 2017.. Feeding the microbiota: transducer of nutrient signals for the host. . Gut 66::1709–17
    [Google Scholar]
14. 14.

    Vrieze A, Van Nood E, Holleman F, et al. 2012.. Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome. . Gastroenterology 143::913–16.e7
    [Google Scholar]
15. 15.

    Koopen AM, Almeida EL, Attaye I, et al. 2021.. Effect of fecal microbiota transplantation combined with Mediterranean diet on insulin sensitivity in subjects with metabolic syndrome. . Front. Microbiol. 12::662159
    [Google Scholar]
16. 16.

    Valles-Colomer M, Menni C, Berry SE, et al. 2023.. Cardiometabolic health, diet and the gut microbiome: a meta-omics perspective. . Nat. Med. 29::551–61
    [Google Scholar]
17. 17.

    Tang WHW, Li DY, Hazen SL. 2019.. Dietary metabolism, the gut microbiome, and heart failure. . Nat. Rev. Cardiol. 16::137–54
    [Google Scholar]
18. 18.

    Jiang Y, Pang S, Liu X, et al. 2024.. The gut microbiome affects atherosclerosis by regulating reverse cholesterol transport. . J. Cardiovasc. Transl. Res. 17::624–37
    [Google Scholar]
19. 19.

    Wahlstrom A, Sayin SI, Marschall HU, Backhed F. 2016.. Intestinal crosstalk between bile acids and microbiota and its impact on host metabolism. . Cell Metab. 24::41–50
    [Google Scholar]
20. 20.

    Boulange CL, Neves AL, Chilloux J, et al. 2016.. Impact of the gut microbiota on inflammation, obesity, and metabolic disease. . Genome Med. 8::42
    [Google Scholar]
21. 21.

    Duncan SH, Conti E, Ricci L, Walker AW. 2023.. Links between diet, intestinal anaerobes, microbial metabolites and health. . Biomedicines 11::1338
    [Google Scholar]
22. 22.

    Bravo JA, Julio-Pieper M, Forsythe P, et al. 2012.. Communication between gastrointestinal bacteria and the nervous system. . Curr. Opin. Pharmacol. 12::667–72
    [Google Scholar]
23. 23.

    Ross FC, Mayer DE, Gupta A, et al. 2024.. Existing and future strategies to manipulate the gut microbiota with diet as a potential adjuvant treatment for psychiatric disorders. . Biol. Psychiatry 95::348–60
    [Google Scholar]
24. 24.

    Lynch JB, Hsiao EY. 2023.. Toward understanding links between the microbiome and neurotransmitters. . Ann. N. Y. Acad. Sci. 1524::10–16
    [Google Scholar]
25. 25.

    Valles-Colomer M, Falony G, Darzi Y, et al. 2019.. The neuroactive potential of the human gut microbiota in quality of life and depression. . Nat. Microbiol. 4::623–32
    [Google Scholar]
26. 26.

    Meyer K, Lulla A, Debroy K, et al. 2022.. Association of the gut microbiota with cognitive function in midlife. . JAMA Netw. Open 5::e2143941
    [Google Scholar]
27. 27.

    Costea PI, Zeller G, Sunagawa S, et al. 2017.. Towards standards for human fecal sample processing in metagenomic studies. . Nat. Biotechnol. 35::1069–76
    [Google Scholar]
28. 28.

    Maier L, Goemans CV, Wirbel J, et al. 2021.. Unravelling the collateral damage of antibiotics on gut bacteria. . Nature 599::120–24
    [Google Scholar]
29. 29.

    Imhann F, Bonder MJ, Vich Vila A, et al. 2016.. Proton pump inhibitors affect the gut microbiome. . Gut 65::740–48
    [Google Scholar]
30. 30.

    Vieira-Silva S, Falony G, Belda E, et al. 2020.. Statin therapy is associated with lower prevalence of gut microbiota dysbiosis. . Nature 581::310–15
    [Google Scholar]
31. 31.

    McGovern AS, Hamlin AS, Winter G. 2019.. A review of the antimicrobial side of antidepressants and its putative implications on the gut microbiome. . Aust. N. Z. J. Psychiatry 53::1151–66
    [Google Scholar]
32. 32.

    López-Otín C, Blasco MA, Partridge L, et al. 2013.. The hallmarks of aging. . Cell 153::1194–217
    [Google Scholar]
33. 33.

    López-Otín C, Blasco MA, Partridge L, et al. 2023.. Hallmarks of aging: an expanding universe. . Cell 186::243–78
    [Google Scholar]
34. 34.

    Schmauck-Medina T, Moliere A, Lautrup S, et al. 2022.. New hallmarks of ageing: a 2022 Copenhagen ageing meeting summary. . Aging 14::6829–39
    [Google Scholar]
35. 35.

    McCann A, Jeffery IB, Ouliass B, et al. 2019.. Exploratory analysis of covariation of microbiota-derived vitamin K and cognition in older adults. . Am. J. Clin. Nutr. 110::1404–15
    [Google Scholar]
36. 36.

    Dai L, Mafra D, Shiels PG, et al. 2023.. Vitamin K and hallmarks of ageing: focus on diet and gut microbiome. . Nutrients 15::2727
    [Google Scholar]
37. 37.

    Ma L, Zhang L, Li J, et al. 2023.. The potential mechanism of gut microbiota-microbial metabolites-mitochondrial axis in progression of diabetic kidney disease. . Mol. Med. 29::148
    [Google Scholar]
38. 38.

    Prajapati SK, Shah R, Alford N, et al. 2023.. The triple alliance: microbiome, mitochondria, and metabolites in the context of age-related cognitive decline and Alzheimer's disease. . J. Gerontol. A Biol. Sci. Med. Sci. 78::2187–202
    [Google Scholar]
39. 39.

    Barrett M, Hand CK, Shanahan F, et al. 2020.. Mutagenesis by microbe: the role of the microbiota in shaping the cancer genome. . Trends Cancer 6::277–87
    [Google Scholar]
40. 40.

    Janney A, Powrie F, Mann EH. 2020.. Host–microbiota maladaptation in colorectal cancer. . Nature 585::509–17
    [Google Scholar]
41. 41.

    Nougayrede JP, Homburg S, Taieb F, et al. 2006.. Escherichia coli induces DNA double-strand breaks in eukaryotic cells. . Science 313::848–51
    [Google Scholar]
42. 42.

    Lopez LR, Bleich RM, Arthur JC. 2021.. Microbiota effects on carcinogenesis: initiation, promotion, and progression. . Annu. Rev. Med. 72::243–61
    [Google Scholar]
43. 43.

    Sheehan D, Shanahan F. 2017.. The gut microbiota in inflammatory bowel disease. . Gastroenterol. Clin. N. Am. 46::143–54
    [Google Scholar]
44. 44.

    Ravi A, Garg P, Sitaraman SV. 2007.. Matrix metalloproteinases in inflammatory bowel disease: boon or a bane?. Inflamm. Bowel Dis. 13::97–107
    [Google Scholar]
45. 45.

    Donohoe DR, Garge N, Zhang X, et al. 2011.. The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon. . Cell Metab. 13::517–26
    [Google Scholar]
46. 46.

    Kibe R, Kurihara S, Sakai Y, et al. 2014.. Upregulation of colonic luminal polyamines produced by intestinal microbiota delays senescence in mice. . Sci. Rep. 4::4548
    [Google Scholar]
47. 47.

    Yu T, Guo F, Yu Y, et al. 2017.. Fusobacterium nucleatum promotes chemoresistance to colorectal cancer by modulating autophagy. . Cell 170::548–63.e16
    [Google Scholar]
48. 48.

    Woo V, Alenghat T. 2022.. Epigenetic regulation by gut microbiota. . Gut Microbes 14::2022407
    [Google Scholar]
49. 49.

    Bollati V, Schwartz J, Wright R, et al. 2009.. Decline in genomic DNA methylation through aging in a cohort of elderly subjects. . Mech. Ageing Dev. 130::234–39
    [Google Scholar]
50. 50.

    Sharma M, Li Y, Stoll ML, Tollefsbol TO. 2019.. The epigenetic connection between the gut microbiome in obesity and diabetes. . Front. Genet. 10::1329
    [Google Scholar]
51. 51.

    Ansari I, Raddatz G, Gutekunst J, et al. 2020.. The microbiota programs DNA methylation to control intestinal homeostasis and inflammation. . Nat. Microbiol. 5::610–19
    [Google Scholar]
52. 52.

    Furusawa Y, Obata Y, Fukuda S, et al. 2013.. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. . Nature 504::446–50
    [Google Scholar]
53. 53.

    Chang PV, Hao L, Offermanns S, Medzhitov R. 2014.. The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition. . PNAS 111::2247–52
    [Google Scholar]
54. 54.

    Kadosh E, Snir-Alkalay I, Venkatachalam A, et al. 2020.. The gut microbiome switches mutant p53 from tumour-suppressive to oncogenic. . Nature 586::133–38
    [Google Scholar]
55. 55.

    Franceschi C, Bonafe M, Valensin S, et al. 2000.. Inflamm-aging. An evolutionary perspective on immunosenescence. . Ann. N. Y. Acad. Sci. 908::244–54
    [Google Scholar]
56. 56.

    Bulut O, Kilic G, Dominguez-Andres J. 2022.. Immune memory in aging: a wide perspective covering microbiota, brain, metabolism, and epigenetics. . Clin. Rev. Allergy Immunol. 63::499–529
    [Google Scholar]
57. 57.

    Ghosh TS, Das M, Jeffery IB, O'Toole PW. 2020.. Adjusting for age improves identification of gut microbiome alterations in multiple diseases. . eLife 9::e30240
    [Google Scholar]
58. 58.

    Bana B, Cabreiro F. 2019.. The microbiome and aging. . Annu. Rev. Genet. 53::239–61
    [Google Scholar]
59. 59.

    Pedersen HK, Gudmundsdottir V, Nielsen HB, et al. 2016.. Human gut microbes impact host serum metabolome and insulin sensitivity. . Nature 535::376–81
    [Google Scholar]
60. 60.

    Bauer PV, Hamr SC, Duca FA. 2016.. Regulation of energy balance by a gut–brain axis and involvement of the gut microbiota. . Cell. Mol. Life Sci. 73::737–55
    [Google Scholar]
61. 61.

    Oh HYP, Visvalingam V, Wahli W. 2019.. The PPAR–microbiota–metabolic organ trilogy to fine-tune physiology. . FASEB J. 33::9706–30
    [Google Scholar]
62. 62.

    Long SL, Gahan CGM, Joyce SA. 2017.. Interactions between gut bacteria and bile in health and disease. . Mol. Aspects Med. 56::54–65
    [Google Scholar]
63. 63.

    Ghosh TS, Shanahan F, O'Toole PW. 2022.. The gut microbiome as a modulator of healthy ageing. . Nat. Rev. Gastroenterol. Hepatol. 19::565–84
    [Google Scholar]
64. 64.

    Wilmanski T, Diener C, Rappaport N, et al. 2021.. Gut microbiome pattern reflects healthy ageing and predicts survival in humans. . Nat. Metab. 3::274–86
    [Google Scholar]
65. 65.

    O'Toole PW, Jeffery IB. 2015.. Gut microbiota and aging. . Science 350::1214–15
    [Google Scholar]
66. 66.

    Galkin F, Mamoshina P, Aliper A, et al. 2020.. Human gut microbiome aging clock based on taxonomic profiling and deep learning. . iScience 23::101199
    [Google Scholar]
67. 67.

    Arumugam M, Raes J, Pelletier E, et al. 2011.. Enterotypes of the human gut microbiome. . Nature 473::174–80
    [Google Scholar]
68. 68.

    Wu GD, Chen J, Hoffmann C, et al. 2011.. Linking long-term dietary patterns with gut microbial enterotypes. . Science 334::105–8
    [Google Scholar]
69. 69.

    Jeffery IB, Lynch DB, O'Toole PW. 2016.. Composition and temporal stability of the gut microbiota in older persons. . ISME J. 10::170–82
    [Google Scholar]
70. 70.

    Biagi E, Nylund L, Candela M, et al. 2010.. Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians. . PLOS ONE 5::e10667
    [Google Scholar]
71. 71.

    Rampelli S, Soverini M, D'Amico F, et al. 2020.. Shotgun metagenomics of gut microbiota in humans with up to extreme longevity and the increasing role of xenobiotic degradation. . mSystems 5::e00124-20
    [Google Scholar]
72. 72.

    Collino S, Montoliu I, Martin FP, et al. 2013.. Metabolic signatures of extreme longevity in northern Italian centenarians reveal a complex remodeling of lipids, amino acids, and gut microbiota metabolism. . PLOS ONE 8::e56564
    [Google Scholar]
73. 73.

    Rampelli S, Candela M, Turroni S, et al. 2013.. Functional metagenomic profiling of intestinal microbiome in extreme ageing. . Aging 5::902–12
    [Google Scholar]
74. 74.

    Ruiz-Ruiz S, Sanchez-Carrillo S, Ciordia S, et al. 2020.. Functional microbiome deficits associated with ageing: chronological age threshold. . Aging Cell 19::e13063
    [Google Scholar]
75. 75.

    Pang S, Chen X, Lu Z, et al. 2023.. Longevity of centenarians is reflected by the gut microbiome with youth-associated signatures. . Nat. Aging 3::436–49
    [Google Scholar]
76. 76.

    Luan Z, Fu S, Qi S, et al. 2024.. A metagenomics study reveals the gut microbiome as a sex-specific modulator of healthy aging in Hainan centenarians. . Exp. Gerontol. 186::112356
    [Google Scholar]
77. 77.

    Duvallet C, Gibbons SM, Gurry T, et al. 2017.. Meta-analysis of gut microbiome studies identifies disease-specific and shared responses. . Nat. Commun. 8::1784
    [Google Scholar]
78. 78.

    Tzemah-Shahar R, Turjeman S, Sharon E, et al. 2023.. Signs of aging in midlife: physical function and sex differences in microbiota. . GeroScience 46::1477–88
    [Google Scholar]
79. 79.

    Jackson MA, Jeffery IB, Beaumont M, et al. 2016.. Signatures of early frailty in the gut microbiota. . Genome Med. 8::8
    [Google Scholar]
80. 80.

    Ghosh TS, Shanahan F, O'Toole PW. 2022.. Toward an improved definition of a healthy microbiome for healthy aging. . Nat. Aging 2::1054–69
    [Google Scholar]
81. 81.

    O'Toole PW, Ghosh TS, Goswami S, et al. 2023.. Translating the microbiome: What's the target?. Gastroenterology 165::317–19
    [Google Scholar]
82. 82.

    Walter J, Armet AM, Finlay BB, Shanahan F. 2020.. Establishing or exaggerating causality for the gut microbiome: lessons from human microbiota-associated rodents. . Cell 180::221–32
    [Google Scholar]
83. 83.

    Ghosh TS, Rampelli S, Jeffery IB, et al. 2020.. Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across five European countries. . Gut 69::1218–28
    [Google Scholar]
84. 84.

    Ye H, Ghosh TS, Hueston CM, et al. 2023.. Engraftment of aging-related human gut microbiota and the effect of a seven-species consortium in a pre-clinical model. . Gut Microbes 15::2282796
    [Google Scholar]
85. 85.

    Perez M, Ntemiri A, Tan H, et al. 2021.. A synthetic consortium of 100 gut commensals modulates the composition and function in a colon model of the microbiome of elderly subjects. . Gut Microbes 13::1919464
    [Google Scholar]
86. 86.

    Tran TTT, Cousin FJ, Lynch DB, et al. 2019.. Prebiotic supplementation in frail older people affects specific gut microbiota taxa but not global diversity. . Microbiome 7::39
    [Google Scholar]
87. 87.

    Shanahan F, Ghosh TS, O'Toole PW. 2021.. The healthy microbiome—what is the definition of a healthy gut microbiome?. Gastroenterology 160::483–94
    [Google Scholar]
88. 88.

    Sehgal K, Cifu AS, Khanna S. 2022.. Treatment of Clostridioides difficile infection. . JAMA 328::881–82
    [Google Scholar]
89. 89.

    Gweon TG, Lee YJ, Kim KO, et al. 2022.. Clinical practice guidelines for fecal microbiota transplantation in Korea. . J. Neurogastroenterol. Motil. 28::28–42
    [Google Scholar]
90. 90.

    Baunwall SMD, Lee MM, Eriksen MK, et al. 2020.. Faecal microbiota transplantation for recurrent Clostridioides difficile infection: an updated systematic review and meta-analysis. . eClinicalMedicine 29::100642
    [Google Scholar]
91. 91.

    Ianiro G, Bibbo S, Porcari S, et al. 2021.. Fecal microbiota transplantation for recurrent C. difficile infection in patients with inflammatory bowel disease: experience of a large-volume European FMT center. . Gut Microbes 13::1994834
    [Google Scholar]
92. 92.

    Suchman K, Luo Y, Grinspan A. 2022.. Fecal microbiota transplant for Clostridioides difficile infection is safe and efficacious in an immunocompromised cohort. . Dig. Dis. Sci. 67::4866–73
    [Google Scholar]
93. 93.

    He R, Li P, Wang J, et al. 2022.. The interplay of gut microbiota between donors and recipients determines the efficacy of fecal microbiota transplantation. . Gut Microbes 14::2100197
    [Google Scholar]
94. 94.

    Matson V, Chervin CS, Gajewski TF. 2021.. Cancer and the microbiome—influence of the commensal microbiota on cancer, immune responses, and immunotherapy. . Gastroenterology 160::600–13
    [Google Scholar]
95. 95.

    Li W, Deng X, Chen T. 2021.. Exploring the modulatory effects of gut microbiota in anti-cancer therapy. . Front. Oncol. 11::644454
    [Google Scholar]
96. 96.

    Wieczorska K, Stolarek M, Stec R. 2020.. The role of the gut microbiome in colorectal cancer: Where are we? Where are we going?. Clin. Colorectal Cancer 19::5–12
    [Google Scholar]
97. 97.

    Shoer S, Shilo S, Godneva A, et al. 2023.. Impact of dietary interventions on pre-diabetic oral and gut microbiome, metabolites and cytokines. . Nat. Commun. 14::5384
    [Google Scholar]
98. 98.

    Zeevi D, Korem T, Zmora N, et al. 2015.. Personalized nutrition by prediction of glycemic responses. . Cell 163::1079–94
    [Google Scholar]
99. 99.

    Rein M, Ben-Yacov O, Godneva A, et al. 2022.. Effects of personalized diets by prediction of glycemic responses on glycemic control and metabolic health in newly diagnosed T2DM: a randomized dietary intervention pilot trial. . BMC Med. 20::56
    [Google Scholar]
100. 100.

     Guizar-Heredia R, Noriega LG, Rivera AL, et al. 2023.. A new approach to personalized nutrition: postprandial glycemic response and its relationship to gut microbiota. . Arch. Med. Res. 54::176–88
     [Google Scholar]
101. 101.

     Tor-Roca A, Sanchez-Pla A, Korosi A, et al. 2023.. A Mediterranean diet-based metabolomic score and cognitive decline in older adults: a case–control analysis nested within the Three-City Cohort Study. . Mol. Nutr. Food Res. 68::e2300271
     [Google Scholar]
102. 102.

     Ardisson Korat AV, Shea MK, Jacques PF, et al. 2024.. Dietary protein intake in midlife in relation to healthy aging—results from the prospective Nurses’ Health Study cohort. . Am. J. Clin. Nutr. 119::271–82
     [Google Scholar]
103. 103.

     Ntemiri A, Ghosh TS, Gheller ME, et al. 2020.. Whole blueberry and isolated polyphenol-rich fractions modulate specific gut microbes in an in vitro colon model and in a pilot study in human consumers. . Nutrients 12::2800
     [Google Scholar]