Gut Microbiota in Health and Disease: A Path to Personalized Medicine

Main Article Content

Sowjanya Pulipati
Srinivasa Babu Puttagunta
S Aswini
Y Nandini
K Lavanya

Abstract

This paper reviews groundbreaking research uncovering the precise dynamics of how nutrients in food affect the gut microbiota and how the gut microbiota in turn affects health in individualized ways. Throughout this paper, the nuances of these dynamics are explored, and the concept of precision nutrition and its practical implications are laid out. Microbes significantly impact how the body processes nutrients from food. It is clear that nutrients and chemicals in food directly influence the structure of gut bacterial communities, protecting against dysbiosis and benefiting health. However, it was not fully understood about the precise dynamics of how nutrients in food impact the gut microbiota and how these microbes in turn affect health, in individualized ways. Recently, in a series of ground-breaking studies, researchers filled in many details of this big picture, investigating detailed mechanisms of action and execution. This research offers the promise of personalized dietary guidance based on an individual’s unique gut microbiota. Microbes are deeply intertwined with health and well-being. The microbiome can be considered a vital organ because of its critical functions for the host. One crucial function is the role that commensal microbes play in the pharmacological bioactivation of inactive compounds, including drugs. This complicated series of actions further validates the need for a better understanding of the genetics in response to therapeutic agents.

Article Details

Sowjanya Pulipati, Srinivasa Babu Puttagunta, S Aswini, Y Nandini, & K Lavanya. (2025). Gut Microbiota in Health and Disease: A Path to Personalized Medicine. Archives of Case Reports, 231–244. https://doi.org/10.29328/journal.acr.1001152
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Copyright (c) 2025 Pulipati S, et al.

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1. Shang Z, Pai L, Patil S. Unveiling the dynamics of gut microbial interactions: a review of dietary impact and precision nutrition in gastrointestinal health. Front Nutr. 2024;11:1395664. Available from: https://doi.org/10.3389/fnut.2024.1395664

2. Abeltino A, Hatem D, Serantoni C, Riente A, De Giulio MM, De Spirito M, et al. Unraveling the gut microbiota: implications for precision nutrition and personalized medicine. Nutrients. 2024;16(22):3806. Available from: https://www.mdpi.com/2072-6643/16/22/3806

3. Bianchetti G, De Maio F, Abeltino A, Serantoni C, Riente A, Santarelli G, … Maulucci G. Unraveling the gut microbiome–diet connection: exploring the impact of digital precision and personalized nutrition on microbiota composition and host physiology. Nutrients. 2023;15(18):3931. Available from: https://www.mdpi.com/2072-6643/15/18/3931

4. Sisk Hackworth L, Kelley ST, Thackray VG. Sex, puberty, and the gut microbiome. Reproduction. 2023;165(2):R61–R74. Available from: https://rep.bioscientifica.com/view/journals/rep/165/2/REP-22-0303.xml

5. Barreto HC, Gordo I. Intrahost evolution of the gut microbiota. Nat Rev Microbiol. 2023;21(9):590-603. Available from: https://doi.org/10.1038/s41579-023-00890-6

6. Rinninella E, Raoul P, Cintoni M, Franceschi F, Miggiano GAD, Gasbarrini A, Mele MC. What is the healthy gut microbiota composition? A changing ecosystem across age, environment, diet, and diseases. Microorganisms. 2019;7(1):14. Available from: https://www.mdpi.com/2076-2607/7/1/14

7. Miyauchi E, Shimokawa C, Steimle A, Desai MS, Ohno H. The impact of the gut microbiome on extra intestinal autoimmune diseases. Nat Rev Immunol. 2023;23(1):9-23. Available from: https://www.nature.com/articles/s41577-022-00727-y

8. Di Tommaso N, Santopaolo F, Gasbarrini A, Ponziani FR. The gut–vascular barrier as a new protagonist in intestinal and extraintestinal diseases. Int J Mol Sci. 2023;24(2):1470. Available from: https://www.mdpi.com/1422-0067/24/2/1470

9. Hong M, Cheng L, Liu Y, Wu Z, Zhang P, Zhang X. Mechanisms underlying the interaction between chronic neurological disorders and microbial metabolites via tea polyphenols therapeutics. Front Microbiol. 2022;13:823902. Available from: https://www.frontiersin.org/articles/10.3389/fmicb.2022.823902

10. Rinninella E, Raoul P, Cintoni M, Franceschi F, Miggiano GAD, Gasbarrini A, Mele MC. What is the healthy gut microbiota composition? A changing ecosystem across age, environment, diet, and diseases. Microorganisms. 2019;7(1):14. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6351938/

11. Sarkar A, Yoo JY, Dutra VO, Morgan KH, Groer M. The association between early-life gut microbiota and long-term health and diseases. J Clin Med. 2021;10(3):459. Available from: https://www.mdpi.com/2077-0383/10/3/459

12. Turroni F, Milani C, Ventura M, van Sinderen D. The human gut microbiota during the initial stages of life: insights from bifidobacteria. Curr Opin Biotechnol. 2022;73:81-87. Available from: https://doi.org/10.1016/j.copbio.2021.07.012

13. Martino C, Dilmore AH, Burcham ZM, Metcalf JL, Jeste D, Knight R. Microbiota succession throughout life from the cradle to the grave. Nat Rev Microbiol. 2022;20(12):707-720. Available from: https://doi.org/10.1038/s41579-022-00768-z

14. Guo J, Ren C, Han X, Huang W, You Y, Zhan J. Role of IgA in the early-life establishment of the gut microbiota and immunity: implications for constructing a healthy start. Gut Microbes. 2021;13(1):1–21. Available from: https://doi.org/10.1080/19490976.2021.1908101

15. Olsson LM, Boulund F, Nilsson S, Khan MT, Gummesson A, Fagerberg L, et al. Dynamics of the normal gut microbiota: a longitudinal one year population study in Sweden. Cell Host Microbe. 2022;30(5):726–739. Available from: https://doi.org/10.1016/j.chom.2022.03.002

16. Liu Q, Mak JWY, Su Q, Yeoh YK, Lui GCY, Ng SSS, et al. Gut microbiota dynamics in a prospective cohort of patients with post acute COVID 19 syndrome. Gut. 2022;71(3):544–552. Available from: https://doi.org/10.1136/gutjnl-2021-325989

17. Luo Y, Ren W, Smidt H, Wright ADG, Yu B, Schyns G, et al. Dynamic distribution of gut microbiota in pigs at different growth stages: composition and contribution. Microbiol Spectr. 2022;10(3):e00688-21. Available from: https://doi.org/10.1128/spectrum.00688-21

18. Aldars García L, Marin AC, Chaparro M, Gisbert JP. The interplay between the immune system and microbiota in inflammatory bowel disease: a narrative review. Int J Mol Sci. 2021;22(6):3076. Available from: https://doi.org/10.3390/ijms22063076

19. Ullah H, Arbab S, Tian Y, Liu CQ, Chen Y, Qijie L, et al. The gut microbiota–brain axis in neurological disorders. Front Neurosci. 2023;17:1225875. Available from: https://doi.org/10.3389/fnins.2023.1225875

20. Ghosh TS, Shanahan F, O’Toole PW. Toward an improved definition of a healthy microbiome for healthy aging. Nat Aging. 2022;2:253–266. Available from: https://doi.org/10.1038/s43587-022-00306-9

21. Hoskinson C, Dai DL, Del Bel KL, Becker AB, Moraes TJ, Mandhane PJ, et al. Delayed gut microbiota maturation in the first year of life is a hallmark of pediatric allergic disease. Nat Commun. 2023;14(1):4785. Available from: https://doi.org/10.1038/s41467-023-40336-4

22. Ranheim Sveen T, Hannula SE, Bahram M. Microbial regulation of feedbacks to ecosystem change. Trends Microbiol. 2024;32(1):68-78. Available from: https://doi.org/10.1016/j.tim.2023.06.006

23. Pan X, Raaijmakers JM, Carrión VJ. Importance of Bacteroidetes in host–microbe interactions and ecosystem functioning. Trends Microbiol. 2023; 31(9):959-97. Available from: https://doi.org/10.1016/j.tim.2023.03.018

24. Vernocchi P, Del Chierico F, Putignani L. Gut microbiota metabolism and interaction with food components. Metabolites. 2020; 21(10):3688. Available from: https://doi.org/10.3390/ijms21103688

25. Sarfraz MH, Shahid A, Asghar S, Aslam B, Ashfaq UA, Raza H, et al. Personalized nutrition, microbiota, and metabolism: a triad for eudaimonia. Metabolites. 2022; 9:1038830. Available from: https://doi.org/10.3389/fmolb.2022.1038830

26. Arnolds L, Lozupone CA. Striking a balance with help from our little friends – how the gut microbiota contributes to immune homeostasis. Semin Immunol. 2016;28(5):517–524. Available from: https://pubmed.ncbi.nlm.nih.gov/27698623/

27. Correale J, Hohlfeld R, Baranzini SE. The role of the gut microbiota in multiple sclerosis. Nat Rev Neurol. 2022;18(7):and page(s). Available from: https://doi.org/10.1038/s41582-022-00697-8

28. Ramanan D, Pratama A, Zhu Y, Venezia O, Sassone Corsi M, Chowdhary K, et al. Regulatory T cells in the face of the intestinal microbiota. Nat Rev Immunol. 2023;23(11):749-762. Available from: https://doi.org/10.1038/s41577-023-00890-w

29. Suchiita A, Gupta N, Nandi K, Sonkar S, Chandra L. Harmony within: unravelling the microbiome–immune system symbiosis for health. Adv Gut Microbiome Res. 2025;1:9927379. Available from: https://onlinelibrary.wiley.com/doi/pdf/10.1155/agm3/9927379

30. Khor B, Snow M, Herrman E, Ray N, Mansukhani K, Patel KA, et al. Interconnections between the oral and gut microbiomes: reversal of microbial dysbiosis and the balance between systemic health and disease. Microorganisms. 2021;9(3):496. Available from: https://doi.org/10.3390/microorganisms9030496

31. Bisgaard TH, Allin KH, Keefer L, Ananthakrishnan AN, Jess T. Depression and anxiety in inflammatory bowel disease: epidemiology, mechanisms, and treatment. Nat Rev Gastroenterol Hepatol. 2022;19(11):717-726. Available from: https://doi.org/10.1038/s41575-022-00634-6

32. Kho YZ, Lal KS. The human gut microbiome – a potential controller of wellness and disease. 2018;9:1835. Available from: https://doi.org/10.3389/fmicb.2018.01835

33. Sies H, Belousov VV, Chandel NS, Davies MJ, Jones DP, Mann GE, et al. Defining the roles of specific reactive oxygen species (ROS) in cell biology and physiology. Nat Rev Mol Cell Biol. 2022;23(7):499-515. Available from: https://doi.org/10.1038/s41580-022-00456-z

34. Andrabi SM, Sharma NS, Karan A, Shahriar SS, Cordon B, Ma B, Xie J. Nitric oxide: physiological functions, delivery, and biomedical applications. Adv Sci. 2023;10(30):2303259. Available from: https://doi.org/10.1002/advs.202303259

35. Infante Villamil S, Huerlimann R, Jerry DR. Microbiome diversity and dysbiosis in aquaculture. Rev Aquac. 2021;13(2):1077-1096. Available from: https://ui.adsabs.harvard.edu/abs/2021RvAq...13.1077I/abstract

36. Wang F, Liu Q, Wu H, Tang T, Zhao T, Li Z. The dysbiosis gut microbiota induces the alternation of metabolism and imbalance of Th17/Treg in OSA patients. Arch Microbiol. 2022; 204(4):217. Available from: https://doi.org/10.1007/s00203-022-02825-w

37. Haneishi Y, Furuya Y, Hasegawa M, Picarelli A, Rossi M, Miyamoto J. Inflammatory bowel diseases and gut microbiota. Int J Mol Sci. 2023;24(4):3817. Available from: https://doi.org/10.3390/ijms24043817

38. Santana PT, Rosas SLB, Ribeiro BE, Marinho Y, de Souza HS. Dysbiosis in inflammatory bowel disease: pathogenic role and potential therapeutic targets. Int J Mol Sci. 2022;23(7):3464. Available from: https://doi.org/10.3390/ijms23073464

39. Pisani A, Rausch P, Bang C, Ellul S, Tabone T, Marantidis Cordina C, et al. Dysbiosis in the gut microbiota in patients with inflammatory bowel disease during remission. Microbiol Spectr. 2022;10(3):e00616-22. Available from: https://doi.org/10.1128/spectrum.00616-22

40. Ballini A, Scacco S, Boccellino M, Santacroce L, Arrigoni R. Microbiota and obesity: where are we now? 2020;9(12):415. Available from: https://doi.org/10.3390/biology9120415

41. Hou K, Wu ZX, Chen XY, Wang JQ, Zhang D, Xiao C, et al. Microbiota in health and disease. Signal Transduct Target Ther. 2022;7(1):135. Available from: https://doi.org/10.1038/s41392-022-00974-4

42. Liu J, Tan Y, Cheng H, Zhang D, Feng W, Peng C. Functions of gut microbiota metabolites, current status, and future perspectives. Aging Dis. 2022;13(4):1106. Available from: https://doi.org/10.14336/ad.2022.0104

43. Afzaal M, Saeed F, Shah YA, Hussain M, Rabail R, Socol CT, et al. Human gut microbiota in health and disease: unveiling the relationship. Front Microbiol. 2022;13:999001. Available from: https://doi.org/10.3389/fmicb.2022.999001

44. Christovich A, Luo X. Gut microbiota, leaky gut, and autoimmune diseases. 2022; 13:946248. Available from: https://doi.org/10.3389/fimmu.2022.946248

45. Mousa WK, Chehadeh F, Husband S. Microbial dysbiosis in the gut drives systemic autoimmune diseases. Front Immunol. 2022;13: 906258. Available from: https://doi.org/10.3389/fimmu.2022.906258

46. Topi S, Bottalico L, Charitos IA, Colella M, Di Domenico M, Palmirotta R, Santacroce L. Biomolecular mechanisms of autoimmune diseases and their relationship with the resident microbiota: friend or foe? Pathophysiology. 2022;29(3):507-536. Available from: https://doi.org/10.3390/pathophysiology29030041

47. Wang X, Yuan W, Yang C, Wang Z, Zhang J, Xu D, Sun W. Emerging role of gut microbiota in autoimmune diseases. Front Immunol. 2024;15:1365554. Available from: https://doi.org/10.3389/fimmu.2024.1365554

48. Wu HJ, Zegarra Ruiz D, Diehl GE. Intestinal microbes in autoimmune and inflammatory disease. 2020;11:597966. Available from: https://doi.org/10.3389/fimmu.2020.597966

49. Halper Stromberg A, Jabri B. Maladaptive consequences of inflammatory events shape individual immune identity. Nat Immunol. 2022; 23(12):1675-1686. Available from: https://doi.org/10.1038/s41590-022-01342-8

50. Yau C, Danska JS. Cracking the type 1 diabetes code: genes, microbes, immunity, and the early life environment. Immunol Rev. 2024; 325(1):23-45. Available from: https://doi.org/10.1111/imr.13362

51. Sun J, Chen F, Wu G. Potential effects of gut microbiota on host cancers: focus on immunity, DNA damage, cellular pathways, and anticancer therapy. 2023; 17(10):1535-1551. Available from: https://doi.org/10.1038/s41396-023-01483-0

52. Xu Z, Lv Z, Chen F, Zhang Y, Xu Z, Huo J, Lu A. Dysbiosis of human tumor microbiome and aberrant residence of Actinomyces in tumor associated fibroblasts in young onset colorectal cancer. Front Immunol. 2022;13:1008975. Available from: https://doi.org/10.3389/fimmu.2022.1008975

53. Lin Z, Mao D, Jin C, Wang J, Lai Y, Zhang Y, Sheng L. The gut microbiota correlates with the disease characteristics and immune status of patients with untreated diffuse large B cell lymphoma. Front Immunol. 2023;14:1105293. Available from: https://doi.org/10.3389/fimmu.2023.1105293

54. Song EJ, Shin JH. Personalized diets based on the gut microbiome as a target for health maintenance: from current evidence to future possibilities. 2022;32(12):1497-1505. Available from: https://doi.org/10.4014/jmb.2209.09050

55. Kuntz MK, Gilbert JA. Introducing the microbiome into precision medicine. 2016; 38(1):81-91. Available from: https://doi.org/10.1016/j.tips.2016.10.001

56. Nogal B, Blumberg JB, Blander G, Jorge M. Gut microbiota–informed precision nutrition in the generally healthy individual: are we there yet? 2021; 5(9):nzab107. Available from: https://doi.org/10.1093/cdn/nzab107

57. Vyas U, Ranganathan N. Probiotics, prebiotics, and synbiotics: gut and beyond. 2012; 2012:872716. Available from: https://doi.org/10.1155/2012/872716

58. Schmidt TS, Li SS, Maistrenko OM, Akanni W, Coelho LP, Dolai S, et al. Drivers and determinants of strain dynamics following fecal microbiota transplantation. Nat Med. 2022;28(9):1902 1912. Available from: https://doi.org/10.1038/s41591-022-01913-0

59. Shtossel O, Turjeman S, Riumin A, Goldberg MR, Elizur A, Bekor Y, … Louzoun Y. Recipient independent, high accuracy FMT response prediction and optimization in mice and humans. Microbiome. 2023;11(1):181. Available from: https://doi.org/10.1186/s40168-023-01623-w

60. Lin A, Jiang A, Huang L, Li Y, Zhang C, Zhu L,et al. From chaos to order: optimizing fecal microbiota transplantation for enhanced immune checkpoint inhibitors efficacy. Gut Microbes. 2025;17(1):2452277. Available from: https://doi.org/10.1080/19490976.2025.2452277

61. Tian H, Wang X, Fang Z, Li L, Wu C, Bi D, et al. Fecal microbiota transplantation in clinical practice: present controversies and prospects. HLife. 2024;2(6):269 283. Available from: https://doi.org/10.1016/j.hlife.2024.01.006

62. Brüssow H. Problems with the concept of gut microbiota dysbiosis. 2019;13(2):423-434. Available from: https://doi.org/10.1111/1751-7915.13479

63. Foster Nyarko E, Pallen MJ. The microbial ecology of Escherichia coli in the vertebrate gut. FEMS Microbiol Rev. 2022;46(3):fuac008. Available from: https://doi.org/10.1093/femsre/fuac008

64. Sharon I, Quijada NM, Pasolli E, Fabbrini M, Vitali F, Agamennone V, … Turroni S. The core human microbiome: does it exist and how can we find it? a critical review of the concept. Nutrients. 2022;14(14):2872. Available from: https://doi.org/10.3390/nu14142872

65. Abdullah MM, Vazquez Vidal I, Baer DJ, House JD, Jones PJ, Desmarchelier C. Common genetic variations involved in the inter-individual variability of circulating cholesterol concentrations in response to diets: a narrative review of recent evidence. Nutrients. 2021;13(2):695. Available from: https://doi.org/10.3390/nu13020695

66. Lange L, Berg G, Cernava T, Champomier Vergès MC, Charles T, Cocolin L, … Sessitsch A. Microbiome ethics, guiding principles for microbiome research, use, and knowledge management. 2022;17(1):50. Available from: https://doi.org/10.1186/s40793-022-00444-y

67. Sainz T, Pignataro V, Bonifazi D, Ravera S, Mellado MJ, Pérez Martínez A, Escudero A, Ceci A, Calvo C. Human microbiome in children, at the crossroad of social determinants of health and personalized medicine. 2021;8(12):1191. Available from: https://doi.org/10.3390/children8121191

68. Wei L, Singh R, Ro S, Ghoshal UC. Gut microbiota dysbiosis in functional gastrointestinal disorders: underpinning the symptoms and pathophysiology. JGH Open. 2021;5(9):976-987. Available from: https://doi.org/10.1002/jgh3.12528

69. Stolfi C, Maresca C, Monteleone G, Laudisi F. Implications of intestinal barrier dysfunction in gut dysbiosis and diseases. Biomedicines. 2022;10(2):289. Available from: https://doi.org/10.3390/biomedicines10020289

70. Li XY, Meng L, Shen L, Ji HF. Regulation of gut microbiota by vitamin C, vitamin E, and β carotene. Food Res Int. 2023;169:112749. Available from: https://doi.org/10.1016/j.foodres.2023.112749

71. Hossain KS, Amarasena S, Mayengbam S. B vitamins and their roles in gut health. Microorganisms. 2022;10(6):1168. Available from: https://doi.org/10.3390/microorganisms10061168

72. Brun P. The profiles of dysbiotic microbial communities. 2019;5(1):87-101. Available from: https://doi.org/10.3934/microbiol.2019.1.87

73. Ruiz Malagón AJ, Rodríguez Sojo MJ, Redondo E, Rodríguez Cabezas ME, Gálvez J, Rodríguez Nogales A. Systematic review: the gut microbiota as a link between colorectal cancer and obesity. Obes Rev. 2025;26(4):e13872. Available from: https://onlinelibrary.wiley.com/doi/full/10.1111/obr.13872

74. Geng J, Ni Q, Sun W, Li L, Feng X. The links between gut microbiota and obesity and obesity related diseases. Biomed Pharmacother. 2022;153:113415. Available from: https://doi.org/10.1016/j.biopha.2022.112678

75. Caballero Flores G, Pickard JM, Núñez G. Microbiota-mediated colonization resistance: mechanisms and regulation. Nat Rev Microbiol. 2023;21(6):347 360. Available from: https://doi.org/10.1038/s41579-022-00833-7

76. Ross FC, Patangia D, Grimaud G, Lavelle A, Dempsey EM, Ross RP, Stanton C. The interplay between diet and the gut microbiome: implications for health and disease. Nat Rev Microbiol. 2024;22(11):671 686. Available from: https://doi.org/10.1038/s41579-024-01068-4

77. Davis EC, Castagna VP, Sela DA, Hillard MA, Lindberg S, Mantis NJ, … Järvinen KM. Gut microbiome and breast-feeding: implications for early immune development. J Allergy Clin Immunol. 2022;150(3):523 534. Available from: https://doi.org/10.1016/j.jaci.2022.07.014