Gastrointestinal microbiome: The two-way communication within us
The gut is considered the largest organ with a significant function in regulating immune homeostasis throughout the life of an individual. The presence of “good” microbes in the gut tract makes the individual healthier, for example, in Parkinson’s disease a decrease in beneficial microbes such as Blautia and Roseburia is observed contrary to a high population of Akkermansia and Verrucomicrobiaceae which is associated with mucin degradation. The first and foremost microbial colonization in the human gut occurs at the fetal stage in utero. Further, a vast amount of the resident microbial population is also transferred in utero from the oral cavity of the mother. The medical practices of birth, that is, the cesarean delivery or the vaginal delivery regulate the microbiome composition of the newborn. Unregulated dietary changes in human lifestyle along with antibiotics and environmental exposures can alter the gut microbiome. Typically, with less recognized implications for health and the likelihood of disease occurrence, the unhealthy gut impairs the normal functioning of the microbiota. Further, it has been extensively investigated that the intestinal tract harbors the largest and most diverse microbial population, and forms the Enteric Nervous System. Elucidation of the factors that influence this mutualistic relationship is therefore vital for understanding the Gut–Brain communication.
Kaur I, Narang PK, Goyal B. Gastrointestinal microbiome: The two-way communication within us. J Appl Biol Biotech 2025. Article in Press. http://doi.org/10.7324/JABB.2026.270878
1. Valdes AM, Walter J, Segal E, Spector TD. Role of the gut microbiota in nutrition and health. BMJ. 2018;361:k2179. https://doi.org/10.1136/bmj.k2179
2. Flint HJ.The impact of nutrition on the human microbiome. Nutr Rev. 2012;70(Suppl 1):S10-3. https://doi.org/10.1111/j.1753-4887.2012.00499.x
3. Borre YE, O’Keeffe GW, Clarke G, Stanton C, Dinan TG, Cryan JF. Microbiota and neurodevelopmental windows: Implications for brain disorders. Trends Mol Med. 2014;20(9):509-518. https://doi.org.10.1016/j.molmed.2014.05.002
4. Bäckhed F, Fraser CM, Ringel Y, Sanders ME, Sartor RB, Sherman PM, et al. Defining a healthy human gut microbiome: Current concepts, future directions, and clinical applications. Cell Host Microbe. 2012;12(5):611-22. https://doi.org.10.1016/j.chom.2012.10.012
5. Tap J, Mondot S, Levenez F, Pelletier E, Caron C, Furet J, et al. Towards the human intestinal microbiota phylogenetic core. Environ Microbiol. 2009;11(10):2574-84. https://doi.org.10.1111/j.1462-2920.2009.01982.x
6. Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci. 2011;108(Suppl 1):4554-61. https://doi.org.10.1073/pnas.1000087107
7. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464(7285):59-65. https://doi.org.10.1038/nature08821
8. O’Callaghan A, Van Sinderen D. Bifidobacteria and their role as members of the human gut microbiota. Front Microbiol. 2016;7:925. https://doi.org.10.3389/fmicb.2016.00925
9. Kim G, Yoon Y, Park JH, Park JW, Noh MG, Kim H, et al. Bifidobacterial carbohydrate/nucleoside metabolism enhances oxidative phosphorylation in white adipose tissue to protect against diet-induced obesity. Microbiome. 2022;10:188. https://doi.org/10.1186/s40168-022-01374-0
10. Power SE, O’Toole PW, Stanton C, Ross RP, Fitzgerald GF. Intestinal microbiota, diet and health. Br J Nutr. 2014;111(3):387-402. https://doi.org.10.1017/S0007114513002560
11. Tang Q, Jin G, Wang G, Liu T, Liu X, Wang B, et al. Current sampling methods for gut microbiota: A call for more precise devices. Front Cell Infect Microbiol. 2020;10:151. https://doi.org.10.3389/fcimb.2020.00151
12. Hooper LV, Gordon JI. Commensal host-bacterial relationships in the gut. Science. 2001;292(5519):1115-8. https://doi.org.10.1126/science.1058709
13. Cooke G, Behan J, Costello M. Newly identified vitamin K-producing bacteria isolated from the neonatal faecal flora. Microbial Ecol Health Dis. 2006;18(3-4):133-8. https://doi.org/10.1080/08910600601048894
14. Geleijnse JM, Vermeer C, Grobbee DE, Schurgers LJ, Knapen MH, Van Der Meer IM, et al. Dietary intake of menaquinone is associated with a reduced risk of coronary heart disease: The Rotterdam study. J Nutr. 2004;134(11):3100-5. https://doi.org.10.1093/jn/134.11.3100
15. Andrès E, Loukili NH, Noel E, Kaltenbach G, Abdelgheni MB, Perrin AE, et al. Vitamin B12 (cobalamin) deficiency in elderly patients. CMAJ.2004;171(3):251-9. https://doi.org.10.1503/cmaj.1031155
16. Gominak C. Vitamin D deficiency changes the intestinal microbiome reducing B vitamin production in the gut. The resulting lack of pantothenic acid adversely affects the immune system, producing a “pro-inflammatory” state associated with atherosclerosis and autoimmunity. Med Hypotheses. 2016;94:103-7. https://doi.org/10.1016/j.mehy.2016.07.007
17. Mayer EA, Savidge T, Shulman RJ.Brain-gut microbiome interactions and functional bowel disorders. Gastroenterology. 2014;146(6):1500-12. https://doi.org/10.1053/j.gastro.2014.02.037
18. Staels B, Fonseca VA. Bile acids and metabolic regulation: Mechanisms and clinical responses to bile acid sequestration. Diabetes Care. 2009;32(Suppl 2):S237. https://doi.org.10.2337/dc09-S355
19. Ridlon JM, Ikegawa S, Alves JM, Zhou B, Kobayashi A, Iida T, et al. Clostridium scindens: A human gut microbe with a high potential to convert glucocorticoids into androgens. J Lipid Res. 2013;54(9):2437-49. https://doi.org/10.1194/jlr.M038869
20. Ciccia F, Guggino G, Rizzo A, Alessandro R, Luchetti MM, Milling S, et al. Dysbiosis and zonulin upregulation alter gut epithelial and vascular barriers in patients with ankylosing spondylitis. Ann Rheum Dis. 2017;76(6):1123-32. https://doi.org/10.1136/annrheumdis-2016-210000.
21. Cox LM, Weiner HL. Microbiota signaling pathways that influence neurologic disease. Neurotherapeutics. 2018;15(1):135-45. https://doi.org.10.1007/s13311-017-0598-8
22. Makris AP, Karianaki M, Tsamis KI, Paschou SA. The role of the gut-brain axis in depression: Endocrine, neural, and immune pathways. Hormones (Athens). 2021;20(1):1-12. https://doi.org.10.1007/s42000-020-00236-4
23. Twardowska A, Makaro A, Binienda A, Fichna J, Salaga M. Preventing bacterial translocation in patients with leaky gut syndrome: Nutrition and pharmacological treatment options. Int J Mol Sci. 2022;23(6):3204. https://doi.org.10.3390/ijms23063204
24. Paone P, Cani PD. Mucus barrier, mucins and gut microbiota: The expected slimy partners? Gut. 2020;69(12):2232-43. https://doi.org.10.1136/gutjnl-2020-322260
25. Bischoff SC, Barbara G, Buurman W, Ockhuizen T, Schulzke JD, Serino M, et al. Intestinal permeability—a new target for disease prevention and therapy. BMC Gastroenterol. 2014;14:189. https://doi.org.10.1186/s12876-014-0189-7
26. Chen Y, Cui W, Li X, Yang H. Interaction between commensal bacteria, immune response and the intestinal barrier in inflammatory bowel disease. Front Immunol. 2021;12:761981. https://doi.org.10.3389/fimmu.2021.761981
27. Zhao X, Zeng H, Lei L, Tong X, Yang L, Yang Y, et al. Tight junctions and their regulation by non-coding RNAs. Int J Biol Sci. 2021;17(3):712. https://doi.org.10.7150/ijbs.45885
28. Molotla-Torres DE, Guzmán-Mejía F, Godínez-Victoria M, Drago- Serrano ME. Role of stress on driving the intestinal paracellular permeability. Curr Issues Mol Biol. 2023;45(11):9284-305. https://doi.org/10.3390/cimb45110581
29. France MM, Turner JR. The mucosal barrier at a glance. J Cell Sci. 2017;130(2):307-14. https://doi.org/10.1242/jcs.193482
30. Durantez Á, Gómez S. Agujeros. Intestino Síndrome de Hipermeabilidad Intestinal; 2018. p. 35. Available from: https://drdurantez.es/blog/2018/09/04/agujeros-en-el-intestino-sindrome-dehipermeabilidad-intestinal [Last accessed on 2025 Mar 10].
31. Iweala OI, Nagler CR. The microbiome and food allergy. Annu Rev Immunol. 2019;37(1):377-403. https://doi.org/10.1146/annurev-immunol-042718-041621
32. Nusrat A, Turner JR, Madara JL. Molecular physiology and pathophysiology of tight junctions. IV. Regulation of tight junctions by extracellular stimuli: Nutrients, cytokines, and immune cells. Am J Physiol. 2000;279(1):G851-7. https://doi.org/10.1152/ajpgi.2000.279.5.G851
33. Quiroz-Olguín G, Gutiérrez-Salmeán G, Posadas-Calleja JG, Padilla- Rubio MF, Serralde-Zúñiga AE. The effect of enteral stimulation on the immune response of the intestinal mucosa and its application in nutritional support. Eur J Clin Nutr. 2021;75(11):1533-9. https://doi.org.10.1038/s41430-021-00877-7
34. Li T, Wang C, Liu Y, Li B, Zhang W, Wang L, et al. Neutrophil extracellular traps induce intestinal damage and thrombotic tendency in inflammatory bowel disease. J Crohn’s Colitis. 2020;14(2):240-53. https://doi.org.10.1093/ecco-jcc/jjz132
35. Adak A, Khan MR. An insight into gut microbiota and its functionalities. Cell Mol Life Sci. 2019;76:473-93. https://doi.org.10.1007/s00018-018-2943-4
36. Koboziev I, Reinoso Webb C, Furr KL, Grisham MB. Role of the enteric microbiota in intestinal homeostasis and inflammation. Free Radical Biol Med. 2014;68:122-33. https://doi.org.10.1016/j.freeradbiomed.2013.11.008
37. Cani PD, Osto M, Geurts L, Everard A. Involvement of gut microbiota in the development of low-grade inflammation and type 2 diabetes associated with obesity. Gut Microbes 2012;3(4):279-88. https://doi.org.10.4161/gmic.19625
38. Cui X, Cong Y. Role of Gut microbiota in the development of some autoimmune diseases. J Inflamm Res. 2025;18:4409-19. https://doi.org/10.2147/JIR.S515618
39. Belizário JE, Faintuch J.Microbiome and gut dysbiosis. Exp Suppl. 2018;109:459-76. https://doi.org.10.1007/978-3-319-74932-7_13
40. Carabotti M, Scirocco A, Maselli MA, Severi C. The gut-brain axis: Interactions between enteric microbiota, central and enteric nervous systems. Ann Gastroenterol. 2015;28(2):203-9.
41. De Goffau MC, Lager S, Sovio U, Gaccioli F, Cook E, Peacock SJ, et al. Human placenta has no microbiome but can contain potential pathogens. Nature. 2019;572(7769):329-34. https://doi.org.10.1038/s41586-019-1451-5
42. Bokulich NA, Chung J, Battaglia T, Henderson N, Jay M, Li H, Blaser MJ.Antibiotics, birth mode, and diet shape microbiome maturation during early life. Sci Transl Med. 2016;8(343):343ra82. https://doi.org.10.1126/scitranslmed.aad7121
43. La Rosa PS, Warner BB, Zhou Y, Weinstock GM, Sodergren E, Hall-Moore CM, et al. Patterned progression of bacterial populations in the premature infant gut. Proc Natl Acad Sci. 2014;111(34):12522- 7. https://doi.org.10.1073/pnas.1409497111
44. Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, et al. Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci. 2014;108(Suppl 1):4578-85. https://doi.org/10.1073/pnas.1000081107
45. Perez-Munoz ME, Arrieta MC, Ramer-Tait AE, Walter J.A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: Implications for research on the pioneer infant microbiome. Microbiome. 2017;5(1):48. https://doi.org/10.1186/s40168-017-0268-4
46. Bushman FD. De-discovery of the placenta microbiome. Am J Obstet Gynecol. 2019;220(3):213-4. https://doi.org.10.1016/j.ajog.2018.11.1093
47. Xie Z, Chen Z, Chai Y, Yao W, Ma G. Unveiling the placental bacterial microbiota: Implications for maternal and infant health. Front Physiol. 2025;1(16):1544216. https://doi.org.10.3389/fphys.2025.1544216
48. Park JY, Yun H. Comprehensive characterization of maternal, fetal, and neonatal microbiomes supports prenatal colonization of the gastrointestinal tract. Sci Rep. 2023;13(1):4652. https://doi.org/10.1038/s41598-023-31049-1
49. Broens PM, Van Rooij IA, Bagci S, Brosens E, Tibboel D, De Klein A, et al. More than fetal urine: Enteral uptake of amniotic fluid as a major predictor for fetal growth during late gestation. Eur J Pediatr. 2016;175:825-31. https://doi.org.10.1007/s00431-016-2713-y
50. Trahair J.Digestive system. In: Harding R, Bocking AD, editors. Fetal Growth and Development. Cambridge UK: Cambridge University Press; 2001. p. 137-153.
51. Gitlin D, Kumate J, Morales C, Noriega L, Arévalo N. The turnover of amniotic fluid protein in the human conceptus. Am J Obstet Gynecol. 1972;113:632-45. https://doi.org.10.1016/0002-9378(72)90632-1
52. Stinson LF, Boyce MC, Payne MS, Keelan JA. The Not-so-Sterile Womb: Evidence That the Human Fetus Is Exposed to Bacteria Prior to Birth. Frontiers in Microbiology. 2019;10:1124. doi: https://doi.org.10.3389/fmicb.2019.01124
53. Brown J, De Vos WM, DiStefano PS, Doré J, Huttenhower C, Knight R, et al. Translating the human microbiome. Nat Biotechnol. 2013;31(4):304-8. https://doi.org.10.1038/nbt.2543
54. Dunn AB, Jordan S, Baker BJ, Carlson NS. The maternal infant microbiome: Considerations for labor and birth. MCN Am J Matern Child Nurs. 2017;42(6):318-25. https://doi.org.10.1097/NMC.0000000000000373
55. Walker RW, Clemente JC, Peter I, Loos RJ.The prenatal gut microbiome: Are we colonized with bacteria in utero? Pediatr Obes. 2017;12(Suppl 1):3-17. https://doi.org.10.1111/ijpo.12217
56. Kerr CA, Grice DM, Tran CD, Bauer DC, Li D, Hendry P, et al. Early life events influence whole-of-life metabolic health via gut microflora and gut permeability. Crit Rev Microbiol. 2015;41(3):326-40. https://doi.org.10.3109/1040841X.2013.837863
57. Ma G, Chen Z, Xie Z, Liu J, Xiao X. Mechanisms underlying changes in intestinal permeability during pregnancy and their implications for maternal and infant health. J Reprod Immunol. 2025;168:104423. https://doi.org.10.1016/j.jri.2025.104423
58. Amabebe E, Anumba DO. The vaginal microenvironment: The physiologic role of lactobacilli. Front Med (Lausanne). 2018;5:181. https://doi.org.10.3389/fmed.2018.00181
59. Amir M, Brown JA, Rager SL, Sanidad KZ, Ananthanarayanan A, Zeng MY. Maternal microbiome and infections in pregnancy. Microorganisms. 2020;8(12):1996. https://doi.org.10.3390/microorganisms8121996
60. Tang M, Weaver NE, Frank DN, Ir D, Robertson CE, Kemp JF, et al. Longitudinal Reduction in diversity of maternal gut microbiota during pregnancy is observed in multiple low-resource settings: Results from the women first trial. Front Microbiol. 2022;13:823757. https://doi.org.10.3389/fmicb.2022.823757
61. Koren O, Goodrich JK, Cullender TC, Spor A, Laitinen K, Bäckhed HK, et al. Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell. 2012;150(3):470-480. https://doi.org.10.1016/j.cell.2012.07.008
62. Walters WA, Xu Z, Knight R. Meta-analyses of human gut microbes associated with obesity and IBD. FEBS Lett. 2014;588(22):4223-33. https://doi.org.10.1016/j.febslet.2014.09.039
63. Edwards SM, Cunningham SA, Dunlop AL, Corwin EJ.The maternal gut microbiome during pregnancy. MCN Am J Matern Child Nurs. 2017;42(6):310-7. https://doi.org.10.1097/NMC.0000000000000372
64. Liang X, Wang R, Luo H, Liao Y, Chen X, Xiao X, et al. The interplay between the gut microbiota and metabolism during the third trimester of pregnancy. Front Microbiol. 2022;13:1059227. https://doi.org.10.3389/fmicb.2022.1059227
65. Neuman H, Koren O. The pregnancy microbiome. Nestle Nutr Inst Workshop Ser. 2017;88:1-9. https://doi.org/10.1159/000455207
66. Vijay-Kumar M, Aitken JD, Carvalho FA, Cullender TC, Mwangi S, Srinivasan S, et al. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science. 2010;328(5975):228-31. https://doi.org.10.1126/science.1179721
67. Tilg H, Moschen AR. Adipocytokines: Mediators linking adipose tissue, inflammation and immunity. Nat Rev Immunol. 2006;6(10):772-83. https://doi.org/10.1038/nri1937
68. Huang B, Fettweis JM, Brooks JP, Jefferson KK, Buck GA. The changing landscape of the vaginal microbiome. Clin Lab Med. 2014;34(4):747-61. https://doi.org.10.1016/j.cll.2014.08.006
69. Biasucci G, Rubini M, Riboni S, Morelli L, Bessi E, Retetangos C. Mode of delivery affects the bacterial community in the Newborn gut. Early Hum Dev. 2010;86(Supp 1):13-15. https://doi.org.10.1016/j.earlhumdev.2010.01.004
70. Penders J, Thijs C, Vink C, Stelma FF, Snijders B, Kummeling I, et al. Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics. 2006;118(2):511-21. https://doi.org.10.1542/peds.2005-2824
71. Pivrncova E, Kotaskova I, Thon V. Neonatal diet and gut microbiome development after C-section during the first three months after birth: A systematic review. Front Nutr. 2022;9:941549. https://doi.org.10.3389/fnut.2022.941549
72. Shao Y, Forster SC, Tsaliki E, Vervier K, Strang A, Simpson N, et al. Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth. Nature. 2019;574(7776):117-21. https://doi.org.10.1038/s41586-019-1560-1
73. Guaraldi F, Salvatori G. Effect of breast and formula feeding on gut microbiota shaping in newborns. Front Cell Infect Microbiol. 2012;2:94. https://doi.org.10.3389/fcimb.2012.0094
74. Walker WA, Iyengar RS. Breast milk, microbiota, and intestinal immune homeostasis. Pediatr Res. 2015;77:220-8. https://doi.org.10.1038/pr.2014.160
75. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota. PLoS Biol. 2007;5(7):e177. https://doi.org.10.1371/journal.pbio.0050177
76. McCann A, Ryan FJ, Stockdale SR, Dalmasso M, BlakeT, Ryan CA, et al. Viromes of one year old infants reveal the impact of birth mode on microbiome diversity. PeerJ.2016;6:e4694. https://doi.org.10.7717/peerj.4694
77. Shennon I, Wilson BC, Behling AH, Portlock T, Haque R, Forrester T, et al. The infant gut microbiome and cognitive development in malnutrition. Clin Nutr. 2024;43(5):1181-9. https://doi.org.10.1016/j.clnu.2024.03.029
78. Zhou L, Qiu W, Wang J, Zhao A, Zhou C, Sun T, et al. Effects of vaginal microbiota transfer on the neurodevelopment and microbiome of cesarean-born infants: A blinded randomized controlled trial. Cell Host Microbe. 2023;31(7):1232-47. https://doi.org/10.1016/j.chom.2023.05.022
79. Rodríguez JM, Murphy K, Stanton C, Ross RP, Kober OI, Kober OI, et al. The composition of the gut microbiota throughout life, with an emphasis on early life. Microb Ecol Health Dis. 2015;26:26050. https://doi.org.10.3402/mehd.v26.26050
80. Claesson MJ, Cusack S, O’Sullivan O, Greene-Diniz R, De Weerd H, Flannery E, et al. Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proc Natl Acad Sci. 2011;108(Suppl 1):4586-591. https://doi.org/10.1073/pnas.1000097107
81. Odamaki T, Kato K, Sugahara H, Hashikura N, Takahashi S, Xiao JZ, et al. Age-related changes in gut microbiota composition from newborn to centenarian: A cross-sectional study. BMC Microbiol. 2016;16:90. https://doi.org.10.1073/pnas.1000097107
82. Salazar N, Arboleya S, Valdés, L, Stanton C, Ross P, Ruiz L, et al. The human intestinal microbiome at extreme ages of life. Dietary intervention as a way to counteract alterations. Front Genet. 2014;5:406. https://doi.org/10.3389/fgene.2014.00406
83. Jackson MA, Jeffery IB, Beaumont M, Bell JT, Clark AG, Ley RE, et al. Signatures of early frailty in the gut microbiota. Genome Med. 2016;8:8. https://doi.org.10.1186/s13073-016-0262-7
84. Zhang D, Huang Y, Ye D. Intestinal dysbiosis: An emerging cause of pregnancy complications? Med Hypotheses. 2015;84(3):223-26. https://doi.org/10.1016/j.mehy.2014.12.029
85. Zmora N, Suez J, Elinav E. You are what you eat: Diet, health and the gut microbiota. Nat Rev Gastroenterol Hepatol. 2019;16:35-56. https://doi.org/10.1038/s41575-018-0061-2
86. Planer JD, Peng Y, Kau AL, Blanton LV, Ndao IM, Tarr PI, et al. Development of the gut microbiota and mucosal IgA responses in twins and gnotobiotic mice. Nature. 2016;534(7606):263-6. https://doi.org.10.1038/nature17940
87. Mkilima T. Engineering artificial microbial consortia for personalized gut microbiome modulation and disease treatment. Ann N Y Acad Sci. 2025;1548(1):29-55. https://doi.org.10.1111/nyas.15352
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