STM Journals Peer-reviewed research from Consortium e-Learning Network

Research and Reviews : A Journal of Immunology Review Article

Gut Feelings: Unravelling the Secrets of the Microbial Universe Within

  1. Yashashwi Shrivastav Department of Pharmacy, IPS Academy College of Pharmacy, Rajendra Nagar, A.B. Road, Indore
  2. Sanika Balekar Department of Business analytics, IPS Academy Institute of Business Management and Research, Rajendra Nagar, A.B. Road, Indore
  3. Neelam Balekar Department of Pharmacy, IPS Academy College of Pharmacy, Rajendra Nagar, A.B. Road, Indore

Abstract

The human digestive system hosts a varied and dynamic community of microorganisms, commonly known as the gut microbiota. This complex community, which includes various organisms such as bacteria, archaea, viruses, and fungi, is essential and important for numerous bodily functions such as metabolism, immune response, and cognitive development. The composition and vast diversity of the gut microbiome are shaped by diet, lifestyle, and genetic factors. Disruptions in this balance, known as dysbiosis, have been associated with various health issues, including obesity, inflammatory bowel diseases, and metabolic disorders. Recent breakthroughs in molecular technologies, such as metagenomics and metabolomics, have allowed scientists to unravel the intricate composition and functions of the gut microbiome, offering new insights into its influence and effect on human health and various diseases. Beyond digestion and nutrient absorption, the gut microbiome plays key roles in immune system regulation, maintaining gut barrier integrity, and supporting overall bodily balance. Therapeutic strategies designed to alter the gut microbiome, such as probiotics, prebiotics, and fecal microbiota transplants, have shown promise in addressing a range of health issues. Additionally, growing research indicates that yoga may benefit gut health by reducing stress, enhancing digestion, and supporting microbial balance. Future studies will likely focus on developing microbiome-based diagnostics, personalized treatments, and innovative therapies such as postbiotics, phage therapy, and engineered microbiota. By deepening the understanding of interactions between both the gut microbiome and human health, new opportunities for diagnosis, prognosis, and targeted therapies can emerge, transforming healthcare in the process.

Keywords

References (52)

  1. 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 Dec;26(1):26050. doi:10.3402/mehd. v26.26050. PMID: 25651996; PMCID: PMC4315782.
  2. Malard F, Dore J, Gaugler B, Mohty M. Introduction to host microbiome symbiosis in health and disease. Mucosal Immunology. 2021 May 1;14(3):547–54. Epub 2020 Dec. PMID: 33299088; PMCID: PMC7724625.
  3. Busnelli M, Manzini S, Sirtori CR, Chiesa G, Parolini C. Effects of Vegetable Proteins on Hypercholesterolemia and Gut Microbiota Modulation. Nutrients. 2018;10(9):1249. doi:10.3390/nu10091249
  4. Jones ML, Ganopolsky JG, Martoni CJ, Labbé A, Prakash S. Emerging science of the human microbiome. Gut Microbes. 2014;5(4):446-457. doi:10.4161/gmic.29810
  5. Ruiz L, Delgado S, Ruas-Madiedo P, Margolles A, Sánchez B. Proteinaceous Molecules Mediating Bifidobacterium-Host Interactions. Frontiers in Microbiology. 2016;7. doi:10.3389/fmicb.2016.01193
  6. Shreiner AB, Kao JY, Young VB. The gut microbiome in health and in disease. Current Opinion in Gastroenterology. 2015;31(1):69-75. doi:10.1097/mog.0000000000000139
  7. Otaru N, Ye K, Mujezinovic D, Berchtold L, Constancias F, Cornejo FA, et al. GABA Production by Human Intestinal Bacteroides spp.: Prevalence, Regulation, and Role in Acid Stress Tolerance. Frontiers in Microbiology. 2021;12. doi:10.3389/fmicb.2021.656895
  8. Tuddenham S, Sears CL. The intestinal microbiome and health. Current Opinion in Infectious Diseases. 2015;28(5):464-470. doi:10.1097/qco.0000000000000196
  9. Selber-Hnatiw S, Rukundo B, Ahmadi M, Akoubi H, Al-Bizri H, Aliu AF, et al. Human Gut Microbiota: Toward an Ecology of Disease. Frontiers in Microbiology. 2017;8. doi:10.3389/fmicb.2017.01265
  10. Montalto, Massimo Montalto, Ferruccio D’Onofrio, A. Gallo, Alessia Cazzato, Giovanni Gasbarrini. Intestinal microbiota and its functions. Digestive and Liver Disease Supplements 3 (2009) 30–34.
  11. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences. 2010;108(supplement_1):4516-4522. doi:10.1073/pnas.1000080107
  12. Johnson JS, Spakowicz DJ, Hong BY, Petersen LM, Demkowicz P, Chen L, et al. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nature communications. 2019 Nov;10(1):5029.
  13. Structure, function and diversity of the healthy human microbiome. Nature 486, no. 7402 (2012): 207–214.
  14. Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, et al. A genomic catalog of Earth’s microbiomes. Nature Biotechnol. 2021 Apr;39(4):499–509.
  15. 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 Mar;464(7285):59–65.
  16. Almeida A, Mitchell AL, Boland M, Forster SC, Gloor GB, Tarkowska A, et al. A new genomic blueprint of the human gut microbiota. Nature. 2019 Apr;568(7753):499–504.
  17. Franzosa EA, Morgan XC, Segata N, Waldron L, Reyes J, Earl AM, et al. Relating the metatranscriptome and metagenome of the human gut. Proceedings of the National Academy of Sciences. 2014 Jun;111(22):E2329–38.
  18. Zhang X, Deeke SA, Ning Z, Starr AE, Butcher J, Li J, et al. Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-05357-4
  19. Zhang W, An Y, Qin X, Wu X, Wang X, Hou H, et al. Gut microbiota-derived metabolites in colorectal cancer: the bad and the challenges. Frontiers in Oncology. 2021 Oct; 11:739648.
  20. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nature biotechnology. 2018 Nov;36(10):996–1004.
  21. Sonnenburg JL, Bäckhed F. Diet–microbiota interactions as moderators of human metabolism. Nature. 2016 Jul;535(7610):56–64.
  22. LeBlanc JG, Milani C, De Giori GS, Sesma F, Van Sinderen D, Ventura M. Bacteria as vitamin suppliers to their host: a gut microbiota perspective. Current opinion in biotechnology. 2013 Apr ;24(2):160–8.
  23. Acharya A, Shetty SS. Role of gut microbiota derived short chain fatty acid metabolites in modulating female reproductive health. Human Nutrition & Metabolism. 2024 Mar 8:200256.
  24. Belkaid Y, Harrison OJ. Homeostatic immunity and the microbiota. Immunity. 2017 Apr ;46(4):562–76.
  25. Kelly D, Conway S, Aminov R. Commensal gut bacteria: mechanisms of immune modulation. Trends in immunology. 2005 Jun;26(6):326–33.
  26. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, et al. A core gut microbiome in obese and lean twins. nature. 2009 Jan ;457(7228):480–4.
  27. Cryan JF, O’Riordan KJ, Cowan CS, Sandhu KV, Bastiaanssen TF, Boehme M, et al. The microbiota-gut-brain axis. Physiol Rev. 2019 Aug.
  28. Menees S, Chey W. The gut microbiome and irritable bowel syndrome. F1000Research. 2018;7:1029. doi:10.12688/f1000research.14592.1
  29. Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 2019;569(7758):655-662. doi:10.1038/s41586-019-1237-9
  30. Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, et al. Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice. Science. 2013;341(6150). doi:10.1126/science.1241214
  31. Gurung M, Li Z, You H, Rodrigues R, Jump DB, Morgun A, et al. Role of gut microbiota in type 2 diabetes pathophysiology. EBioMedicine. 2020;51:102590. doi:10.1016/j.ebiom.2019.11.051
  32. Cryan JF, O'Riordan KJ, Cowan CSM, Sandhu KV, Bastiaanssen TFS, Boehme M, et al. The Microbiota-Gut-Brain Axis. Physiological Reviews. 2019;99(4):1877-2013. doi:10.1152/physrev.00018.2018
  33. Vogt NM, Kerby RL, Dill-McFarland KA, Harding SJ, Merluzzi AP, Johnson SC, et al. Gut microbiome alterations in Alzheimer’s disease. Scientific Reports. 2017;7(1). doi:10.1038/s41598-017-13601-y
  34. West CE. Gut microbiota and allergic disease. Current Opinion in Clinical Nutrition and Metabolic Care. 2014;17(3):261-266. doi:10.1097/mco.0000000000000044
  35. Belkaid Y, Hand TW. Role of the Microbiota in Immunity and Inflammation. Cell. 2014;157(1):121-141. doi:10.1016/j.cell.2014.03.011
  36. Sanders ME, Merenstein DJ, Reid G, Gibson GR, Rastall RA. Probiotics and prebiotics in intestinal health and disease: from biology to the clinic. Nature Reviews Gastroenterology & Hepatology. 2019;16(10):605-616. doi:10.1038/s41575-019-0173-3
  37. Vangay P, Johnson AJ, Ward TL, Al-Ghalith GA, Shields-Cutler RR, Hillmann BM, et al. US Immigration Westernizes the Human Gut Microbiome. Cell. 2018;175(4):962-972.e10. doi:10.1016/j.cell.2018.10.029
  38. Sharma B, Hankey A, Nagilla N, Meenakshy KB, Nagendra HR. Can yoga practices benefit health by improving organism regulation? Evidence from electrodermal measures of acupuncture meridians. Int J Yoga. 2014 Jan;7(1):32–40.
  39. Shree Ganesh HR, Subramanya P, Rao M R, Udupa V. Role of yoga therapy in improving digestive health and quality of sleep in an elderly population: A randomized controlled trial. J Bodyw Mov Ther. 2021 Jul; 27:692–697.
  40. Raman M, Vishnubhotla R, Ramay HR, Gonçalves MC, Shin AS, Pawale D, et al. Isha yoga practices, vegan diet, and participation in Samyama meditation retreat: impact on the gut microbiome & metabolome–a non-randomized trial. BMC Complementary Medicine and Therapies. 2023 Apr;23(1):107.
  41. Allegretti JR, Mullish BH, Kelly C, Fischer M. The evolution of the use of faecal microbiota transplantation and emerging therapeutic indications. The Lancet. 2019;394(10196):420-431. doi:10.1016/s0140-6736(19)31266-8
  42. Wegh CAM, Geerlings SY, Knol J, Roeselers G, Belzer C. Postbiotics and Their Potential Applications in Early Life Nutrition and Beyond. International Journal of Molecular Sciences. 2019;20(19):4673. doi:10.3390/ijms20194673
  43. Kortright KE, Chan BK, Koff JL, Turner PE. Phage Therapy: A Renewed Approach to Combat Antibiotic-Resistant Bacteria. Cell Host & Microbe. 2019;25(2):219-232. doi:10.1016/j.chom.2019.01.014
  44. Lu TK, Mimee M, Citorik RJ, et al. Engineering the Microbiome for Human Health Applications. In: National Academies of Sciences, Engineering, and Medicine; Division on Earth and Life Studies; Board on Chemical Sciences and Technology; Chemical Sciences Roundtable. The Chemistry of Microbiomes: Proceedings of a Seminar Series. Washington (DC): National Academies Press (US); 2017 Jul. 10. Available from: https://www.ncbi.nlm.nih.gov/books/NBK447358/
  45. Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nature Reviews Genetics. 2016;17(6):333-351. doi:10.1038/nrg.2016.49
  46. Li Y, Jin Y, Zhang J, Pan H, Wu L, Liu D, et al. Recovery of human gut microbiota genomes with third-generation sequencing. Cell Death & Disease. 2021;12(6). doi:10.1038/s41419-021-03829-y
  47. Scalbert A, Brennan L, Fiehn O, Hankemeier T, Kristal BS, van Ommen B, et al. Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research. Metabolomics. 2009;5(4):435-458. doi:10.1007/s11306-009-0168-0
  48. Emwas AH, Roy R, McKay RT, Tenori L, Saccenti E, Gowda GAN, et al. NMR Spectroscopy for Metabolomics Research. Metabolites. 2019;9(7):123. doi:10.3390/metabo9070123
  49. Peng B, Li H, Peng XX. Functional metabolomics: from biomarker discovery to metabolome reprogramming. Protein & Cell. 2015;6(9):628-637. doi:10.1007/s13238-015-0185-x
  50. Oulas A, Pavloudi C, Polymenakou P, Pavlopoulos GA, Papanikolaou N, Kotoulas G, et al. Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies. Bioinformatics and Biology Insights. 2015;9:BBI.S12462. doi:10.4137/bbi.s12462
  51. Kanehisa M. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research. 2000;28(1):27-30. doi:10.1093/nar/28.1.27
  52. Hernández Medina R, Kutuzova S, Nielsen KN, Johansen J, Hansen LH, Nielsen M, et al. Machine learning and deep learning applications in microbiome research. ISME Communications. 2022;2(1). doi:10.1038/s43705-022-00182-9
Support