The Gut Microbiome: An Overview

Authors

  • Shelly Dimri George C. Marshall High School
  • Angela Rizzo High School Mentor

DOI:

https://doi.org/10.47611/jsrhs.v11i4.3111

Keywords:

Microbiome, Gut brain axis, metabolism, modulating microbiome

Abstract

As a rapidly growing field of research over the past two decades, the Gut Microbiome has emerged as an important player with an integral role in human body functions. Its perturbed function correlates with several diseases such as diabetes, obesity, liver dysfunction, degenerative conditions, and neurological conditions. Studies utilizing the technological advancements with multi-omics methodologies continue to allow the detection and identification of gut microbes and provide mechanistic insights into their functioning. This review provides an overall understanding of the gut microbiome, its function, and communication with the brain and liver via the gut-brain axis and gut-liver axis. This review further discusses its role in some of the common disease states and some ways to potentially modulate the gut microbiome.

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References or Bibliography

Anderson, G., & Maes, M. (2015). The gut–brain axis: The role of melatonin in linking psychiatric, inflammatory and neurodegenerative conditions. Advances in Integrative Medicine, 2(1), 31–37. https://doi.org/10.1016/j.aimed.2014.12.007

Auteri, M., Zizzo, M. G., & Serio, R. (2015). GABA and GABA receptors in the gastrointestinal tract: From motility to inflammation. Pharmacological Research, 93, 11–21. https://doi.org/10.1016/j.phrs.2014.12.001

Bauer, H., Horowitz, R. E., Lewensen, S. M., & Popper, H. (1963). Response of the lymphatic tissue to the microbial flora. Studies on germ free mice. Am. J. Pathol, 42, 471–483.

Bentley, R., & Meganathan, R. (1982). Biosynthesis of vitamin K (menaquinone) in bacteria. Microbiological Reviews, 46(3), 241–280. https://doi.org/10.1128/mr.46.3.241-280.1982

Berg, G., Rybakova, D., Lima, N., Loy, A., Macklin, J. A., Maguin, E., Mauchline, T., McClure, R., Schloter, M. (2020). Microbiome definition re-visited: Old concepts and new challenges. Microbiome, 8(1). https://doi.org/10.1186/s40168-020-00875-0

Betrapally, N. S., Gillevet, P. M., & Bajaj, J. S. (2017). Gut microbiome and liver disease. Translational Research, 179, 49–59. https://doi.org/10.1016/j.trsl.2016.07.005

Bocci, V. (1992). The neglected organ: Bacterial Flora has a crucial immunostimulatory role. Perspectives in Biology and Medicine, 35(2), 251–260. https://doi.org/10.1353/pbm.1992.0004

Brandl, K., Kumar, V., & Eckmann, L. (2017). Gut-liver axis at the frontier of host-microbial interactions. American Journal of Physiology-Gastrointestinal and Liver Physiology, 312(5). https://doi.org/10.1152/ajpgi.00361.2016

Breit, S., Kupferberg, A., Rogler, G., & Hasler, G. (2018). Vagus nerve as modulator of the brain–gut axis in psychiatric and inflammatory disorders. Frontiers in Psychiatry, 9. https://doi.org/10.3389/fpsyt.2018.00044

Britton, G. J., Contijoch, E. J., Clemente, J. C., Grinspan, A., Sands, B. E., Colombel, J.-F., … Faith, J. J. (2019). Microbiotas from humans with inflammatory bowel disease alter the balance of gut th17 and rorγt+ regulatory T cells and exacerbate colitis in mice. Immunity, 50(1). https://doi.org/10.1016/j.immuni.2018.12.015

Burke, K. E., & Lamont, J. T. (2014). clostridium difficile infection: A worldwide disease. Gut and Liver, 8(1), 1–6. https://doi.org/10.5009/gnl.2014.8.1.1

Cani, P. D., & Knauf, C. (2016). How gut microbes talk to organs: The role of endocrine and nervous routes. Molecular Metabolism, 5(9), 743–752. https://doi.org/10.1016/j.molmet.2016.05.011

Cani, P. D., Amar, J., Iglesias, M, Chamontin, B., Ferrières Jean, Tanti Jean-François, Gibson, G. R., Casteilla, L., … Burcelin Rémy. (2007). Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes, 56(7), 1761–1772. https://doi.org/10.2337/db06-1491

Carding, S., Verbeke, K., Vipond, D. T., Corfe, B. M., & Owen, L. J. (2015). Dysbiosis of the gut microbiota in disease. Microbial Ecology in Health & Disease, 26. https://doi.org/10.3402/mehd.v26.26191

Cassard, A.-M., & Ciocan, D. (2018). Microbiota, a key player in alcoholic liver disease. Clinical and Molecular Hepatology, 24(2), 100–107. https://doi.org/10.3350/cmh.2017.0067

Chen, Z., Radjabzadeh, D., Uitterlinden, A. G., Zhernakova, A., Fu, J., Kraaij, R., & Voortman, T. (2021). Association of insulin resistance and type 2 diabetes with gut microbial diversity. JAMA Network Open, 4(7). https://doi.org/10.1001/jamanetworkopen.2021.18811

Clemente, J. C., Ursell, L. K., Parfrey, L. W., & Knight, R. (2012). The impact of the gut microbiota on human health: An integrative view. Cell, 148(6), 1258–1270. https://doi.org/10.1016/j.cell.2012.01.035

Collins, S. L., & Patterson, A. D. (2020). The gut microbiome: An orchestrator of xenobiotic metabolism. Acta Pharmaceutica Sinica B, 10(1), 19–32. https://doi.org/10.1016/j.apsb.2019.12.001

Covasa, M., Stephens, R. W., Toderean, R., & Cobuz, C. (2019). Intestinal sensing by gut microbiota: Targeting gut peptides. Frontiers in Endocrinology, 10. https://doi.org/10.3389/fendo.2019.00082

de J.R. De-Paula, V., Forlenza, A. S., & Forlenza, O. V. (2018). Relevance of gut microbiota in cognition, behaviour and alzheimer's disease. Pharmacological Research, 136, 29–34. https://doi.org/10.1016/j.phrs.2018.07.007

Di Domenico, M., Ballini, A., Boccellino, M., Scacco, S., Lovero, R., Charitos, I. A., & Santacroce, L. (2022). The intestinal microbiota may be a potential theranostic tool for personalized medicine. Journal of Personalized Medicine, 12(4), 523. https://doi.org/10.3390/jpm12040523

Doulberis, M., Kotronis, G., Gialamprinou, D., Kountouras, J., & Katsinelos, P. (2017). Non-alcoholic fatty liver disease: An update with special focus on the role of gut microbiota. Metabolism, 71, 182–197. https://doi.org/10.1016/j.metabol.2017.03.013

Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K. E., & Relman, D. A. (2005). Diversity of the human intestinal microbial flora. Science, 308(5728), 1635–1638. https://doi.org/10.1126/science.1110591

Fenn, K., Strandwitz, P., Stewart, E. J., Dimise, E., Rubin, S., Gurubacharya, S., Clardy, J., & Lewis, K. (2017). Quinones are growth factors for the human gut microbiota. Microbiome, 5(1). https://doi.org/10.1186/s40168-017-0380-5

Forssten, S. D., & Ouwehand, A. C. (2022). Contribution of the microbiota to Healthy Aging. Comprehensive Gut Microbiota, 69–84. https://doi.org/10.1016/b978-0-12-819265-8.00059-0

Framework for human microbiome research. (2012). Nature, 486(7402), 215–221. https://doi.org/10.1038/nature11209

Frank, D. N., St. Amand, A. L., Feldman, R. A., Boedeker, E. C., Harpaz, N., & Pace, N. R. (2007). Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proceedings of the National Academy of Sciences, 104(34), 13780–13785. https://doi.org/10.1073/pnas.0706625104

Gavini, F., Cayuela, C., & Neut, C. (2001). Differences in the distribution of bifidobacterial and enterobacterial species in human faecal microflora of three different (children, adults, elderly) age groups. Microbial Ecology in Health and Disease, 13(1), 40–45. https://doi.org/10.1080/089106001750071690

Ge, X., Pan, J., Liu, Y., Wang, H., Zhou, W., & Wang, X. (2018). Intestinal crosstalk between microbiota and serotonin and its impact on Gut Motility. Current Pharmaceutical Biotechnology, 19(3), 190–195. https://doi.org/10.2174/1389201019666180528094202

Gensollen, T., Iyer, S. S., Kasper, D. L., & Blumberg, R. S. (2016). How colonization by Microbiota in early life shapes the immune system. Science, 352(6285), 539–544. https://doi.org/10.1126/science.aad9378

Ghattargi, V. C., Sape, K., Kumbhare, S. V., & Shouche, Y. S. (2019). Mining human microbiome for therapeutics. Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications, 573–613. https://doi.org/10.1007/978-981-13-8315-1_18

Gomez de Agüero, M., Hapfelmeier, S., Sauer, U., McCoy, K. D., & Macpherson, A. J. (2016). The maternal microbiota drives early postnatal innate immune development. Science, 351(6279), 1296–1302. https://doi.org/10.1126/science.aad2571

Hapfelmeier, S., Lawson, M. A., Velykoredko, Y., Balmer, M. L., Endt, K., Geuking, M. B., Curtiss, R., McCoy, K. D., & Macpherson, A. J. (2010). Reversible microbial colonization of germ-free mice reveals the dynamics of Iga Immune Responses. Science, 328(5986), 1705–1709. https://doi.org/10.1126/science.1188454

Holscher, H. D. (2017). Dietary fiber and prebiotics and the gastrointestinal microbiota. Gut Microbes, 8(2), 172–184. https://doi.org/10.1080/19490976.2017.1290756

Indiani, C. M., Rizzardi, K. F., Castelo, P. M., Ferraz, L. F., Darrieux, M., & Parisotto, T. M. (2018). Childhood obesity and Firmicutes/bacteroidetes ratio in the gut microbiota: A systematic review. Childhood Obesity, 14(8), 501–509. https://doi.org/10.1089/chi.2018.0040

Izuddin, W. I., Humam, A. M., Loh, T. C., Foo, H. L., & Samsudin, A. A. (2020). Dietary postbiotic lactobacillus plantarum improves serum and ruminal antioxidant activity and upregulates hepatic antioxidant enzymes and ruminal barrier function in post-weaning lambs. Antioxidants, 9(3), 250. https://doi.org/10.3390/antiox9030250

Kaelberer, M. M., Rupprecht, L. E., Liu, W. W., Weng, P., & Bohórquez, D. V. (2020). Neuropod cells: The emerging biology of gut-brain sensory transduction. Annual Review of Neuroscience, 43(1), 337–353. https://doi.org/10.1146/annurev-neuro-091619-022657

Kamada, N., Seo, S.-U., Chen, G. Y., & Núñez, G. (2013). Role of the gut microbiota in immunity and inflammatory disease. Nature Reviews Immunology, 13(5), 321–335. https://doi.org/10.1038/nri3430

Kim, C. Y., Ma, J., & Lee, I. (2022). HiFi metagenomic sequencing enables assembly of accurate and complete genomes from human gut microbiota. https://doi.org/10.1101/2022.02.09.479829

Kim, Y. S., & Ho, S. B. (2010). Intestinal goblet cells and mucins in health and disease: Recent insights and progress. Current Gastroenterology Reports, 12(5), 319–330. https://doi.org/10.1007/s11894-010-0131-2

LeBlanc, J. G., Milani, C., de Giori, G. S., Sesma, F., van Sinderen, D., & Ventura, M. (2013). Bacteria as vitamin suppliers to their host: A gut microbiota perspective. Current Opinion in Biotechnology, 24(2), 160–168. https://doi.org/10.1016/j.copbio.2012.08.005

Ley, R. E., Knight, R., & Gordon, J. I. (2007). The human microbiome: Eliminating the biomedical/environmental dichotomy in Microbial Ecology. Environmental Microbiology, 9(1), 3–4. https://doi.org/10.1111/j.1462-2920.2006.01222_3.x

Ley, R. E., Peterson, D. A., & Gordon, J. I. (2006). Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell, 124(4), 837–848. https://doi.org/10.1016/j.cell.2006.02.017

Ley, R. E., Turnbaugh, P. J., Klein, S., & Gordon, J. I. (2006). Human gut microbes associated with obesity. Nature, 444(7122), 1022–1023. https://doi.org/10.1038/4441022a

Liu, Y., Wang, J., & Wu, C. (2022). Modulation of gut microbiota and immune system by probiotics, pre-biotics, and post-biotics. Frontiers in Nutrition, 8. https://doi.org/10.3389/fnut.2021.634897

Macpherson, A. J., & Uhr, T. (2004). Induction of protective IGA by intestinal dendritic cells carrying commensal bacteria. Science, 303(5664), 1662–1665. https://doi.org/10.1126/science.1091334

Mariat, D., Firmesse, O., Levenez, F., Guimarăes, V. D., Sokol, H., Doré, J., Corthier, G., & Furet, J.-P. (2009). The Firmicutes/bacteroidetes ratio of the human microbiota changes with age. BMC Microbiology, 9(1), 123. https://doi.org/10.1186/1471-2180-9-123

Maurice, C. F., Haiser, H. J., & Turnbaugh, P. J. (2013). Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell, 152(1-2), 39–50. https://doi.org/10.1016/j.cell.2012.10.052

Merriam-Webster. (n.d.). Microbiome definition & meaning. Merriam-Webster. Retrieved June 22, 2022, from https://www.merriam-webster.com/dictionary/microbiome

Metges, C. C. (2000). Contribution of microbial amino acids to amino acid homeostasis of the host. The Journal of Nutrition, 130(7). https://doi.org/10.1093/jn/130.7.1857s

Misiak, B., Łoniewski, I., Marlicz, W., Frydecka, D., Szulc, A., Rudzki, L., & Samochowiec, J. (2020). The HPA axis dysregulation in severe mental illness: Can we shift the blame to gut microbiota? Progress in Neuro-Psychopharmacology and Biological Psychiatry, 102, 109951. https://doi.org/10.1016/j.pnpbp.2020.109951

Mitsuoka, T. (2014). Decline in Microbial Diversity and Richness of the Microbiome with Age. Biosci.Microbiota Food Health, 33, 99–116.

Morais, L. H., Schreiber, H. L., & Mazmanian, S. K. (2020). The gut microbiota–brain axis in behaviour and brain disorders. Nature Reviews Microbiology, 19(4), 241–255. https://doi.org/10.1038/s41579-020-00460-0

Morrison, D. J., & Preston, T. (2016). Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism. Gut Microbes, 7(3), 189–200. https://doi.org/10.1080/19490976.2015.1134082

Nicholson, J. K., Holmes, E., & Wilson, I. D. (2005). Gut microorganisms, mammalian metabolism and personalized health care. Nature Reviews Microbiology, 3(5), 431–438. https://doi.org/10.1038/nrmicro1152

Odamaki, T., Kato, K., Abe, F., & Osawa, R. (2016). Age-related changes in gut microbiota composition from newborn to Centenarian: A cross-sectional study. BMC Microbiology, 16(1). https://doi.org/10.1186/s12866-016-0708-5

O'Hara, A. M., & Shanahan, F. (2006). The gut flora as a forgotten organ. EMBO Reports, 7(7), 688–693. https://doi.org/10.1038/sj.embor.7400731

Owyang, C., & Logsdon, C. D. (2004). New insights into neurohormonal regulation of pancreatic secretion. Gastroenterology, 127(3), 957–969. https://doi.org/10.1053/j.gastro.2004.05.002

Pham,V. T., Dold, S., Rehman, A., Bird, J. K., & Steinert, R. E. (2021). Vitamins, the gut microbiome and gastrointestinal health in humans. Nutrition Research, 95, 35–53. https://doi.org/10.1016/j.nutres.2021.09.001

Ponziani, F. R., Bhoori, S., Calvani, R., Camisaschi, C., Picca, A., Tuccitto, A., Gasbarrini, A., Pompili, M., & Mazzaferro, V. (2018). Hepatocellular carcinoma is associated with gut microbiota profile and inflammation in nonalcoholic fatty liver disease. Hepatology, 69(1), 107–120. https://doi.org/10.1002/hep.30036

Ramakrishna, B. S. (2013). Role of the gut microbiota in human nutrition and metabolism. Journal of Gastroenterology and Hepatology, 28, 9–17. https://doi.org/10.1111/jgh.12294

Ritter, R. C. (2004). Gastrointestinal mechanisms of satiation for food. Physiology & Behavior, 81(2), 249–273. https://doi.org/10.1016/j.physbeh.2004.02.012

Rodríguez-Romero, J. de, Durán-Castañeda, A. C., Cárdenas-Castro, A. P., Sánchez-Burgos, J. A., Zamora-Gasga, V. M., & Sáyago-Ayerdi, S. G. (2022). What we know about protein gut metabolites: Implications and insights for human health and diseases. Food Chemistry: X, 13, 100195. https://doi.org/10.1016/j.fochx.2021.100195

Rogers, Y.-H., & Zhang, C. (2016). Genomic Technologies in Medicine and Health. Medical and Health Genomics, 15–28. https://doi.org/10.1016/b978-0-12-420196-5.00002-2

Round, J. L., & Mazmanian, S. K. (2009). The gut microbiota shapes intestinal immune responses during health and disease. Nature Reviews Immunology, 9(5), 313–323. https://doi.org/10.1038/nri2515

Régnier, M., Hul, M. V., Knauf, C., & Cani, P. D. (2021). Gut microbiome, endocrine control of gut barrier function and Metabolic Diseases. Journal of Endocrinology, 250(1). https://doi.org/10.1530/joe-20-0473e

Sarada, J., Anju, S., Aparna, Y., & Anuradha, K. (2021). Microbiome therapeutics: Emerging concepts and challenges. Microbiome in Human Health and Disease, 217–238. https://doi.org/10.1007/978-981-16-3156-6_11

Schroeder, B. O., & Bäckhed, F. (2016). Signals from the gut microbiota to distant organs in physiology and disease. Nature Medicine, 22(10), 1079–1089. https://doi.org/10.1038/nm.4185

Shah, A., Shanahan, E., Macdonald, G., Fletcher, L., Ghasemi, P., Morrison, M., Jones, M., & Holtmann, G. (2017). Systematic Review and meta-analysis: Prevalence of small intestinal bacterial overgrowth in chronic liver disease. Seminars in Liver Disease, 37(04), 388–400. https://doi.org/10.1055/s-0037-1608832

Shasthry, S. M. (2020). Fecal microbiota transplantation in alcohol related liver diseases. Clinical and Molecular Hepatology, 26(3), 294–301. https://doi.org/10.3350/cmh.2020.0057

Sherman, P. M., Ossa, J. C., & Johnson-Henry, K. (2009). Unraveling mechanisms of action of probiotics. Nutrition in Clinical Practice, 24(1), 10–14. https://doi.org/10.1177/0884533608329231

Smits, L. P., Bouter, K. E. C., de Vos, W. M., Borody, T. J., & Nieuwdorp, M. (2013). Therapeutic potential of fecal microbiota transplantation. Gastroenterology, 145(5), 946–953. https://doi.org/10.1053/j.gastro.2013.08.058

Srivastava, N., Gupta, B., Gupta, S2012., Danquah, M. K., & Sarethy, I. P. (2019). Analyzing functional microbial diversity. Microbial Diversity in the Genomic Era, 79–102. https://doi.org/10.1016/b978-0-12-814849-5.00006-x

Strandwitz, P. (2018). Neurotransmitter modulation by the gut microbiota. Brain Research, 1693, 128–133. https://doi.org/10.1016/j.brainres.2018.03.015

Sun, C., Chen, L., & Shen, Z. (2019). Mechanisms of gastrointestinal microflora on drug metabolism in clinical practice. Saudi Pharmaceutical Journal, 27(8), 1146–1156. https://doi.org/10.1016/j.jsps.2019.09.011

Tanabe, S. (2013). The effect of probiotics and gut microbiota on th17 cells. International Reviews of Immunology, 32(5-6), 511–525. https://doi.org/10.3109/08830185.2013.839665

Tang, R., Wei, Y., Xiao, X., Fan, Z., Wu, M., Qiu, D., Fang, J.-Y., Ansari, A, Ma, X. (2017). Gut microbial profile is altered in primary biliary cholangitis and partially restored after UDCA therapy. Gut, 67(3), 534–541. https://doi.org/10.1136/gutjnl-2016-313332

Tang, W. H., & Hazen, S. L. (2017). The gut microbiome and its role in cardiovascular diseases. Circulation, 135(11), 1008–1010. https://doi.org/10.1161/circulationaha.116.024251

Thomas, C. M., Hong, T., Hu, W., Britton, R. A., Kalkum, M., & Versalovic, J. (2012). Histamine derived from probiotic lactobacillus reuteri suppresses TNF via modulation of PKA and Erk Signaling. PLoS ONE, 7(2). https://doi.org/10.1371/journal.pone.0031951

Tomasello, G., Mazzola, M., Jurjus, A., Carini, F., Damiani, P., Geagea, A. G., Zeeny, M. N., & Leone, A. (2017). The fingerprint of the human gastrointestinal tract microbiota: a hypothesis of molecular mapping. J. Biol Regul Homeost Agents 31(1), 245–249.

Turnbaugh, P. J., Ley, R. E., Hamady, M., Fraser-Liggett, C. M., Knight, R., & Gordon, J. I. (2007). The Human Microbiome Project. Nature, 449(7164), 804–810. https://doi.org/10.1038/nature06244

Udayappan, S. D., Hartstra, A. V., Dallinga-Thie, G. M., & Nieuwdorp, M. (2014). Intestinal microbiota and faecal transplantation as treatment modality for insulin resistance and type 2 diabetes mellitus. Clinical and Experimental Immunology, 177(1), 24–29. https://doi.org/10.1111/cei.12293

U.S. Food and Drug Administration. (2016) Use of fecal microbiota for transplantation (FMT) to treat clostridium.. Retrieved from https://www.fda.gov/news-events/fda-meetings-conferences-and-workshops/use-fecal-microbiota-transplantation-fmt-treat-clostridium-difficile-infection-not-responsive

Wesemann, D. R., Portuguese, A. J., Magee, J. M., Panchakshari, R. A., Rodig, S. J., Kepler, T. B., & Alt, F. W. (2013). Microbial colonization influences early B-lineage development in the gut lamina propria. Nature, 501(7465), 112–115. https://doi.org/10.1038/nature12496

Whipps, J. M. (n.d.). Mycoparasitism and plant disease control. In N. Burge (Ed.), Fungi Biol Control Syst. (pp. 161–187). Essay, Manchester: Manchester University Press.

Woese, C. R., & Fox, G. E. (1977). Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proceedings of the National Academy of Sciences, 74(11), 5088–5090. https://doi.org/10.1073/pnas.74.11.5088

Zhang, X., Zhivaki, D., & Lo-Man, R. (2017). Unique aspects of the perinatal immune system. Nature Reviews Immunology, 17(8), 495–507. https://doi.org/10.1038/nri.2017.54

Zimmermann, M., Zimmermann-Kogadeeva, M., Wegmann, R., & Goodman, A. L. (2019). Mapping human microbiome drug metabolism by gut bacteria and their genes. Nature, 570(7762), 462–467. https://doi.org/10.1038/s41586-019-1291-3

Zou, Y., Wang, J., Lv, H., & Wang, S. (2020). Protection of galacto-oligosaccharide against E. coli O157 colonization through enhancing gut barrier function and modulating gut microbiota. Foods, 9(11), 1710. https://doi.org/10.3390/foods9111710

Published

11-30-2022

How to Cite

Dimri, S., & Rizzo, A. (2022). The Gut Microbiome: An Overview. Journal of Student Research, 11(4). https://doi.org/10.47611/jsrhs.v11i4.3111

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HS Review Articles