Encyclopedia of Evolutionary Psychological Science

Living Edition
| Editors: Todd K. Shackelford, Viviana A. Weekes-Shackelford

Gut Microbiome

  • Kate E. LynchEmail author
Living reference work entry
DOI: https://doi.org/10.1007/978-3-319-16999-6_2782-1



The human gut microbiome is a community of roughly 40 trillion bacteria, fungi, archaea, and protozoa which reside within the human gastrointestinal tract. Variations in gut microbiome composition have been implicated in a variety of psychological, physiological, and behavioral traits.


A variety of environments, including many human organs, contain within them communities of microorganisms, including bacteria, fungi, archaea, protozoa and viruses. This community is collectively referred to as the microbiome or microbiota. Traditionally, the term microbiota was used to refer to the community of organisms, and microbiome to refer to the collective genomes of organisms within those communities. While the term microbiome can still refer to a set of collective genetic material, these two terms are also now used synonymously to refer to the community of organisms within a given environment (Ursell et al. 2012). The human gastrointestinal tract...

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  1. Alcock, J., Maley, C. C., & Aktipis, C. A. (2014). Is eating behavior manipulated by the gastrointestinal microbiota? Evolutionary pressures and potential mechanisms. BioEssays, 36(10), 940–949.  https://doi.org/10.1002/bies.201400071.CrossRefPubMedPubMedCentralGoogle Scholar
  2. Becattini, S., Taur, Y., & Pamer, E. G. (2016). Antibiotic-induced changes in the intestinal microbiota and disease. Trends in Molecular Medicine, 22(6), 458–478.  https://doi.org/10.1016/j.molmed.2016.04.003.CrossRefPubMedPubMedCentralGoogle Scholar
  3. Bercik, P., et al. (2011). The anxiolytic effect of Bifidobacterium longum NCC3001 involves vagal pathways for gut–brain communication. Neurogastroenterol Motil 23, 1132–1139.CrossRefGoogle Scholar
  4. Carabotti, M., Scirocco, A., Maselli, M. A., & Severi, C. (2015). The gut-brain axis: Interactions between enteric microbiota, central and enteric nervous systems. Annals of Gastroenterology: Quarterly Publication of the Hellenic Society of Gastroenterology, 28(2), 203.Google Scholar
  5. Chen, X., D’Souza, R., & Hong, S. T. (2013). The role of gut microbiota in the gut-brain axis: Current challenges and perspectives. Protein & Cell, 4(6), 403–414.  https://doi.org/10.1007/s13238-013-3017-x.CrossRefGoogle Scholar
  6. Costello, E. K., Lauber, C. L., Hamady, M., Fierer, N., Gordon, J. I., & Knight, R. (2009). Bacterial community variation in human body habitats across space and time. Science, 326(5960), 1694–1697.  https://doi.org/10.1126/science.1177486.CrossRefPubMedPubMedCentralGoogle Scholar
  7. Dash, S., Clarke, G., Berk, M., & Jacka, F. N. (2015). The gut microbiome and diet in psychiatry: Focus on depression. Current Opinion in Psychiatry, 28(1), 1–6.  https://doi.org/10.1097/YCO.0000000000000117.CrossRefPubMedGoogle Scholar
  8. de Theije, C. G., Wopereis, H., Ramadan, M., van Eijndthoven, T., Lambert, J., Knol, J., Garssen, J., Kraneveld, A. D., & Oozeer, R. (2014). Altered gut microbiota and activity in a murine model of autism spectrum disorders. Brain, Behavior, and Immunity, 37, 197–206.  https://doi.org/10.1016/j.bbi.2013.12.005.CrossRefPubMedGoogle Scholar
  9. Diaz Heijtz, R., Wang, S., Anuar, F., Qian, Y., Björkholm, B., Samuelsson, A., Hibberd, M. L., Forssberg, H., & Pettersson, S. (2011). Normal gut microbiota modulates brain development and behavior. Proceedings of the National Academy of Sciences of the United States of America, 108, 3047–3052.CrossRefGoogle Scholar
  10. Dominguez-Bello, M. G., Costello, E. K., Contreras, M., Magris, M., Hidalgo, G., Fierer, N., & Knight, R. (2010). Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proceedings of the National Academy of Sciences, 107(26), 11971–11975.  https://doi.org/10.1073/pnas.1002601107.CrossRefGoogle Scholar
  11. Foster, J. A., & Neufeld, K. A. M. (2013). Gut–brain axis: How the microbiome influences anxiety and depression. Trends in Neurosciences, 36(5), 305–312.  https://doi.org/10.1016/j.tins.2013.01.005.CrossRefPubMedGoogle Scholar
  12. Guarner, F., & Malagelada, J. R. (2003). Gut flora in health and disease. The Lancet, 361(9356), 512–519.  https://doi.org/10.1016/S0140-6736(03)12489-0.CrossRefGoogle Scholar
  13. Hooks, K. B., Konsman, J. P., & O’Malley, M. A. (2019). Microbiota-gut-brain research: A critical analysis. Behavioral and Brain Sciences, 42.  https://doi.org/10.1017/S0140525X18002133.
  14. Human Microbiome Project Consortium. (2012). Structure, function and diversity of the healthy human microbiome. Nature, 486(7402), 207–214.  https://doi.org/10.1038/nature11234.CrossRefGoogle Scholar
  15. Kelly, J. R., et al. (2016). Transferring the blues: Depression-associated gut microbiota induces neurobehavioural changes in the rat. Journal of Psychiatric Research, 82, 109–118.  https://doi.org/10.1016/j.jpsychires.2016.07.019.CrossRefPubMedGoogle Scholar
  16. Kostic, A. D., Xavier, R. J., & Gevers, D. (2014). The microbiome in inflammatory bowel disease: Current status and the future ahead. Gastroenterology, 146(6), 1489–1499.  https://doi.org/10.1053/j.gastro.2014.02.009.CrossRefPubMedPubMedCentralGoogle Scholar
  17. Ley, R. E., et al. (2006). Microbial ecology: Human gut microbes associated with obesity. Nature, 444, 1022–1023.  https://doi.org/10.1038/4441022a.CrossRefPubMedGoogle Scholar
  18. Liang, S., Wu, X., & Jin, F. (2018). Gut brain psychology: Rethinking psychology from the microbiota–gut–brain axis. Frontiers in Integrative Neuroscience, 12, 33.CrossRefGoogle Scholar
  19. Lynch, K. E., Parke, E. C., & O’Malley, M. A. (2019). How causal are microbiomes? A comparison with the Helicobacter pylori explanation of ulcers. Biology and Philosophy, pitt philsci, 15777.Google Scholar
  20. Mueller, N. T., Bakacs, E., Combellick, J., Grigoryan, Z., & Dominguez-Bello, M. G. (2015). The infant microbiome development: Mom matters. Trends in Molecular Medicine, 21(2), 109–117.  https://doi.org/10.1016/j.molmed.2014.12.002.CrossRefPubMedGoogle Scholar
  21. Palmer, C., Bik, E. M., DiGiulio, D. B., Relman, D. A., & Brown, P. O. (2007). Development of the human infant intestinal microbiota. PLoS Biology, 5(7), e177.  https://doi.org/10.1371/journal.pbio.0050177.CrossRefPubMedPubMedCentralGoogle Scholar
  22. Power, S. E., O’Toole, P. W., Stanton, C., Ross, R. P., & Fitzgerald, G. F. (2014). Intestinal microbiota, diet and health. British Journal of Nutrition, 111(3), 387–402.  https://doi.org/10.1017/S0007114513002560.CrossRefPubMedGoogle Scholar
  23. Schwabe, R. F., & Jobin, C. (2013). The microbiome and cancer. Nature Reviews Cancer, 13(11), 800.  https://doi.org/10.1038/nrc3610.CrossRefPubMedPubMedCentralGoogle Scholar
  24. Sender, R., Fuchs, S., & Milo, R. (2016). Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans. Cell, 164(3), 337–340.  https://doi.org/10.1016/j.cell.2016.01.013.CrossRefPubMedGoogle Scholar
  25. Shen, S., & Wong, C. H. (2016). Bugging inflammation: Role of the gut microbiota. Clinical & Translational Immunology, 5(4), e72.  https://doi.org/10.1038/cti.2016.12.CrossRefGoogle Scholar
  26. Sudo, N., Chida, Y., Aiba, Y., Sonoda, J., Oyama, N., Yu, X.-N., Kubo, C., & Koga, Y. (2004). Postnatal microbial colonization programs the hypothalamic-pituitary-adrenal system for stress response in mice. Journal of Physiology, 558(1), 263–275.  https://doi.org/10.1113/jphysiol.2004.063388.CrossRefPubMedGoogle Scholar
  27. 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.  https://doi.org/10.1038/nature06244.CrossRefPubMedPubMedCentralGoogle Scholar
  28. Turnbaugh, P. J., et al. (2009). A core gut microbiome in obese and lean twins. Nature, 457, 480–484.  https://doi.org/10.1038/nature07540.CrossRefPubMedGoogle Scholar
  29. Ursell, L. K., Metcalf, J. L., Parfrey, L. W., & Knight, R. (2012). Defining the human microbiome. Nutrition Reviews, 70(suppl_1), S38–S44.CrossRefGoogle Scholar

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© Springer Nature Switzerland AG 2020

Authors and Affiliations

  1. 1.Department of PhilosophyUniversity of SydneySydneyAustralia

Section editors and affiliations

  • Todd K. Shackelford
    • 1
  1. 1.Department of PsychologyOakland UniversityRochesterUSA