Physiol Rev 99: 1877–2013, 2019 Published August 28, 2019; doi:10.1152/physrev.00018.2018 THE MICROBIOTA-GUT-BRAIN AXIS John F. Cryan, Kenneth J. O’Riordan, Caitlin S. M. Cowan, Kiran V. Sandhu, Thomaz F. S. Bastiaanssen, Marcus Boehme, Martin G. Codagnone, Sofia Cussotto, Christine Fulling, Anna V. Golubeva, Katherine E. Guzzetta, Minal Jaggar, Caitriona M. Long-Smith, Joshua M. Lyte, Jason A. Martin, Alicia Molinero-Perez, Gerard Moloney, Emanuela Morelli, Enrique Morillas, Rory O’Connor, Joana S. Cruz-Pereira, Veronica L. Peterson, Kieran Rea, Nathaniel L. Ritz, Eoin Sherwin, Simon Spichak, Emily M. Teichman, Marcel van de Wouw, Ana Paula Ventura-Silva, Shauna E. Wallace-Fitzsimons, Niall Hyland, Gerard Clarke, and Timothy G. Dinan APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland; and Department of Physiology, University College Cork, Cork, Ireland Cryan JF, O’Riordan KJ, Cowan CSM, Sandhu KV, Bastiaanssen TFS, Boehme M, Codagnone MG, Cussotto S, Fulling C, Golubeva AV, Guzzetta KE, Jaggar M, Long-Smith CM, Lyte JM, Martin JA, Molinero-Perez A, Moloney G, Morelli E, Morillas E, O’Connor R, Cruz-Pereira JS, Peterson VL, Rea K, Ritz NL, Sherwin E, Spichak S, Teichman EM, van de Wouw M, Ventura-Silva AP, Wallace-Fitzsi- Lmons SE, Hyland N, Clarke G, Dinan TG. The Microbiota-Gut-Brain Axis. Physiol Rev 99: 1877–2013, 2019. Published August 28, 2019; doi:10.1152/physrev.00018.2018.—The importance of the gut-brain axis in maintaining homeostasis has long been appreciated. However, the past 15 yr have seen the emergence of the microbiota (the trillions of microorganisms within and on our bodies) as one of the key regulators of gut-brain function and has led to the appreciation of the importance of a distinct microbiota-gut-brain axis. This axis is gaining ever more traction in fields investigating the biological and physiological basis of psychiatric, neurodevelopmental, age-re- lated, and neurodegenerative disorders. The microbiota and the brain communicate with each other via various routes including the immune system, tryptophan metabolism, the vagus nerve and the enteric nervous system, involving microbial metabolites such as short-chain fatty acids, branched chain amino acids, and peptidoglycans. Many factors can influence microbiota composition in early life, including infection, mode of birth delivery, use of antibiotic medications, the nature of nutritional provision, environmental stressors, and host genetics. At the other extreme of life, microbial diversity diminishes with aging. Stress, in particular, can significantly impact the microbiota-gut-brain axis at all stages of life. Much recent work has implicated the gut microbiota in many conditions including autism, anxiety, obesity, schizophrenia, Parkinson’s disease, and Alzheimer’s disease. Animal models have been para- mount in linking the regulation of fundamental neural processes, such as neurogenesis and myelination, to microbiome activation of microglia. Moreover, translational human studies are ongoing and will greatly enhance the field. Future studies will focus on understanding the mechanisms underlying the microbiota-gut-brain axis and attempt to elucidate microbial-based intervention and therapeutic strat- egies for neuropsychiatric disorders. brain-gut; microbiome; neurogastroenterology; second brain; stress I. INTRODUCTION 1877 I. INTRODUCTION II. STUDYING THE... 1881 “All disease begins in the gut.” III. MICROBIOTA-GUT-BRAIN AXIS... 1907 –Hippocrates of Kos (Hippokráte៮shoKṓos: IV. PATHWAYS OF COMMUNICATION 1911 c. 460–c. 370 BCE) V. MICROBIOTA AND SYNAPTIC... 1929 VI. FACTORS INFLUENCING THE... 1932 It was over 2,000 years ago when the Greek physician VII. BEHAVIOR AND THE... 1941 Hippocrates, oft-lauded as the father of modern medi- VIII. DISEASES AND DISEASE PROCESSES 1947 cine, is purported to have made this proclamation. Al- IX. BEYOND THE “BACTERIOME” 1961 though the attribution to Hippocrates has been ques- X. CONCLUSIONS 1963 tioned, its inherent wisdom continues to influence re- 0031-9333/19 Copyright © 2019 the American Physiological Society 1877 Downloaded from www.physiology.org/journal/physrev by ${individualUser.givenNames} ${individualUser.surname} (082.071.017.116) on January 29, 2020. CRYAN ET AL. them for future energy requirements. Encapsulating his This is a comprehensive review of current knowledge of the body of research, Bernard developed the concept of milieu influence that the microbiota has on brain and behavior. In intérieur, stating that “The stability of the internal environ- particular, we focus on the pathways involved and the models ment is the condition for the free and independent life” used in the field. Moreover, we highlight what still remains to be understood to fully realize the potential for the development of (139). This would later become the foundation for our un- microbiota-based therapeutic strategies for brain disorders. derstanding of corporeal homeostasis. Bernard, as one of the earliest pioneers of animal experi- mentation, also paved the way for future scientific discov- searchers and practitioners in medicine (and beyond) ery. Among those following in this tradition was Ivan Pav- regardless of its authenticity (443). lov, whose defining studies of classical conditioning were directly inspired by William Beaumont’s observations of Although the links between rural Michigan and ancient digestion. Under the tutelage of Carl Ludwig in Leipzig, Greece are not obvious, it was there in the 1800s that an Germany, Ivan Pavlov helped develop the Pavlov pouch unfortunate injury to a Canadian fur-trader Alexis St. Mar- (1173), a piece of exteriorized dog intestine used to study tin created a serendipitous opportunity to advance the study the processes of digestion in dogs. He perfected the tech- of the gut and digestion in line with the sentiments of Hip- nique by maintaining the innervation to the exteriorized pocrates and the other great Greek physician-philosopher, intestine section to allow more accurate measurement of Galen of Pergamon (1001). St. Martin was accidentally shot digestive processes in real time over extended periods; it is at close range and, during his treatment by the United States believed that this is one of the first recorded uses of a Army surgeon William Beaumont, became one of the most chronic model of animal experimentation in modern sci- famous patients in gastroenterology (115). The surgery left ence. These studies set the basis for our understanding of St. Martin with a fistula in his gut, a window into the intes- the critical role that the gut-brain axis plays in homeostatic tine, for Beaumont to study. The doctor took careful notes processes in health and disease. With the advent of brain throughout the recovery period and discovered the manner imaging technology in the 1980s, the full appreciation of in which many aspects of digestion occurred via experi- the bidirectionality of this axis emerged. Studies showed ments where he inserted food into St. Martin’s stomach, that distension of the gut resulted in activation of key path- then later removing it to observe the extent of digestion. He ways within the brain and that such pathways are exagger- took gastric secretion samples and sent them to chemists ated in disorders such as irritable bowel syndrome (IBS), a of the day for analysis, a very uncommon medical process functional gastrointestinal (GI) disorder with dysregulated for the mid-19th century. This was one of the first recorded observations of human digestion taking place in real time. microbiota-gut-brain axis (503, 784, 1009). Moreover, the Even more fascinating were Beaumont’s notes of “pain and gut-brain axis is seen as an important node in mammalian uneasiness” at corporeal sites far from the wound, linking interoception (351). digestion with disease, and emotionality. Moreover, when St. Martin became angry or irritable, it greatly affected the Finally, in the past decades, a new player has emerged as a rate of digestion, indicating that the subject’s emotional key regulator of the gut-brain axis, the trillions of microbes state affected digestion, i.e., there was a brain-gut axis. within the gut, the microbiota. Five separate lines of evi- Notwithstanding the discomfort of his patient, Beaumont’s dence converged to establish this. First, studies in germ-free work moved the field beyond the 2nd-century teachings of (GF) animals showed that the brain is affected in the ab- Galen (1001) to pioneer a new era of precise clinical data sence of microbiota (see FIGURE 1 and TABLE 2) (308, 437, collection, observation, and recording of conclusions for 569, 654, 1092, 1434). Second, animals given specific future reference. Other great historical scientists, including strains of bacteria had alterations in behavior (132, 209, Charles Darwin (74) and Claude Bernard (138), continued 429, 1021, 1321, 1560), and human studies of such strains the effort to formally establish and standardize the use of confirmed the potential translatability of such findings (38, the scientific method in medicine. While Darwin was fastid- 1198, 1493). Third, population-based studies of people ex- iously investigating, collecting, and cataloging biological posed to infection, most notably in Walkerton in Canada, specimens to build evidence for his famed theory of natural demonstrated alterations in gut-brain symptoms (1477). selection