ISSUE #012 - Mar 06, 2019

Gut Microbiota-brain Axis

Hong‑Xing Wang, Yu‑Ping Wang

by HongXing Wang1, YuPing Wang1,2

1Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing 100053, China

2Center of Epilepsy, Beijing Institute for Brain Disorders, Laboratory of Brain Disorders, Capital Medical University, Beijing 100069, China


The latest research showed that changes in gut microbiota could affect the brain’s physiological, behavioral, and cognitive functions.[15] In 2013, the United States launched a special research project on gut microbiota‑brain axis. Since then, this field, especially the interaction between gut microbiota and the brain, has gradually become the focus of neuroscience.[24] Although the exact mechanism of gut microbiota‑brain axis has not yet been fully understood and clarified, the evidence from animals and human studies has showed that gut microbiota can play an important role in brain behavior and cognitive development by producing hormones, immune factors, and metabolites, which also indicated that altering the gut microbiota may improve or even cure brain diseases.[614]

The gut microbiota and the brain interact with each other, and the gut microbiota can be regarded as an independent variable in gut microbiota‑brain axis, its effect on the brain regarded as a dependent variable. Therefore, this article focused on the influence of gut microbiota on the brain and described the latest progress in gut microbiota, cognitive process of influence of gut microbiota on the brain in neuroscience domain, and the possible measurement and detection of gut microbiota.


Gut microbiota is a complex community that helps to maintain dynamic metabolic ecological balance.[15] There are an estimated 100 trillion bacteria in an adult’s body, 80% of which exist in the gut, about ten times as many as cells in human body. The gut microbiome host more than 100 bacterial species that encode 150 times as many genes as the human genome.[16,17] It is well‑recognized that human microbiome is composed of more than 5000 strains of microbes and greater than 1000 kinds of microflora.[16,17] The bacteria, mainly anaerobic bacteria, dominate this environment, and others including virus, protozoa, archaea, and fungi also involve in this environment.[18,19] The microbiome is mainly defined by two bacterial phylotypes, Bacteroidetes and Firmicutes, and the amounts of Proteobacteria, Actinomyces, Fusobacterium, and Verrucomicrobia are relatively small.[20]

Gut microbiota is changing with human development and influenced by various stress factors. Babies receive the initial microbiome from their mothers.[20,21] After 1‑year‑old, the infants form a complex gut microbiome like adults.[22,23] The compositions of gut microbiota are not fixed, and change with increasing age. The dynamic changes are markedly different among different individuals, but the common effect is a macrobalance.[24] The changes of beneficial bacteria can significantly affect the health of individuals, while some factors such as infection, drug, illness, and diet may change the microbiome.[2527]

Some evidence showed that stress in the first few years of life could lead to the change of microbiota, and this change is a risk factor for stress‑related disorders in adulthood.[28,29] Maternal separation could lead to the reducing number of Lactobacillus in the feces of baby rats three days later, which had a long‑term effect on the gut microbiome.[28] Prenatal stress changed the compositions of microbiota by reducing the total number of Bifidobacterium and Lactobacillus in the rhesus monkey.[30] Moreover, prenatal antibiotic treatment increased offspring’s susceptibility to experimental colitis.[31] These results indicated that stress could change the gut microbiome.

Gut microbiota has multiple functions. First, gut microbiota constitutes the intestinal barrier, promotes the continuous existence of gut microbiota, stimulates intestinal epithelial cell regeneration, and produces mucus and nourishes mucosa by producing short‑chain fatty acids (SCFAs).[32] Gut microbiota is involved in the maturation of immune system by stimulating innate immune system in the early stage of life, which leads to the maturity of intestinal‑related lymphoid tissue, inspires the acquired immunity by stimulating local and systemic immune responses,[33] intestinal synthesis and metabolism of certain nutrients, hormones and vitamins, and plays an important role in drug and poison removal. Under physiological conditions, gut microbiota continues to stimulate the immune system, leading to a state of “low degree of physiological inflammation”, which is a rapid and effective mechanism for defending against pathogens.[34] In addition, bacterial colony also plays a role of protective competition in gut, producing nutrition for the survival of pathogen and cytokines that can inhibit the growth of the microorganism.[35]


The effect of gut microbiota on the brain was seldom recognized by people at first, except the pathogenic microorganism in the gut can pass through the blood‑brain barrier and affect the brain, for instance, rabies virus could elicit aggression, agitation, and a fear of water when it enters the brain.[3] However, a public health emergency aroused people’s attention to the possible relationship between the gut microbiota and the brain. In the year 2000, the flood occurred in the town of Walkerton, Canada, making the drinking water polluted by Escherichia coli and Campylobacter jejuni. Among the 4561 infected participants, 2451 of them completed a reassessment 8 years later, and 1166 of them were diagnosed with irritable bowel syndrome (IBS). Among these IBS patients, anxiety and depression were found to be independent risk factors for continuous IBS.[13] But at that time, the interaction between gut microbiota and the brain had not been taken seriously by neuroscientists.

In the year 2011, a study by Diaz Heijtz et al.[5] showed that compared with conventional mice who were growing in specific‑pathogen‑free (SPF) environment, germ‑free (GF) mice under the experimental conditions had less anxiety‑like behaviors and increased 5‑HT synthesis in the thalamus. When moving the adult GF mice to SPF environment, its reduced anxiety‑like behavior did not increase, but its offspring’s anxiety behavior returned to the normal state, which indicated that there was a critical time window for the influence of gut microbiota on behavior development. At that time, although there were an increasing number of related studies, most of them were conducted by gastrointestinal scientists alone, few were performed by gastrointestinal scientists together with psychologists. The focuses of the studies were peripheral and behavioral variations rather than variation in the brain. However, the study of Diaz Heijtz et al. sparked an interest of scientists in this field, and they hoped to directly study the underlying mechanism about the role of gut microbiota in the brain.

In the year 2013, the National Institute of Mental Health (NIMH) launched a special project on exploring the mechanism involved in gut microbiota‑brain communication, with a view to develop new medications or noninvasive treatments for mental diseases. Since then, studies on the influence of gut microbiota on the brain have been increasing, and gut microbiota‑brain axis has become one of the focuses of neuroscience. The core of the axis was the interaction between the gut microbiota and the brain.[2‑4] Gut microbiota has an important influence on the brain through the neural network, neuroendocrine system, and immune system.[24,6,7]

During 2014 and 2015, NIMH offered a special fund of 1 million US dollars to study the gut microbiota‑brain axis. In the year 2015, the United States Navy Institute planned to provide a special fund of 14.5 million US dollars in the next 6–7 years to research the role of the gut in cognitive and stress disorders. The European Union has launched a 5‑year MyNewGut project (10.1 million US dollars) for research on brain development and related disorders.[3]


Currently, the exact mechanism of communication between the gut microbiota and the brain has not yet been fully understood and clarified. Generally speaking, gut microbiota exerts effects on the brain not only through the nervous system (gut‑brain’s neuroanatomical pathway) but also through the endocrine system, immune system, and metabolic system. A bidirectional communication between the gut and the brain is referred to as the gut‑brain axis.[36,37] Interaction of gut microbiota and gut‑brain axis is referred to as the gut microbiota‑gut‑brain axis (hereinafter referred to as the gut microbiota‑brain axis).[38,39] In the gut microbiota‑brain axis, because gut microbiota can be used as an independent variable and changed intentionally, more emphases are placed on the role of microbes in gut microbiota‑brain axis.[40]

Neuroanatomical pathways

The gut can interact with the brain through two neuroanatomical pathways. The one is mutual information exchange directly between gut and brain by the autonomic nervous system (ANS) and vagus nerve (VN) in the spinal cord; another one is a bidirectional communication between gut and brain through the bi‑communication between enteric nervous system (ENS) in the gut and ANS and VN within the spinal cord. The neural anatomical pathways for controlling gut functions form a hierarchic four‑level integrative organization:[41,42] the first level is the ENS, including myenteric ganglia, submucous ganglion, and gut glial cells;[43,44] the second level is prevertebral ganglia regulating peripheral visceral reflex responses;[45] The third level is the ANS in the spinal cord (from T5‑L2 sympathetic nerve and S2‑S4 parasympathetic nervous system) and brain stem nucleus tractus solitarius and dorsal motor nucleus of VN, which receive and give the origin of afferent and efferent fiber of VN, respectively. The most important effect of the dorsal motor nucleus of VN is prominent in the upper gastrointestinal tract, and the cholinergic neurons on myenteron of upper gastrointestinal tract regulate vagal excitability effect;[46] and the fourth level is the higher brain centers. Information from cortex and subcortical centers including basal ganglia and funnels down to peculiar brainstem nuclei. Brainstem nuclei control many gut functions. The afferent fiber of VN stops at the brain stem nucleus tractus solitarius, which then gives fiber upward and arrives at thalamus, lobus limbicus, and insular cortex through parabrachial nucleus. Spinal afferent fiber goes upward within spinothalamic tract and spinal tract to the thalamus (spinothalamic tract) and gracile nucleus and cuneate nucleus of medulla oblongata (spinal tract), respectively, then project fiber to thalamus through lemniscus medialis. Fiber is gave from thalamus and projected to the primary sensorimotor areas and insular cortex. Damages and abnormalities at the above‑mentioned levels can influence the regulation of intestinal function, including local intestinal reflexes, and external neural control.[42]

Direct neural communication between gut microbiota and the brain is mainly realized through VN, i.e., bacteria stimulates afferent neurons of ENS,[47] and the vagal signal from the gut can stimulate the anti‑inflammatory response, preventing against pyosepticemia caused by microorganisms. Further research showed that many effects of gut microbiota or potential probiotics on brain functions were independent on vagal activation,[39,48] and bacteria settled in the gut played a critically important role in individual’s postnatal development and the maturation of the immune system, the endocrine system, and the nervous system.[47]

Neuroendocrinehypothalamicpituitaryadrenal axis

Gut microbiota is helpful to the maturation of neuroendocrine. Lacking gut microbiota and low/lack of expression of toll‑like receptors (TLRs) contribute to producing a neuroendocrine response to the pathogen in the gut.[49,50] For example, the response of TLR4‑knockout mouse to lipopolysaccharide (LPS) produced by Gram‑negative bacteria was reduced.[51] Griseofulvin (GF) mouse is one of the most appropriate models to study the hypothalamic‑pituitary‑adrenal (HPA) axis regulated by the microorganism. Compared with SPF mice, mild restraint stress led to significantly elevated corticosterone and adrenocorticotropic hormone in GF mice. GF mouse’s stress response could be partially reversed by fecal microbial transplant, and completely reversed over time by single Bifidobacterium infantis.[52] The study clearly showed the feces containing gut microbiota were vital for the postnatal development of appropriate stress reaction, and the timing that microbiota appeared in early life was a very narrow window, which was extremely important for normal development of HPA axis.

Gut microbiota can affect neural circuits and behavior related with the stress response. Compared with SPF mice, GF male mice had the reduced brain‑derived neurotrophic factor (BDNF) and 2A subtype of N‑methyl‑D‑aspartic acid receptor (NMDA receptor) expressions in cortex and hippocampus.[52] Neufeld et al.[53] have found that Mrna of BDNF in the hippocampal area was improved in female mice, which conflicted with the results reported by the earlier studies. Clarke et al.[54] have also found that mRNA of hippocampus BDNF in male mice was reduced and the 5‑HT functional system was significantly changed, but these changes could not be found in female mice. These findings suggested that the regulation of gut microbiota‑brain axis may be dependent on gender. Many studies have shown the changes of hippocampal NMDA and 5‑HT1A receptor of GF animals.[52] These receptors affect the release and expression of the corticotropin‑releasing hormone of the hypothalamus and then change the function of HPA.

Stress and HPA axis can affect the composition of the gut microbiome. Early stress and maternal separation could lead to a long‑term change of HPA, and also had a long effect on the microbiome.[55,56] When compared with rats nonseparated from the mother, the diversity of 16S ribosomal RNA in adult rats, who received mother separation for 3 h/day from day 2 to day 12 after birth, revealed that stress significantly changed microbiome in feces.[28] Microbiome composition in mouse exposed to a long‑term restraint stress was significantly different from that of a nonstressed mouse.[57] Recently, using the above method and the repeated social interaction, stress can reduce the quantity of Bacteroides at cecum and increase the number of Clostridium.[58] Stress also increased interleukin‑6 and monocyte chemotactic protein 1 (MCP‑1) levels in blood, and MCP‑1 was significantly related with the changes of three kinds of stress‑induced bacteria of Enterococcus faecalis, Pseudobutyrivibrio, and aerogenic bacteria Dorea strain.

Gut immune system

Development of gut immune system depends on gut microbiota.[59,60] GF mice almost had no immune activity, but they could generate immune function when giving certain microbiota.[61] For example, the segmented filamentous bacterium in the gut can restore the full functions of gut B and T lymphocytes.[6264] Bacteria communicate with the host through a variety of ways, and the receptors‑TLRs of host cell play a key role in the communication between bacteria and host. There are ten kinds of TLRs in the human innate immune system, which have been identified as pattern recognition receptors.[65] These receptors are a part of the innate immune system,  which is the first step to produce cytokine response and is also widely distributed on neurons.[66] Hence, neurons also respond to bacterial and viral components. Intestinal epithelial cells can transport microbial composition or metabolites into the inner environment, and the nervous system also interacts with these bacterial and viral components.[67] The balance of gut microbiota may change the regulation of inflammatory response, and this mechanism may also get involved in the regulation of emotion and behavior.[41,61,6870]

Neurotransmitters and neural regulators synthesized by intestinal bacteria

Gut bacteria can synthesize gamma amino acid, butyric acid, 5‑HT, dopamine, and SCFAs,[48,71] and these substances can exchange between cells of microorganism,[48] especially intestinal cells in the gut can produce many 5‑HT that have an effect on the brain. Bacterial enzymes can also produce neurotoxin products such as D‑lactic acid and ammonia.[3,72] Hence, a lot of necessary neurotransmitters in the body are generated by the gut microbiota, exerting influence on the human body including the brain, among which many of neurotransmitters in the human gut microbiota are also critical molecules.[73]

Intestinal mucosal barrier and bloodbrain barrier (barrier system)

Evidence from rodent studies showed that stress changed intestinal mucosal barrier function, made LPS and other cytokines entering blood circulation, and stimulated TLR4 and other TLRs producing inflammatory cytokine.[74] Peripheral produced inflammatory factors could increase the permeability of blood‑brain barrier, thus make it possible for peripheral produced inflammatory factors to directly influence the brain.[75]

Therefore, vast evidence of animals and human studies showed that gut microbiota plays a critical role in the brain development and function.[76,77]

Use of Microbiome and Metagenomics to Analyze Composition and Characteristics in Gut Microbiota Respectively

Evidence of the animal studies showed that gut microbiota composition and metabolic products could be obtained through feces analysis.[73]

Microbiome define the composition and functional characteristics of gut microbiota

To effectively understand the role of symbiotic microorganisms of mammals, in particular bacteria, on health and disease, terms and indicators must be used to describe complex ecological gut microbiota. Some bacteria phyla represent its characteristics in gut, and symbiotic bacteria represent the possible diversity, there are about 1000 different bacteria in the gut.[7880] Two main bacteria phyla are Bacteroidetes and Firmicutes, which account for at least 70–75% of the microbiome.[7981] There are also Proteobacteria, Actinomyces, Fusobacterium, and Verrucomicrobia, which are relatively small in number.[81] How to describe a variety of gut microbiota? Scientists use microbiome to give an overview description, and microbiome refers to the living bacteria in the gut and its genetic materials, including the archaea, protozoa, fungi, and virus.[41,82]

Dynamic characteristics and diversity of microbiome are beyond people’s imagination. Currently, scientists have only begun to understand the distribution and diversity of bacteria phyla which are helpful for health and disease. Metagenomics approach has already revealed that certain bacterial colonies could be as phenotype which shared with a human.[81] Beyond hierarchical features of bacteria phyla, detailed analysis showed that there was a big bacteria variation between the individuals who were relating or nonrelating.[82,83] The microbiome is a dynamic entity, influenced by factors such as gene, diet, metabolites, age, geography, use of antibiotics, and stress.[26,8491] Hence, the characteristics of gut microbiota are a good representative of individual’s environment, which is helpful for understanding individual disease risk, disease progression, and treatment effect. These tools are now being used in the human and animals studies.

Metagenomics is used to be an appropriate technique to characterize gut microbiota

The recent developments in molecular biology and metagenomics allow researchers to better understand the structure and function of gut microbiota. Metagenomics is an emerging subject that uses the method of nonmicrobial culture to study microbial colony in the environment,[92] the main research objects are bacteria, archaea, fungi, viruses, and other microbes in bacterial colony, and its main purpose is to reveal the deeper genetic and evolutionary laws through analysis of aspects of microbial diversity, population structure and its dynamic change, relationship between members, and the relationship with environment within microbial colony. Metagenomics allows us to discover new genes and proteins, or even new method that is more accurate than traditional microorganisms or molecular biology, and complete comprehensive nonculturable microbial genome in a shorter time.[92]

The differences between metagenomics sequencing and 16S/18S rDNA sequencing are as follows:[93] 16S/18S rDNA gene sequencing is mainly bacterial 16S rRNA or fungal 18S rRNA gene sequencing, and the cores of study are species taxonomy, species abundance, and system evolution within samples. Metagenomics sequencing takes microbiota genome in the environmental samples as research object, directly extracts DNA of all microbiota from environmental samples, constructs metagenomic library, uses high‑throughput sequencing technology to analyze population genetic composition, function and participated metabolic pathway of all microbiota contained in environmental samples, interprets the diversity and abundance of the microbial population, seeks for the relationship between microbiota and the environment and relationship between microbiota and the host, and explores and studies new genes with specific functions.

The metagenomic study can be used for evolution analysis, gene discovery, environmental and ecological research, and disease and individual medicine,[78,94,95] especially in individual medical field. Vast evidence showed that population and diversity of human gut microbiota have obvious correlation with the occurrence of human diseases, such as obesity, cardiovascular disease, and tumor, but the impact on health and disease of the human brain is underway.


In summary, gut microbiota‑brain axis is a “bottom‑up” term as opposed to a “top‑down” term of “brain‑gut‑microbiota axis”, no matter what is called, its meaning refers to a bidirectional communication network between gut and brain. Its composition includes gut microbiota and their metabolic products, ENS, sympathetic and parasympathetic branches, neural‑immune system, neuroendocrine system, and central nervous system. Moreover, there might have possible five routes of communicating between gut microbiota and brain, including the gut‑brain’s neural network, neuroendocrine‑HPA axis, gut immune system, some neurotransmitters and neural regulators synthesized by gut bacteria, and barriers including intestinal mucosal barrier and blood‑brain barrier [Figure 1]. In this communicating network, the brain affects gut movement, sensory and secretion function, and viscera signal from the gut also affects brain function. For example, incoming and outgoing branches of VN play an important role in gut message transmission. Vagal activation has  anti‑inflammatory effect. Positive effects of many gut microbiota and probiotics on brain function are dependent on the vagal activity.

It is believed that the gut microbiota‑brain axis will provide more information and possible route for people to know the brain, understand the brain, and protect the brain.

Financial support and sponsorship

This study was supported by grants from Beijing Municipal Administration of Hospitals Clinical Medicine Development of Special Funding Support (No. XMLX201401), the National Natural Science Foundation of China (No. 81301138), National High‑Tech R&D Program of China (863 Program, No. 2015AA020514), National Hundred, Thousand, and Ten Thousand Talents Project of Beijing (No. 2010‑005).

Conflicts of interest

There are no conflicts of interest.


  1. Jenkins TA, Nguyen JC, Polglaze KE, Bertrand Influence of tryptophan and serotonin on mood and cognition with a possible role of the gut‑brain axis. Nutrients 2016;8. pii: E56. doi: 10.3390/ nu8010056.
  2. Schmidt C. Mental health: Thinking from the gut. Nature 2015;518:S12‑ doi: 10.1038/518S13a.
  3. Smith The tantalizing links between gut microbes and the brain. Nature 2015;526:312‑4. doi: 10.1038/526312a.
  4. Mayer EA, Knight R, Mazmanian SK, Cryan JF, Tillisch K. Gut microbes and the brain: Paradigm shift in neuroscience. J Neurosci 2014;34:15490‑ doi: 10.1523/JNEUROSCI.3299‑14.2014.
  5. Diaz Heijtz R, Wang S, Anuar F, Qian Y, Björkholm B, Samuelsson A, et Normal gut microbiota modulates brain development and behavior. Proc Natl Acad Sci U S A 2011;108:3047‑52. doi: 10.1073/ pnas.1010529108.
  6. Ogbonnaya ES, Clarke G, Shanahan F, Dinan TG, Cryan JF, O’Leary Adult hippocampal neurogenesis is regulated by the microbiome. Biol Psychiatry 2015;78:e7‑9. doi: 10.1016/j. biopsych.2014.12.023.
  7. Jašarevic E, Howerton CL, Howard CD, Bale TL. Alterations in the vaginal microbiome by maternal stress are associated with metabolic reprogramming of the offspring gut and brain. Endocrinology 2015;156:3265‑ doi: 10.1210/en.2015‑1177.
  8. Yano JM, Yu K, Donaldson GP, Shastri GG, Ann P, Ma L, et al. Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. Cell 2015;161:264‑ Erratum in: Cell 2015;163:258. doi: 10.1016/j.cell.2015.02.047.
  9. Braniste V, Al‑Asmakh M, Kowal C, Anuar F, Abbaspour A, Tóth M, et The gut microbiota influences blood‑brain barrier permeability in mice. Sci Transl Med 2014;6:263ra158. Erratum in: Sci Transl Med 2014;6:266er7. doi: 10.1126/scitranslmed.3009759.
  10. Bercik P, Denou E, Collins J, Jackson W, Lu J, Jury J, et The intestinal microbiota affect central levels of brain‑derived neurotropic factor and behavior in mice. Gastroenterology 2011;141:599‑609, 609.e1‑3. doi: 10.1053/j.gastro.2011.04.052.
  11. Arentsen T, Raith H, Qian Y, Forssberg H, Diaz Heijtz R. Host microbiota modulates development of social preference in mice. Microb Ecol Health Dis 2015;26:29719. doi: 10.3402/mehd. 29719.
  12. Lee YK, Menezes JS, Umesaki Y, Mazmanian SK. Proinflammatory T‑cell responses to gut microbiota promote experimental autoimmune encephalomyelitis. Proc Natl Acad Sci U S A 2011;108 Suppl 1:4615‑ doi: 10.1073/pnas.1000082107.
  13. Marshall JK, Thabane M, Garg AX, Clark WF, Moayyedi P, Collins SM; Walkerton Health Study Investigators. Eight year prognosis of postinfectious irritable bowel syndrome following waterborne bacterial dysentery. Gut 2010;59:605‑ doi: 10.1136/ gut.2009.202234.
  14. De Angelis M, Piccolo M, Vannini L, Siragusa S, De Giacomo A, Serrazzanetti DI, et al. Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified. PLoS One 2013;8:e76993. doi: 10.1371/journal. pone.0076993.
  15. Alander M, Satokari R, Korpela R, Saxelin M, Vilpponen‑Salmela T, Mattila‑Sandholm T, et al. Persistence of colonization of human colonic mucosa by a probiotic strain, Lactobacillus rhamnosus GG, after oral consumption. Appl Environ Microbiol 1999;65:351‑
  16. de Vos WM, de Vos Role of the intestinal microbiome in health and disease: From correlation to causation. Nutr Rev 2012;70 Suppl 1:S45‑56. doi: 10.1111/j.1753‑4887.2012.00505.x.
  17. Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight Diversity, stability and resilience of the human gut microbiota. Nature 2012;489:220‑30. doi: 10.1038/nature11550.
  18. Dave M, Higgins PD, Middha S, Rioux The human gut microbiome: Current knowledge, challenges, and future directions. Transl Res 2012;160:246‑57. doi: 10.1016/j.trsl.2012.05.003.
  19. O’Toole Changes in the intestinal microbiota from adulthood through to old age. Clin Microbiol Infect 2012;18 Suppl 4:44‑6. doi: 10.1111/j.1469‑0691.2012.03867.x.
  20. Grenham S, Clarke G, Cryan JF, Dinan TG. Brain‑gut‑microbe communication in health and disease. Front Physiol 2011;2:94. doi: 10.3389/fphys.2011.00094.
  21. Relman DA. The human microbiome: Ecosystem resilience and health. Nutr Rev 2012;70 Suppl 1:S2‑ doi: 10.1111/j.1753‑4887.20 12.00489.x.
  22. Vallès Y, Gosalbes MJ, de Vries LE, Abellán JJ, Francino Metagenomics and development of the gut microbiota in infants. Clin Microbiol Infect 2012;18 Suppl 4:21‑6. doi: 10.1111/j.1469‑0691.20 12.03876.x.
  23. Vaishampayan PA, Kuehl JV, Froula JL, Morgan JL, Ochman H, Francino Comparative metagenomics and population dynamics of the gut microbiota in mother and infant. Genome Biol Evol 2010;2:53‑66. doi: 10.1093/gbe/evp057.
  24. Claesson MJ, Jeffery IB, Conde S, Power SE, O’Connor EM, Cusack S, et al. Gut microbiota composition correlates with diet and health in the elderly. Nature 2012;488:178‑ doi: 10.1038/ nature11319.
  25. Cryan JF, O’Mahony SM. The microbiome‑gut‑brain axis: From bowel to behavior. Neurogastroenterol Motil 2011;23:187‑ doi: 10.1111/j.1365‑2982.2010.01664.x.
  26. Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon The effect of diet on the human gut microbiome: A metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 2009;1:6ra14. doi: 10.1126/scitranslmed.3000322.
  27. Davey KJ, O’Mahony SM, Schellekens H, O’Sullivan O, Bienenstock J, Cotter PD, et al. Gender‑dependent consequences of chronic olanzapine in the rat: Effects on body weight, inflammatory, metabolic and microbiota parameters. Psychopharmacology (Berl) 2012;221:155‑ doi: 10.1007/s00213‑011‑2555‑2.
  28. O’Mahony SM, Marchesi JR, Scully P, Codling C, Ceolho AM, Quigley EM, et al. Early life stress alters behavior, immunity, and microbiota in rats: Implications for irritable bowel syndrome and psychiatric illnesses. Biol Psychiatry 2009;65:263‑ doi: 10.1016/j. biopsych.2008.06.026.
  29. Sudo N. Stress and gut microbiota: Does postnatal microbial colonization program the hypothalamic‑pituitary‑adrenal system for stress response? Int Congr Ser 2006;1287:350‑ doi: 10.1016/j. ics.2005.12.019.
  30. Bailey MT, Coe CL. Maternal separation disrupts the integrity of the intestinal microflora in infant rhesus monkeys. Dev Psychobiol 1999;35:146‑
  31. Munyaka PM, Khafipour A, Wang H, Eissa N, Khafipour E, Ghia JE. Prenatal antibiotic treatment increases offspring’s susceptibility to experimental colitis: A role of the gut microbiota. Gastroenterology 2015;148:S708. org/10.1016/S0016‑5085(15)32404‑5.
  32. Burger‑van Paassen N, Vincent A, Puiman PJ, van der Sluis M, Bouma J, Boehm G, et al. The regulation of intestinal mucin MUC2 expression by short‑chain fatty acids: Implications for epithelial protection. Biochem J 2009;420:211‑ doi: 10.1042/BJ20082222.
  33. Nell S, Suerbaum S, Josenhans The impact of the microbiota on the pathogenesis of IBD: Lessons from mouse infection models. Nat Rev Microbiol 2010;8:564‑77. doi: 10.1038/nrmicro2403.
  34. Rakoff‑Nahoum S, Paglino J, Eslami‑Varzaneh F, Edberg S, Medzhitov R. Recognition of commensal microflora by toll‑like receptors is required for intestinal homeostasis. Cell 2004;118:229‑ doi: 10.1016/j.cell.2004.07.002.
  35. Sekirov I, Russell SL, Antunes LC, Finlay Gut microbiota in health and disease. Physiol Rev 2010;90:859‑904. doi: 10.1152/ physrev.00045.2009.
  36. Montiel‑Castro AJ, González‑Cervantes RM, Bravo‑Ruiseco G, Pacheco‑López The microbiota‑gut‑brain axis: Neurobehavioral correlates, health and sociality. Front Integr Neurosci 2013;7:70. doi: 10.3389/fnint.2013.00070.
  37. Cryan JF, Dinan Mind‑altering microorganisms: The impact of the gut microbiota on brain and behaviour. Nat Rev Neurosci 2012;13:701‑12. doi: 10.1038/nrn3346.
  38. Rhee SH, Pothoulakis C, Mayer EA. Principles and clinical implications of the brain‑gut‑enteric microbiota axis. Nat Rev Gastroenterol Hepatol 2009;6:306‑ doi: 10.1038/nrgastro.2009.35.
  39. Bauer KC, Huus KE, Finlay BB. Microbes and the mind: Emerging hallmarks of the gut microbiota‑brain axis. Cell Microbiol 2016;18:632‑ doi: 10.1111/cmi.12585.
  40. Al Omran Y, Aziz Q. The brain‑gut axis in health and Adv Exp Med Biol 2014;817:135‑53. doi:10.1007/978‑1‑4939‑0897‑4_6.
  41. Foster JA, McVey Neufeld KA. Gut‑brain axis: How the microbiome influences anxiety and depression. Trends Neurosci 2013;36:305‑ doi: 10.1016/j.tins.2013.01.005.
  42. Mulak A, Bonaz B. Brain‑gut‑microbiota axis in Parkinson’s disease. World J Gastroenterol 2015;21:10609‑ doi: 10.3748/wjg.v21. i37.10609.
  43. Schemann M, Neunlist M. The human enteric nervous system. Neurogastroenterol Motil 2004;16 Suppl 1:55‑ doi: 10.1111/j.1743‑ 3150.2004.00476.x.
  44. Anlauf M, Schäfer MK, Eiden L, Weihe Chemical coding of the human gastrointestinal nervous system: Cholinergic, VIPergic, and catecholaminergic phenotypes. J Comp Neurol 2003;459:90‑111. doi: 10.1002/cne.10599.
  45. Szurszewski JH. Physiology of mammalian prevertebral ganglia. Annu Rev Physiol 1981;43:53‑ doi:10.1146/annurev. ph.43.030181.000413.
  46. Chang HY, Mashimo H, Goyal RK. Musings on the wanderer: What’s new in our understanding of vago‑vagal reflex? Current concepts of vagal efferent projections to the gut. Am J Physiol Gastrointest Liver Physiol 2003;284:G357‑66. doi: 10.1152/ajpgi.00478.2002.
  47. Borre YE, O’Keeffe GW, Clarke G, Stanton C, Dinan TG, Cryan Microbiota and neurodevelopmental windows: Implications for brain disorders. Trends Mol Med 2014;20:509‑18. doi: 10.1016/j. molmed.2014.05.002.
  48. Forsythe P, Bienenstock J, Kunze Vagal pathways for microbiome‑brain‑gut axis communication. Adv Exp Med Biol 2014;817:115‑33. doi: 10.1007/978‑1‑4939‑0897‑4_5.
  49. Dissanayake D, Hall H, Berg‑Brown N, Elford AR, Hamilton SR, Murakami K, et al. Nuclear factor‑B1 controls the functional maturation of dendritic cells and prevents the activation of autoreactive T cells. Nat Med 2011;17:1663‑ doi: 10.1038/nm.2556.
  50. O’Hara AM, Shanahan The gut flora as a forgotten organ. EMBO Rep 2006;7:688‑93. doi: 10.1038/sj.embor.7400731.
  51. Gosselin D, Rivest S. MyD88 signaling in brain endothelial cells is essential for the neuronal activity and glucocorticoid release during systemic inflammation. Mol Psychiatry 2008;13:480‑ doi: 10.1038/
  52. Sudo N, Chida Y, Aiba Y, Sonoda J, Oyama N, Yu XN, et al. Postnatal microbial colonization programs the hypothalamic‑pituitary‑adrenal system for stress response in mice. J Physiol 2004;558(Pt 1):263‑ doi: 10.1113/jphysiol.2004.063388.
  53. Neufeld KM, Kang N, Bienenstock J, Foster JA. Reduced anxiety‑like behavior and central neurochemical change in germ‑free mice. Neurogastroenterol Motil 2011;23:255‑64, e119. doi: 1111/j.136 5‑2982.2010.01620.x.
  54. Clarke G, Grenham S, Scully P, Fitzgerald P, Moloney RD, Shanahan F, et al. The microbiome‑gut‑brain axis during early life regulates the hippocampal serotonergic system in a sex‑dependent manner. Mol Psychiatry 2013;18:666‑ doi: 10.1038/mp.2012.77.
  55. Desbonnet L, Garrett L, Clarke G, Bienenstock J, Dinan TG. The probiotic Bifidobacteria infantis: An assessment of potential antidepressant properties in the rat. J Psychiatr Res 2008;43:164‑ doi: 10.1016/j.jpsychires.2008.03.009.
  56. Barouei J, Moussavi M, Hodgson Effect of maternal probiotic intervention on HPA axis, immunity and gut microbiota in a rat model of irritable bowel syndrome. PLoS One 2012;7:e46051. doi: 10.1371/ journal.pone.0046051.
  57. Bangsgaard Bendtsen KM, Krych L, Sørensen DB, Pang W, Nielsen DS, Josefsen K, et al. Gut microbiota composition is correlated to grid floor induced stress and behavior in the BALB/c mouse. PLoS One 2012;7:e46231. doi: 1371/journal.pone.0046231.
  58. Bailey MT, Dowd SE, Galley JD, Hufnagle AR, Allen RG, Lyte Exposure to a social stressor alters the structure of the intestinal microbiota: Implications for stressor‑induced immunomodulation. Brain Behav Immun 2011;25:397‑407. doi: 10.1016/j. bbi.2010.10.023.
  59. Furusawa Y, Obata Y, Fukuda S, Endo TA, Nakato G, Takahashi D, et al. Commensal microbe‑derived butyrate induces the differentiation of colonic regulatory T cells. Nature 2013;504:446‑ doi: 10.1038/ nature12721.
  60. Mayer EA, Tillisch K, Gupta A. Gut/brain axis and the J Clin Invest 2015;125:926‑38. doi: 10.1172/JCI76304.
  61. Forsythe P, Sudo N, Dinan T, Taylor VH, Bienenstock J. Mood and gut feelings. Brain Behav Immun 2010;24:9‑ doi: 10.1016/j. bbi.2009.05.058.
  62. Umesaki Y, Okada Y, Matsumoto S, Imaoka A, Setoyama H. Segmented filamentous bacteria are indigenous intestinal bacteria that activate intraepithelial lymphocytes and induce MHC class II molecules and fucosyl asialo GM1 glycolipids on the small intestinal epithelial cells in the ex‑germ‑free mouse. Microbiol Immunol 1995;39:555‑ doi: 10.1111/j.1348‑0421.1995.tb02242.x.
  63. Umesaki Y, Setoyama H, Matsumoto S, Imaoka A, Itoh K. Differential roles of segmented filamentous bacteria and clostridia in development of the intestinal immune system. Infect Immun 1999;67:3504‑
  64. Talham GL, Jiang HQ, Bos NA, Cebra JJ. Segmented filamentous bacteria are potent stimuli of a physiologically normal state of the murine gut mucosal immune system. Infect Immun 1999;67:1992‑
  65. Takeuchi O, Akira Pattern recognition receptors and inflammation. Cell 2010;140:805‑20. doi: 10.1016/j.cell.2010.01.022.
  66. McKernan DP, Dennison U, Gaszner G, Cryan JF, Dinan TG. Enhanced peripheral toll‑like receptor responses in psychosis: Further evidence of a pro‑inflammatory phenotype. Transl Psychiatry 2011;1:e36. doi: 1038/tp.2011.37.
  67. O’Brien SM, Scott LV, Dinan TG. Cytokines: Abnormalities in major depression and implications for pharmacological treatment. Hum Psychopharmacol 2004;19:397‑ doi: 10.1002/hup.609.
  68. Levkovich T, Poutahidis T, Smillie C, Varian BJ, Ibrahim YM, Lakritz JR, et al. Probiotic bacteria induce a ‘glow of health’. PLoS One 2013;8:e53867. doi: 1371/journal.pone.0053867.
  69. Hooper LV, Littman DR, Macpherson AJ. Interactions between the microbiota and the immune system. Science. 2012;336:1268‑ doi:10.1126/science.1223490.
  70. Kopp MV, Goldstein M, Dietschek A, Sofke J, Heinzmann A, Urbanek Lactobacillus GG has in vitro effects on enhanced interleukin‑10 and interferon‑gamma release of mononuclear cells but no in vivo effects in supplemented mothers and their neonates. Clin Exp Allergy 2008;38:602‑10. doi: 10.1111/j.1365‑2222.2007.02 911.x.
  71. Lyte Microbial endocrinology: Host‑microbiota neuroendocrine interactions influencing brain and behavior. Gut Microbes 2014;5:381‑9. doi: 10.4161/gmic.28682.
  72. Manicassamy S, Reizis B, Ravindran R, Nakaya H, Salazar‑Gonzalez RM, Wang YC, et al. Activation of beta‑catenin in dendritic cells regulates immunity versus tolerance in the intestine. Science 2010;329:849‑ Erratum in: Science 2011;334:594. doi: 10.1126/science.1188510.
  73. Dinan TG, Stanton C, Cryan Psychobiotics: A novel class of psychotropic. Biol Psychiatry 2013;74:720‑6. doi: 10.1016/j. biopsych.2013.05.001.
  74. Ait‑Belgnaoui A, Durand H, Cartier C, Chaumaz G, Eutamene H, Ferrier L, et al. Prevention of gut leakiness by a probiotic treatment leads to attenuated HPA response to an acute psychological stress in rats. Psychoneuroendocrinology 2012;37:1885‑ doi: 10.1016/j. psyneuen.2012.03.024.
  75. McCusker RH, Kelley Immune‑neural connections: How the immune system’s response to infectious agents influences behavior. J Exp Biol 2013;216(Pt 1):84‑98. doi: 10.1242/jeb.073411.
  76. Galland L. The gut microbiome and the brain. J Med Food 2014;17:1261‑ doi: 10.1089/jmf.2014.7000.
  77. Tillisch K, Labus JS. Neuroimaging the microbiome‑gut‑brain axis. Adv Exp Med Biol 2014;817:405‑ doi: 10.1007/978‑1‑4939‑0897‑4_18.
  78. 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;464:59‑ doi: 10.1038/ nature08821.
  79. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, et al. Diversity of the human intestinal microbial Science 2005;308:1635‑8. doi: 10.1126/science.1110591.
  80. Lay C, Sutren M, Rochet V, Saunier K, Doré J, Rigottier‑Gois Design and validation of 16S rRNA probes to enumerate members of the Clostridium leptum subgroup in human faecal microbiota. Environ Microbiol 2005;7:933‑46. doi: 10.1111/j.1462‑2920.2005.00763.x.
  81. Diamant M, Blaak EE, de Vos Do nutrient‑gut‑microbiota interactions play a role in human obesity, insulin resistance and type 2 diabetes? Obes Rev 2011;12:272‑81. doi: 10.1111/j.1467‑789X.2010. 00797.x.
  82. Dash S, Clarke G, Berk M, Jacka FN. The gut microbiome and diet in psychiatry: Focus on depression. Curr Opin Psychiatry 2015;28:1‑ doi: 10.1097/YCO.0000000000000117.
  83. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. Bacterial community variation in human body habitats across space and time. Science 2009;326:1694‑ doi: 10.1126/science.1177486.
  84. Savage DC. Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol 1977;31:107‑ doi: 10.1146/annurev. mi.31.100177.000543.
  85. Cho I, Yamanishi S, Cox L, Methé BA, Zavadil J, Li K, et Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature 2012;488:621‑6. doi: 10.1038/nature11400.
  86. Panagiotidis G, Bäckström T, Asker‑Hagelberg C, Jandourek A, Weintraub A, Nord CE. Effect of ceftaroline on normal human intestinal microflora. Antimicrob Agents Chemother 2010;54:1811‑ doi: 10.1128/AAC.01716‑09.
  87. Schloss PD, Iverson KD, Petrosino JF, Schloss The dynamics of a family’s gut microbiota reveal variations on a theme. Microbiome 2014;2:25. doi: 10.1186/2049‑2618‑2‑25.
  88. Benson AK, Kelly SA, Legge R, Ma F, Low SJ, Kim J, et al. Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proc Natl Acad Sci U S A 2010;107:18933‑ doi: 10.1073/ pnas.1007028107..
  89. Karlsson CL, Onnerfält J, Xu J, Molin G, Ahrné S, Thorngren‑Jerneck K. The microbiota of the gut in preschool children with normal and excessive body weight. Obesity (Silver Spring) 2012;20:2257‑ doi: 10.1038/oby.2012.110.
  90. Serino M, Fernández‑Real JM, García‑Fuentes E, Queipo‑Ortuño M, Moreno‑Navarrete JM, Sánchez A, et al. The gut microbiota profile is associated with insulin action in humans. Acta Diabetol 2013;50:753‑ Erratum in: Acta Diabetol 2013;50:763. doi: 10.1007/s00592‑012‑0410‑5.
  91. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez‑Bello MG, Contreras M, et Human gut microbiome viewed across age and geography. Nature 2012;486:222‑7. doi: 10.1038/nature11053.
  92. Escobar‑Zepeda A, Vera‑Ponce de León A, Sanchez‑Flores A. The road to metagenomics: From microbiology to DNA sequencing technologies and bioinformatics. Front Genet 2015;6:348. doi: 3389/fgene.2015.00348.
  93. Lozupone CA, Stombaugh J, Gonzalez A, Ackermann G, Wendel D, Vázquez‑Baeza Y, et al. Meta‑analyses of studies of the human microbiota. Genome Res 2013;23:1704‑ doi: 10.1101/ gr.151803.112.
  94. Thomas T, Gilbert J, Meyer Metagenomics – A guide from sampling to data analysis. Microb Inform Exp 2012;2:3. doi: 10.1186/2042‑5783‑2‑3.
  95. Zhang N, He QS. Commensal microbiome promotes resistance to local and systemic infections. Chin Med J 2015;128:2250‑ doi: 10.4103/0366‑6999.162502.

This article was originally published here:  and is reissued here with permission from the author.


ISSUE #012

On Yoga and Neuroscience
Image: On Yoga and Neuroscience

Read and reference at your own pace.
Download this issue of Tarka as a PDF to access the full-length, unabridged articles.

Embodied Philosophy Forum

A Private Facebook Community