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How Smart Is Your Gut?

A major regulator of motivational and emotional states.

Key points

  • Bacteria are capable of learning and remembering.
  • The vagal gut-to-brain axis plays a critical role in motivation and reward.
  • The microbiome has multiple critical effects on our physiological and metabolic processes.

Intelligence is the ability to learn from experience and adapt to, shape, and select environments. On the basis of that definition, scientists are now starting to recognize intelligence in various unicellular and multicellular animals. These organisms or animals, because they are that, have no brains, not even neurons. Yet, they seem capable of learning, decision-making, goal-directed behavior, and memory, at least when it comes to viruses that attack them. They sense and explore their surroundings, communicate with their neighbors, and adaptively reshape themselves.

Great advances in molecular medicine in recent years have led to the discovery of an immense number of microorganisms in the intestine referred to as the gut microbiome. In this post, we shall explore the concept of the brain-gut axis, which links the central and the enteric nervous system, the nervous system of the alimentary canal. Along this route, the exchange of information takes place in both directions.


Once described as mere “bags of enzymes,” bacterial cells were long thought to have little to no internal structure. Bacteria, as opposed to single-cell organisms like slime molds, do not have a membrane-bound nucleus, and their genetic material is typically a single circular DNA chromosome with its associated proteins and RNA located in the cytoplasm in an irregularly-shaped body called the nucleoid.

Researchers at Berkeley studied a strain of Bacillus subtitles’ capacity to ‘remember’ 10 distinct cell histories prior to submitting them to a common stressor. The analysis—much too complicated to describe here—suggested that Bacillus subtilis remembers, for a relatively long time, aspects of its cell history. Though unable to explain the underlying biological mechanisms, the scientists have generated an information theory-based conceptual framework for measuring both the persistence of memory in microbes and the amount of information about the past encoded in their organisms. Since 1983, Roberto Kolter, a professor of microbiology and immunobiology at Harvard Medical School, has led a laboratory that has studied these phenomena. Kolter has stated that under the microscope, the incredible collective intelligence of bacteria reveals itself with spectacular beauty. Imagery from the lab, World in a Drop, is presently on display in an exhibition at the Harvard Museum of Natural History.

The Microbiome

The human gastrointestinal tract (GIT) is populated with as many as 100 trillion bacterial cells. Their collective weight may exceed 5 pounds, about 2.2 kilograms. Recently, there has been a groundswell of research into how these gut bacteria influence critical aspects of our physiology. We are learning that the myriad resident microbes are critical for the development and function of the immune system. Even more importantly, gut microbes affect the complex and distant brain. Findings from animal studies have shown that the microbiota (the sum of all the bacteria, fungi, and viruses inhabiting our gut) can affect brain metabolites, behavior, and neurogenesis, that is, the formation of new neurons.

Signals from the gut travel to the rest of the body along the hypothalamic-pituitary-adrenal axis (HPA). However, the vagus nerve is the primary route that enables stimuli from the brain to pass to the gut and from the gut to the brain. Only recently has it been established that the vagal gut-to-brain axis is also an integral component of the neuronal reward pathway.

In addition to the vagus nerve, the brain-gut-microbiota axis includes the central nervous system, the sympathetic and the parasympathetic system, the neuroendocrine and immune system, and the enteric nervous system.

The enteric nervous system (ENS) is the intrinsic nervous system of the gut. It consists of an extensive network of neurons that lines the walls of the gastrointestinal tract. The complexity of the human ENS, is only exceeded by the brain and spinal cord.

The ENS has the unique ability to control the behaviour of its organ, the gut, without input from the central nervous system. It was this independence of the ENS that led Michael Gershon, at Columbia University, to call it “The Second Brain.” Biologist Michael Schemann, with colleagues at several German universities, reviewed the evidence for what he called the “smartness” of the ENS. He documented the presence in the ENS of habituation, sensitization, conditioned behaviour, and long-term facilitation. As such, the ENS is capable of various forms of implicit learning and remembering. About 88% of the neurons of the ENS are replaced every two weeks. This energetic neurogenesis is driven by the enteric microbiome.

The gastrointestinal tract is now also recognized as a major regulator of motivational and emotional states. Gastrointestinal problems are common among people with depression and anxiety, and studies suggest people with depression have a different gut flora than people without. Intestinal bacteria also produce serotonin, dopamine, and other brain chemicals that regulate mood. The hope is that enhancing good gut microbes—whether with probiotics, fecal transplants, or capsules filled with donor stool, or by adding sauerkraut or other fermented foods to the diet—may be the answer to intractable depression, the kind conventional treatments can’t touch. It could also fundamentally alter the way we conceptualize mental illness. For the longest time, medical experts believed that mental illness was essentially a brain illness, when in fact, it may be much more complex than that.


Studying bacteria, we find credible evidence for host-microbe interaction at virtually all levels of complexity, ranging from direct cell-to-cell communication to extensive systemic signaling, and involving various organs and organ systems, including the central nervous system. As such, the discovery that differential microbial composition is associated with changes in thinking, feeling, and behaving has significantly contributed to extending the well-accepted gut-brain axis concept to the microbiota-gut-brain axis.

The microbiome and its relationship to the enteric nervous system, the brain, and the rest of the body is a perfect example of one of the many unrecognized parts of the Embodied Mind. Out of sight is not out of mind.


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Gershon, Michael D (2020). How smart is the gut? Acta Physiol. 228: e13296;

Dinan, T. G., & Cryan, J. F. (2013). Melancholic microbes: a link between gut microbiota and depression. Neurogastroenterology & Motility, 25(9), 713-719.