The body composition specialist

Could Improving the Health of Your Gut Bacteria Improve Cognition, Mood, and Memory

One of the most fascinating medical discoveries of the 21st century has been the intestinal microbiome and its importance to our health, cognition, and sense of well-being.


As we have come to understand the gut and the gut microbiota more fully, we have found that the gut houses 70% of our immunity cells – a vastly important fact that is so important to know in the age of pandemics.


There is also a vast universe of some 100 million neurons and over 30 different types of neurotransmitters. They’re responsible for sending messages to our brain about our mood, pain perception, our management of fear and anxiety and contribute to the agility and quickness of our mind.


The gut also produces 95% of the serotonin manufactured in the body (which is made in the bowels). Serotonin is in keeping our mood up and happy and in keeping us motivated and with a healthy outlook on life and our future.


All this happens through the circuitry of the gut to the brain, with the gut’s signals flowing upward toward the brain in what scientists now call our enteric nervous system (ENS).


So, one can see how pampering, nourishing, and tending to the gut would be very wise. After all, what is the typical treatment for depression? Selective serotonin reuptake inhibitors (SSRIs), chemical messengers that help boost serotonin levels and lift depressed patients out of depressive states.


But what does it mean that all these neurons and neurotransmitters are located there as opposed to, say, the brain?


Part of It is Probably Evolution


Before we fully evolved the complex and genius minds most of us possess today, scientists believe that we evolved neurons in the gut so that we could stop tapping the brain for digestive commands and information.


As the mind became more independent and the gut could rely upon itself for digestive information about the boring stuff about when to digest food, when to move food to the large intestines, when to poop, etcetera, then our minds could really flourish.


Perhaps that’s when we started doing more things like making fires, houses, and then, civilizations.


Scientists think that the gut is responsible for mood and cognition through two specific avenues:


The millions of neurons embedded in the vagus nerve, protected by the walls of the neurons embedded in the long tube which runs from our gut to our anus


Scientists now believe that this is why electroshock therapy helps many severely depressed patients—the stimulation of the vagus nerve which houses so many neurotransmitters tied to our mood and well-being


The 95% of serotonin housed in our bowels


Depressed patients are helped by increasing serotonin. Many depressed patients, in fact, suffer from gut distress, leading scientists to believe that concentrating on improving gut health can improve the health of our mood and our brain greatly.  


In fact, a prominent scientist at UCLA, Emeran Mayer, believes that in the future, the second brain will be as important to the treatment of depression, anxiety, and mental illness as the first.


So, Is This Where We Get Gut Feelings?


Scientists were surprised to discover that the long vagus nerve (VN) that runs from the gut to the brain actually carries signals from the gut to the brain, instead of vice versa. They originally thought it was the mind controlling everything.


However, our second brain doesn’t control our consciousness nor our conscience, nor is it capable of conducting important thoughts from our gut to our brain. Michael Gershon explains that “[t]he second brain doesn’t help with the great thought processes…religion, philosophy and poetry is left to the brain in the head.”


It is, however, very capable of inducing feelings with us and, in that sense, the old adage about gut feelings is right.




Also, the gut can contribute to and improve the quality of our mind and the state of our mind.


In fact, positive alterations in our gut’s microbiota can positively impact physical and mental health. Today, we’re learning how nutrition and probiotic and prebiotic supplementation can have far-reaching positive impacts on health from gut-related issues like bloating, gas, and heart burn, to improving our mood, thinking, memory, energy, and our sense of well-being.


Kind of Like Splitting the Atom . . .


The discovery of the gut-brain connection and that the vast universe of bacteria within us, the microbiota, has had an impact on science and research as big as the discovery of the genome and the splitting of the atom.


As long-respected John Binenstock, a highly respected physician and mucosal immunologist notes, this amazing discovery just “catapulted into the scene” – as if out of nowhere.


In just the last decade, research on the gut and its impact on the brain, mood, and cognition has just exploded, as scientists hope for new avenues through which they can explore cures to confounding brain illnesses, like autism and Alzheimer’s.


Just recently, we learned that the intestinal microbiota can influence our experience of stress, pain, depression/sadness, happiness – a whole host of feelings (gut feelings?) because as we have learned


the gut directly influences brain chemistry

the gut is swarming with neurotransmitters that directly signal the brain about our mood and feelings

the gut directly influences neural development (the health of our brain cells and neurogenesis: the birth of new brain cells)

enhancing gut health can help us enhance cognitive and executive function


Today, I’m going to focus on all of these aspects of the gut-brain connection and tell you some of the fascinating developments in or understanding of how the gut influences our mind.


Our Second Brain: The Enteric Nervous System (ENS)


Our gut is connected to the brain directly through something called the gut-brain axis or the enteric nervous system (ENS).


–Image courtesy of Nature Review Gastroenterology and Hepatology



The enteric nervous system is really a mesh-like grid – a kind of a cross-hatch bunch of neurons, much like a wire fence – that surrounds the vagus nerve and governs the function of the gastrointestinal tract and, as we’re learning, much more.


If you were to uncoil our small and intestine and colon, you could see all the neurons in their cross-hatch pattern if you had the technology, as you can see below:




Image courtesy of Frontiers in Cell and Developmental Biology.

Scientists believe that the gut-brain connection can affect both mood and behavior. Researchers note that “disruptions in microbial communities have been implicated in several neurological disorders.


Scientists have discovered four main gut-microbiome brain axis pathways:


① the nervous system including the ENS and the VN

② the neuroendocrine and HPA axis

③ the immune system

④ microbiota-derived neuroactive compounds.


Why are these pathways important?


Because collectively, the microbiome of the gut manufactures many mood-regulating neurotransmitters including serotonin, GABA, and dopamine, all of which help control our mood, cognition, sleep patterns, quality of sleep, energy levels, memory and so much more.


Let’s discuss these in more detail, as these mechanisms are the way that the gut influences the brain overall, which impacts both mood and cognition:


1. The ENS/VAGUS Nerve Connection and the Importance of the ANS


First the brain and gut communicate through the autonomic nervous system (ANS) and the vagus nerve. The VN activates the mucosal layers of the gut, which sense stimuli. and retransmit these signals to the brain.


2. The neuroendocrine and HPA Axis


This connection between the gut and brain, in simple terms, regulates immune responses, metabolism, and numerous other physiological processes.


3. The immune system


The immune system, in discussion of the brain-gut connection, is less about protecting us from disease and more about affecting our mood. Here’s where the things you’ve been hearing about the gut, stress, consequential inflammation, and depression become important.


Stress – Again, It’s Basically Fatal, Let’s All Get That


The gut is extremely sensitive to stress. Stress activates the cellular danger response (CDR) and, of course, inflammation, which occurs in response to all stress, sets in. Inflammation can, in return, cause an increased sensitivity to stress, which can cause depression in its worst form—major depressive disorder (MDD). This is ultimately caused by an interaction between the gut microbiota and four important areas of the enteric nervous system.


The gut and the enteric nervous system (ENS)

The gut and the autonomic nervous system (ANS)

The gut and the immune system

The gut and our neuroendocrine signaling systems

The neuroendocrine gut microbiota connection


Researchers are finding that disruptions in gut bacteria can lead to many mood disorders.


People with gastrointestinal disorders, especially (IBS) are highly associated with disruptions in the gut-brain axis that cause mood disorders, specifically anxiety and depression.


In fact, according to Mangiola et. al. (2016), gastrointestinal imbalances and disorders might possibly be the cause of autism. In fact, persons with autism share a correlation between the severity of their autism and the severity of the disruption of their gut bacteria.


In short, we are learning that the gut can influence many areas of our mood and behavior as well as our overall health.


Recent Fascinating Discoveries About the Gut


Scientists are now hard at work on the nutrition-gut-brain connection. Their discoveries are revolutionizing the study of nutrition and health as we know it.


Nutrition, in fact, may be key in curing Alzheimer’s and autism.


Scientists are also investigating other means of normalizing the abnormalities in the gut that typically accompany these disorders.


The trouble is that human studies and diet/nutrition are, inevitably difficult. It’s hard to be certain no one ever cheats or goes outside of the study controls and, secondly, these studies take years and sometimes decades.


The Gut and Circadian Rhythms


Just in 2022, we have discovered something completely new about the gut-brain connection. A recent study has found that the gut microbiota possess their own circadian rhythms and that eating more in alignment with these circadian rhythms leads to lower BMI and better health.


Researchers have found that the gut is constantly changing depending on us – what we eat, how we eat, and – especially and interestingly enough – when we eat.


Amir Zarrinpar, assistant professor of medicine at UC San Diego School of Medicine and a gastroenterologist at UC San Diego Health, notes that

It’s important to realize that the gut microbiome is constantly changing, not only based on what we’re eating and the size of our meals but also based on the time of day . . . And what we’ve learned is that cyclical changes in the gut microbiome are quite important for health since they help with the circadian clock, and with that the regulation and control of glucose, cholesterol and fatty acids — and overall metabolic health.


It has been noted that eating outside of the circadian clock and not fasting overnight caused a disruption in the gut microbiome that has been, in several studies, linked to obesity and diabetes.


For example, in recent animal studies, scientists learned that when they let mice eat whenever they wanted, they became obese and diabetic as opposed to mice allowed to eat the same amount but at limited time intervals.


This is quite revelatory – especially for third shift workers and late-night snack-ers.


Apparently, it’s not so healthy to get everything we want when we want it.


This will be a difficult adjustment for many persons but one that should be considered.


Eating and snacking past our ancient circadian rhythm’s clock sets us up for more hunger, more weight gain, more food cravings – all to replenish the energy we’re losing at night by not fully resting – if you’re digesting, are you really resting and furthermore, because most late-night noshing is done somewhat unconsciously, and we’re not chewing properly or engaging in mindful eating – enjoying each bite. Taking time to enjoy, chew, and digest our food is key to the gut microbiota and our overall health.


Can a Healthy Gut Help Us Fight Depression and Anxiety?


There is overwhelming evidence that imbalances in gut bacteria can impact our mood negatively. This is because serotonin, manufactured in the colon, is so necessary for our mental health.


A large number of recent studies provide evidence of a correlation between the gut microbiota and cognitive function. With anxiety and depressive disorders, it seems disruptions in the gut bacteria are more impacting than any ENS activity of the gut-brain axis.


Our most recent studies evidence that when animals are implanted with excess bad bacteria from IBS patients, animals developed obvious anxiety symptoms, which were immediately relived by supplementation with good bacteria, specifically the Bifidobacterium infantis strain, which has shown to have strong antidepressant effects in animals.


What researchers are finding is that stress might be the crucial modulator in gut-related mood disorders from anxiety to depression with possible implications in bi-polar disorder. Research is and will be developing on this for some time.


Can a Healthier Gut Make Us Smarter?

The research on this is absolutely fascinating.

For example, in a very intriguing study, Myer, Lulla, and Debroy (2022) found that disruptions in gut microbiota, specifically, a reduction of microbiota due to supplementation of antibiotics (I’m sure you’ve heard by now that antibiotics reduce our colony of gut bacteria overall) causes impaired memory, negatively impacted cognition, a reduction in working memory, and negative changes in BDFN (brain derived neurotrophic factor).


When gut health is impacted by antibiotics, the state of the gut is somewhat similar to that of someone with poor eating habits. . .


The negative impact to our BDFN is one of the most damaging effects of gut dysbiosis because we need this neurotransmitter modulator to help our fragile neurons to survive and to keep our brain plasticity ever-improving instead of the opposite.


BDFN is also very important, as researchers Magdelena et al. (2019) for learning and memory and new neuronal growth. ,


Studies on humans have revealed that when supplementing with probiotics, cognition improved significantly when compared to controls., Researchers attribute this to the fact that gut microbiota release molecules which are metabolism by-products which can impact the brain in myriad ways via different pathways.


Furthermore, scientists have proven that changes in gut microbiota directly impact mental performance.


In short, the gut is directly tied to cognitive performance.


Studies on Healthy Versus Non-Healthy Eaters, the Gut, and Cognition


It is often easier to study the habits of admittedly unhealthy eaters than ones who believe they eat healthy, say they always eat healthy, or to know what their definition of “healthy” really is.


This makes studies in nutrition difficult in myriad ways.


In the few studies that have been done on healthy people as opposed to those following an unhealthy diet, following both vegetarian or the Mediterranean diet reduced pathogenic and inflammatory strains of bacteria and a fast-food diet reduced good bacteria necessary in fighting disease and, especially, fungal infections.


As Dr. Kirsten Tillisch, professor of medicine at the David Geffen School of Medicine at UCLA sums it up:


I really feel like all the research to date has pointed us to really basic concepts that add up to what we eat and how we live our lives is going to affect our health, whether it’s our mental health, whether it’s our cardiovascular health, whether it’s our gut health, whether it’s our neurologic health.


As M. G. Gareau (2106) notes, “Cognition was originally thought to be exclusively regulated by the central nervous system (CNS) . . .  


but now other systems, including, for example, the immune system and the intestinal microbiome may also be involved.


Cognitive impairment has been identified in numerous disease states, both gastrointestinal and extraintestinal in nature, many of which have also been characterized as having a role for dysbiosis in disease pathogenesis. This includes, but is not limited to, inflammatory bowel diseases, irritable bowel syndrome, type 1 diabetes, obesity, major depressive disorder, and autism spectrum disorder.


How to Improve Gut Health to Supercharge Our Brainpower and Get Happier


When it comes to boosting both your mood and your cognition, we have found two specific ways we can do this so far both of which share the aim of nourishing and restoring the gut microbiome to a healthy, balanced state.


How does science tell us we can do this? This is where the two ways come in.


1. A microbiota-restoring diet

2. Correct probiotic supplementation


**Both of which should be done under advisement of a specialist or a health coach/trainer who specializes in gut health and precision nutrition.


How Diet Can Restore the Gut to Health      


First, let’s discuss the microbiota-restoring diet.


In a very detailed and informative study conducted by Kate Lawrence and Jeanette Hyde (2017), these researchers learned that following a diet detailed by Hyde in her earlier book, The Gut Makeover Diet (2015) that even after four weeks on this diet, patients on the microbiota-restoring diet experienced “large-scale improvements in physical and emotional well-being and cognitive functioning,” and that patients experienced “rapid, extensive … high-magnitude benefits quite early on in the study.


The benefits they noted were extensive and included digestive, cognitive, and emotional benefits including:


Weight loss of 2.2 to 15.4 pounds

Disappearance of IBS-related symptoms like gas, bloating, diarrhea, and constipation

Improvements in energy, mood, & memory

Enhanced sleep quality


Throughout the four weeks     In the second half of the plan

participants    (weeks 2–4) participants also 


• Eat three main meals per day, no snacks between.

• Undergo a 12-hour overnight fast between dinner and breakfast, with just water permitted between.

• Eat seven American cups’ full of plants (uncooked volume) per day (five as vegetables, two as fruit).

• Eat protein with each meal (either animal, fish, eggs, nuts, or seeds).

• Eat between 20 and 30 different types of plants (fresh herbs, vegetables, and fruits) over the course of a week for variety.

• Can eat butter and ghee.

• Consume probiotic foods such as fermented milk kefir, sauerkraut, tempeh, and miso.

• Increase their intake of Use extra virgin olive oil and coconut oil as their default cooking oils.

• Chew food thoroughly–aiming for approximately 20 chews per mouthful.

• Do not count or restrict calories.

• prebiotic vegetables such as bananas, fennel, asparagus cold potatoes, onions, garlic, leeks, fennel, Jerusalem artichokes, pak choi.

• Consume bone broth/stock.

Excluded from the diet throughout the four weeks


• Refined sugars.

• Grains (e.g. wheat, rice, oats, maize, quinoa) and pulses (e.g. lentils and beans)

• Alcohol

• Caffeine

• Dairy (can be reintroduced after 2 weeks if no adverse symptoms on re-introduction)

Interestingly enough no probiotic or prebiotic supplementation was used here beyond food. Therefore, the prebiotic and probiotic aspects of this diet are critical to improving gut health, as are chewing thoroughly and observing your circadian rhythms by fasting throughout the night (no midnight snacking!)


For more on this fascinating diet and how to follow it properly, see Jeanette Hyde’s The Gut Makeover and The Gut Makeover Recipe Book.


How to Use Probiotics to Restore Balance in the Microbiota


Studies of the human microbiome and microbiota have given us a deepened knowledge and understanding of the association of the microbiome and its implications on the brain and, especially, neurological disorders.


Other research has illuminated the very complex relationship between the gut-brain axis and intestinal microbiota.


We have learned that gut microbes communicate with the gut-brain axis (or the ENS) through production of neuroendocrine molecules such as noradrenaline, adrenaline, serotonin, GABA, and histamine. ,


Researchers have learned in studies that supplementation with specific strains of bacteria stimulates different neurotransmitters that produce different effects in the brain and body from decreasing anxiety and depression to, fascinatingly enough, inhibiting our perception of pain.


For example, Lactobacilli can help inhibit pain via conversion of glutamate into GABA. GABA is an inhibitory neurotransmitter in the CNS which plays a role in pain inhibition. ,


Administration of L. rhamnosus helps to reduce stress-related corticosteroid in the body, which in turn reduces anxiety and stress related behaviors (in animal studies).


Supplementation with probiotics is very complex. It is something that you should undertake after a gut panel done with stool and with a certified specialist or with a fitness trainer knowledgeable and trained in bio-panels and gut health.