Microbiology and Neuroscience

Gut-Based Brains

How the Gut Microbiome can Inform Neurological Patterns

Can you tell me what these 👆🏾 two body parts have in common? You could say that they are both organs/a complex of organs, they are both complex structures, or they are both vital in the human body.

How about these two?

What do neurons and food we eat have to do with each other? Well, there’s a lot more to do than most would think!

However, there’s something called the gut microbiome in the field of neurobiology, which is one of my current interests. The gut microbiome has shown huge potential in influencing neurological conditions.

If you’re a germaphobe, it might be unsettling that there are microbes all around us, and especially with the current pandemic, a lot of us are sweating bullets when we hear about anything that sounds remotely like bacteria or disease.

However, this is way more exciting.

Before we hope into it, here are a couple of technical research papers that I recommend on this topic:

A lot of reading 🤩 — these are some awesome recommendations; search the titles to read them

The Gut ꇲ

The gut, more commonly known as the gastrointestinal tract, is the 30-foot organ complex that acts as a road for us to process our food. In reality, the gut is a tube that starts at the mouth and goes all the way down to the anus (shown in the picture). The gut is a really important functional complex in our body.

Behind the curtain, our gut is responsible for putting our body into working order. As it breaks down the foods we eat, our gut absorbs nutrients that support our body’s functions — from energy production to hormone balance, skin health to mental health, and even toxin and waste elimination.

Essentially, the tube is responsible for the absorption of nutrients that cause really important incidental effects in our bodies.

If you were wondering, the gut looks like this:

The GI Tract of the body is typically sectioned into different organs.

Here’s what each of them look like:

Mouth, Small Intestine, Colon + Large Intestine, Esophagus, Gallbladder, Liver, Stomach, Rectum, Pancreas

Also, am I the only one who thinks the gallbladder looks like a pea, and the pancreas looks like a corn on the cob snack? Maybe I’m just too hungry… anyway:

Mouth: The anatomical section of our body that we put food in (and sometimes other things when we’re younger). Lined with saliva, and contains the vestibule and oral cavity proper. Our lips mark the mucous membrane and skin. The mouth also contains the teeth, tongue, palate, jaw, and the beginning of the neck (including the pharynx, larynx, and esophagus).

Esophagus: The contracting organ through which food passes (only in things with a backbone a.k.a. vertebrates).

Stomach: You know, that pouch muscle thing that breaks down food??!?!? Anyway, your stomach is the organ that receives food from through the esophageal sphincter and then releases some handy-dandy acids and proteins to break the food down.

Pancreas: So, biologically, food = fuel. How do we get fuel from food? The pancreas. This saclike organ in your abdomen is both exocrine and endocrine, meaning that 1.) it helps with digestion by making protein shakes called enzymes to break down fats, sugars, and starches 2.) helps to properly regulate your blood sugar!

Gallbladder: A balloon that takes that gross bile from your liver and stores it. Post-meal: your gallbladder is ready to float; pre-meal: your gallbladder looks like a shriveled sack.

Liver: You’ve seen this one 100000 times. It gets rid of the bad toxins in your body, while simultaneously helping you digest food.

Small intestine: The tiny bowel maze that food goes through, and where the nutrients get absorbed into the bloodstream. It has sponge-walls that create and secrete juices that break down foods (with a little help from the liver + pancreas).

Large intestine/colon: If it’s not food, the large intestine finishes the small intestine’s job. It slurps up all of that salt and water and then isolates the waste. The colon specifically is the last part of digestion. It also gets our 3 pints of liquid stool a day (aka poop), which it condenses into solid.

Rectum: Ready for discharge! Thank you colon (if you get it, you get it — this is what the rectum does).

Basically, this is the equation for the gut:

Eat + Food * (Organs + Nutrients)/ Discharge

*not scientifically proven lol

And that’s the gastrointestinal tract for you! That’s the whole reason it’s gastrointestinal. It involves/runs through the stomach, and the intestines (and other organs).

Anyway, enough about the gut.

What the heck is a “microbiome”, and what does that have to do with the brain?


So, before just hopping directly into the human — and of course gut — microbiome, we must understand what microbes are.

During a time like this, its even more important that we actually understand what they are.

A microbe is just a microorganism that ferments or causes disease via an immune response. The reason the prefix micro-, or μ is so important because it denotes things that are on the microscale, or 10^-6 small.


One of the things that microbes can do is undergo fermentation. This is the process of converting sugar into other molecules, and receiving the necessary field molecules for glycolysis to continue happening to sustain the body. The process, depending on whether lactic acid or ethanol is produced, looks different in terms of specific steps, but has an overall process. The whole idea is that fermentation

💡 takes sugar and converts it into other molecules, while allowing glycolysis (the breaking down of glucose) to continue to make energy

Basically, fermentation is just a fundamental rule in biology where one molecule’s breakdown creates and releases another. It has a lot of applications in causing yeast to make certain proteins from fermentation through gene editing, instead of it just naturally making ethanol, for example.

There are two main types of fermentation, for which I’ve made some cool looking diagrams 😎.

The first is lactic acid fermentation.

A colored diagram showing glycolysis, and the 2 pyruvates produced from it making 2 lactate molecules while releasing NAD+.
Glucose is broken down into two pyruvate, which is then broken down into 2 lactate molecules. The process of breaking down glucose requires 2 NAD+ and 2 ADP molecules, which are then turned into 2 NADH and 2 ATP. The ATP is kept, whle the NADH molecules are used to turn the pyruvates into lactactes, which causes the release of 2 NAD+, which are used to fuel the process of glycolysis once again. All of these reactions are sped up by enzymes.

The second is ethyl alcohol fermentation.

The process of glycolysis making 2 pyruvates from glucose, which turn into 2 acetaldehyde's, which make 2 ethanol, leaves NAD
Glycolysis happens again! Except this time the two pyruvate are broken down into 2 Acetaldehyde, which release 2 CO2 molecules. The Acetaldehydes are broken down in 2 ethanol molecules, which regenerations the 2 NAD+s’ used to fuel glycolysis to create energy again. All of these reactions are sped up by enzymes.

In both photo footers, I say that “all of these reactions are sped up by enzymes”. So let’s look more into what an enzyme does, just quickly.

They speed up reactions 🤩

As you can see, an enzyme is like a puzzle, and the substrate clicks into the active site, where the piece is missing, once they click, the enzyme (made specifically to work only for the substrate — and ones that are SUPER similar ones) speeds up the reaction by reducing the activation energy (energy needed to GO) needed, meaning the reaction will go faster.


So how do microbes cause disease? They come in crowds.

No, literally.

When infection occurs, it’s likely because the bacteria — as a living thing — can multiply, and can multiply to the point where they begin to override the tissues of the original organism and cause them to malfunction. This can cause a variety of effects, commonly killing the cells and tissues completely, and this degeneration causes quite violent reactions, including ejections from the body, fever, etc., etc. The reason for this is that the body is constantly trying to force itself back into a state of equilibrium and fight the bacteria, which is exhaustive and disorienting.

Tissues + Cells = Damaged; Bacteria → More Bacteria, crowds the tissues and cells

Other times, the bacteria can cause toxic responses

where the metabolic processes are destroyed, which create toxic responses, or:

  1. Bacteria make paralytic toxins
  2. Force toxic immune responses

So, basically, though there are good bacteria and microbes that do the opposite, they can still be toxic and harmful. Especially with the current pandemic, make sure to stay safe. Anyway, now that we know about microbes and the gut, let’s talk all about the gut microbiome and brain!

The Gut Microbiome 🧠

A microbiome is the genetic material combination of all microbes — protozoa, bacteria, fungi, viruses — in a biosystem, more importantly, the human body. This is the human microbiome:

Ok. Not so literally. There’s not really a pictorial depiction of the human microbiome, but it is really interesting. I mean the total amount of genetic material in the human microbiome is over 200x the amount of normal genetic material in the human body.

The microbiome also weighs about 5 LBS. To put this *seemingly* small number into perspective, all the DNA weighs about 0.132277 lbs (pounds) in the average adult human body.

So now, let’s look at the

The gut microbiome describes all of the microbes inside of the human digestive tract. In terms of the genomic material itself, this is called the gastrointestinal metagenome. The microbiota is extremely important in sustaining the activity of the gut. They help with the following:

  • digestion processes
  • Vitamins: B-complex, K, thiamine, and riboflavin
  • immune defenses

However, many people’s microbiota, and there has been a recent uptake in lifestyle health community on how to strengthen your gut bacteria, and stay strong, and retain immunity. Solutions include changes in diet and exercise.

But, besides that, your gut has A LOT of [proposed] neurological impacts.

Microbiome + 🧠

So, researchers suspect that your gut microbiota has multiple pathways that allow the gut microbiota to influence the brain. This diagram describes all of the different ways that the GI microbes may communicate with your brain:

There are currently four main speculations as to what the pathways are.

  1. Gut microbes play around with immune cells, and they create cytokines, signaling protein cells, that go to the brain. This signaling can cause neurological changes, as the signals can interact with the brain.
  2. Microbes play around with enteroendocrine cells, which create peptides and molecules that can interfere with the brain. Then, the neuroactive molecules run directly up the vagus nerve, which is a directly signaling nerve to the brain
  3. Gut microbes biosynthesize molecules and neurotransmitters. It’s speculated that these make their way to the brain because they’re able to propagate through the barrier of blood to the brain. Sometimes, this hemo-neuro-barrier is also affected, which causes stimulatory changes.
  4. Recent research has indicated that there were gut bacteria found in brain tissue. This could mean that the gut bacteria have a direct pathway to the brain itself.

But why does this matter?

It has been said that the gut microbiomes plausible interaction with the nervous system (and molecules to the brain) can cause mental disorders, including autism, depression, and epilepsy! It can also edit behavior.

According to this paper (among others), a gut microbiota–brain axis has been discovered, where there is a nervous system network connection through which the gut and brain communicate with each other.

Recently, R&D scientists have been able to inject the brain with viral vectors, viruses without disease-containing genes, and then stimulate it and the gut microbiome.

Hmmm… maybe I’ll parse through that paper in the next video!

Because you gut microbiome might just be affecting your brain if you don’t! 😉

My name is Okezue Bell, and I’m a 14 y/o innovator/entrepreneur in a variety of spaces. I’m investing my time in researching and developing myself (in the super interesting biotech and bioeng space)! Make sure to contact me more:

🔗 LinkedIn: https://www.linkedin.com/in/okezue-a-...

💻 Personal Website: https://www.okezuebell.com

🦜 Twitter: https://twitter.com/okezuebell

Also, I recommend tuning in to my monthly newsletter, non-scientific blog (on website), and letters (in newsletter site)! I post new updates there at least every month!

There’s going to be more…😉

Thanks for reading!

Applied Biology @theksociety, Currently focusing on Alternative Protein x Artificial Intelligence. AI + Security @Fidutam

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