
The gut is the center of everything we are. The more we’ve learned about how stomach pain and bloating interacts with every other organ system the more we’ve realized that medicine had NO idea what it was messing with.
In the first part of this article I gave an overview of the gut and what can go wrong. Since it’s important to remember how your gut gets screwed up in the first place, I’ll give you an overview.
Destroying Your Gut; What Causes Stomach Bloating
There is a long list of things that ruin the gut. Sometimes it’s just for a few hours, sometimes a few days, sometimes a lifetime.
This list can be easily divided into two parts: Things we do that we do to our own gut and those things that mainstream medicine does that causes stomach bloating.
Self-Inflicted Stomach Pain and Bloating
That 8th shot of tequila. That triple-bacon-double-cheese-not-quite-beef-burger with a side of gravy fries. Those leftovers that should’ve been tossed a week prior.
We don’t always make the best choices for our health.
And your gut is on the front line of these bad choices.
Stomach Pain and Bloating: Diet Consequences
Diet is one of the most powerful tools when it comes to good health.
And bad health.
There are the obvious bad choices like a high saturated fat diet loaded with refined carbohydrates and not a vegetable in sight.
There are less obvious ones likes food allergies. Food allergies play a massive role in conditions like GERD/reflux/heartburn. In many cases this is THE problem.
Most common food allergies are dairy, wheat (which includes gluten), soy and corn. There are some other items that can go on the list, but this cuts across the bulk of what people are sensitive to.
If you continue to eat foods that your immune system does not like, the gut is at the front line of the immune reaction, leading to a breakdown of the lining of the gut (more on this later).
To truly heal your gut, you must address food allergies. The best tool for this is NOT a $1,000 blood test that shows that you are allergic to the South Bornean magenta pepper. I’ve never been a terribly big fan of wasting time and effort on bloodwork to determine allergies.
An elimination diet is the gold standard for identifying and fixing food allergies and sensitivities.
In an elimination diet, you avoid all the common food allergies and sensitivities for 2 weeks (it can take this long for the immune system to react to something we eat). During this time, you look for improvements in whatever it is that you’re concerned about. Breathing problems, skin problems, intestinal complaints like diarrhea, constipation or heartburn.
After two weeks, you reintroduce one type of food for just a single serving and be aware for any return of problems. Give yourself a few days before you try the next food item. It’s not uncommon to have problems with more than one type of food type; this is why you reintroduce them one at a time.
For the long haul, living with some type of rotation diet is your best bet. The typical pattern is to give 4 days before eating the same foods again. This keeps the immune system from ramping up from repeated exposures.
I describe this as a Gatland gun. Pull the trigger once or twice and not much happens. But hold the trigger and all hell breaks loose.
The immune system acts much the same way. By putting some time in between food exposures, your immune system is less likely to ramp up and create problems. As an added bonus, you will get a wider variety of foods instead of eating the same foods over and over again.
Stomach Pain and Bloating: Stress Consequences
Our nervous system has a very basic breakdown; the sympathetic (fight or flight) and parasympathetic (rest and digest). These two systems are always in opposition to one another; as one goes up, the other goes down.
This means that, when the fight or flight system is activated from stress, the rest and digest suffers. To put it simpler, stress destroys digestion.
There are few things that will have more damaging consequences to gut health than chronic stress (on this same list is acid-blocking drugs, and for the same reason).
Chronic stress will shut down blood supply to the stomach, leaving the cells of the intestinal tract without the nutrients to heal properly or to produce enzymes needed for optimal digestion.
A Pandora’s box for bad health.
While it is beyond the scope of this article to discuss stress-management techniques, you need to understand that stress needs to be eliminated or managed for your gut to function at its best.
Here are a few tools that may work for you:
- Exercise is a powerful stress reducer, although I generally consider this a tool to manage the physical problems with stress and less for the brain (although there are unquestionable brain-benefits of exercise).
- Biofeedback—there are many tools available like the Muse (a device that connects to your smartphone and monitors brainwaves) and smartphone apps that measure breathing and heart rate.
- Deep prayer
- Yoga
If one of these tools resonates with you, then start TODAY. There is never any excuse good enough to put off managing stress.
Stomach Pain and Bloating: Antibiotic Dangers
Since the identification of penicillin, society has viewed antibiotics as a panacea for all that ails us.
Early on, with life-threatening infections, antibiotics were a powerful tool.
It’s when we started using them for everyday scenarios like ear infections, urinary tract infections, sinus infections and upper respiratory infections that problems began to arise.
Big ones.
The problem is that mainstream medicine is STILL worried about antibiotic resistance. There are sickeningly few discussions about how antibiotics destroy the normal flora.
All of it.
Which wouldn’t be a problem if we weren’t beginning to understand how much of a role normal bacterial flora plays in good health.
It is VERY likely that antibiotics are a major contributor to all immune dysfunctions (autoimmune, allergies) as well as asthma, chronic sinus infections and chronic urinary infections.
What a 180 from what we thought we knew.
The idea that antibiotics play a pivotal role in the very conditions we use antibiotics for is very real and based solidly in what we understand about the bacteria we harbor in our bodies.
I’ll go a little more into detail about just how the antibiotics destroy the gut a little later, but for now, understand that few things will disrupt the balance between your gut and your immune system.
Years ago, I would’ve just recommended 2 weeks of probiotics to follow up a course of antibiotics and call it a day.
Wow was I ignorant of just how complex the microbiome is…
We now know that, even TWO YEARS later, the gut hasn’t recovered from a single course of antibiotics. In reality, few people will ever recover from just one course of antibiotics.
Stomach Pain and Bloating: Acid-Blocking Drugs
I’ve already made it clear how much stress destroys your gut. One of the consequences of stress is lowered stomach acid production.
Digestion and absorption of nutrients is one of the most critical things your body does. Stop this process and you can pretty much kiss good health goodbye.
In part one I covered just how important stomach acid is and how much damage blocking stomach acid production does to your body, so I won’t cover it again here.
Just understand that much like stress, acid-blocking drugs will destroy gut health through many different paths. These drugs should ONLY be used if there is an ulcer present and then only for long enough to protect from immediate danger.
Stomach Pain and Bloating: Anti-Depressants
Selective-Serotonin-Receptor-Inhibitors, or SSRIs have a direct effect on the gut. This little tidbit is one few are aware of, although the major side effects of this class of drugs involves the gut.
Another little tidbit is that up to 90% of the body’s serotonin is produced in the gut, not in the brain. Serotonin has several actions on the gut:
- It blocks stomach acid production in the stomach
- Serotonin speeds up motility in the gut, which can cause diarrhea (which is why one of the side effects of SSRIs is diarrhea). Things that irritate the gut, like toxins and food allergies, lead to more release of serotonin to wash out the irritation.
This is one of the reasons why food allergies can wreak havoc on the gut—because they increase the release of serotonin, messing up a key player in digestion (stomach acid) and causes diarrhea, which affects absorption of nutrients from our food.

Small Intestinal Bacterial Overgrowth, aka SIBO
You may or may not have heard about SIBO, but if you’ve read this far on the topic of gut problems there’s a good chance you’ve got some degree of SIBO going on. But the problems caused by SIBO don’t stop at the gut.
It begins to connect the gut to the immune system and the nervous system and brain. This means that conditions like fibromyalgia, chronic fatigue and migraines are all connected to SIBO.
Here’s the basics.
SIBO: It Starts with Bacterial Overgrowth
I’ve already covered a number of things that lead to problems with the bacteria in the gut. Top of the list include:
- Antibiotic use killing off protective bacteria in the gut, leaving bacteria that cause problems at the “top of the hill”
- Poor motility of the gut (such as a slow-moving or absent Migrating Motor Complex) that doesn’t “sweep clean” the gut
- Acid blocking drugs that allow other the wrong types of bacteria to grow
- Stress that decreases stomach acid production
In general, the small intestine is not a good environment for bacteria to grow.
The above factors, either alone or in combination, lead to a scenario where the overall number of bacteria in the small intestine is much higher than it is designed for.
SIBO: Destroying the Lining of the Gut
The cells lining the small intestine were never designed to handle vacationing bacteria. They’re just not as tough as the cells in the colon. To make this worse, the immune system in this area was not trained to deal with bacteria like the immune cells around the colon.
In a perfect world without immunizations and antibiotics and loaded with breastfeeding moms who have not had antibiotics (like as in….EVER) an infant’s gut gets populated with beneficial bacteria. The immune system gets introduced to these bacteria early in the little one’s life because of this. And the immune symptom learns to play well with the bacteria.
And live in peace and harmony.
Not so with the small intestine. When you get exposed to things on the above list later in your life that allow bacteria to grow in your small intestine, your immune system thinks an attack is underway.
This sets up a situation along the wall of the small intestine that begins to damage the cells and the connections between cells lining the small intestine.
You see, the gut in general is a barrier. Only things that are supposed to get absorbed into the body via the gut get in. Everything else is blocked.
Or should be.
This is not so when the small intestine becomes inflamed from both the action of the immune system and the waste products of the bacteria themselves. The glue holding the cells together begins to fall apart allowing particles to slip by the barrier (for the physiology nerds out there—the gap junctions begin to fail).
Picture how your throat looks in the middle of a wickedly inflamed sore throat. Red, irritated and swollen.
That’s what can happen to the small intestine in this scenario.
And this, dedicated readers and searchers for knowledge as it relates to poor gut and immune health, is where the proverbial hell breaks loose.
SIBO: Letting in Foreign Invaders
I’ve mentioned that stuff gets into the body that isn’t supposed to get in. This can be toxins produced by the bacteria themselves (you’ve heard of botulism, tetanus and C. diff infections? Yeah—these types of toxins). It can be improperly digested food particles (which seems likely because poor digestion is a player in kicking off this fecal storm in the first place).
But KING of the things you don’t want to absorb is fragments of dead bacteria. AKA lipopolysaccharides, or LPS for short.
The immune system HATES bacteria pieces running around free in the blood stream. That’s because things like sepsis from bacterial infections in the bloodstream can be lethal.
And that’s generally a term humans like to avoid, especially when the word is used to describe your health.
SIBO: Pissing Off Your Immune System
Bacterial fragments, the LPS molecules mistakenly absorbed into your body due to a weakened intestinal barrier, piss off the immune system, lighting it up.
And nothing can wreak havoc on your health as much as an irritated, pissed off immune system.
This inflammation can begin right at the lining of the gut. Or the interaction with the immune system can happen as LPS particles get absorbed by the circulation and head straight for the liver (which is the normal path for things we absorb from the gut—stuff heads straight to the liver for processing).
The immune cells in your liver have a special name. The Kupffer cells. Their role is to act as a front-line defense system when things get absorbed into the body from the gut. Which happens sometimes.
You eat sushi from that hole-in-the-wall place with the sushi chef who looks like he just got off the set of Zombieland (and NOT as Woody Harrelson) and regret it for the next 72 hours (or, which seems more an appropriate measure of time for the circumstance, 4,320 minutes).
Or you pick up some funky Ebola-like infection after picking up the candy you dropped on the mall floor and proceeded to eat, positive that the 5-second rule is a real thing.
In these scenarios, the infection creates a temporary (key word: temporary) disruption to the lining of the gut, allowing things to get in and lighting up the immune system. The immune system effectively rises up and squashes the invading army.
It’s when this is an ongoing, persistent, low grade exposure to LPS molecules that your immune system never really gets a break.
This leads to an immune system that is constantly under attack, and the tissues in the warpath suffer the consequences. Just in case you think I’m making this stuff up, links between increased intestinal permeability and fatty liver have been observed in the medical research almost 20 years ago.
Fatty liver is the very early stage of liver damage that can ultimately lead to cirrhosis of the liver and liver failure. Not something you’d put on your Christmas wish list.
Just in case this little scenario is not scary enough for you, don’t worry–it gets worse.
SIBO: Damage to Your Brain
Yes. Because even if you have no empathy for the difficulties your liver is having, certainly you have greater concern about your brain.
Immune populations in our body communicate with one another. In this way we can set the entire body up for fighting off an infection more effectively.
The Kupffer cells in the liver have direct connections to the immune cells in your brain called the glial cells.
And, dedicated readers, inflaming your brain is going to be one of the LEAST fun things you’re going to do this month (unless you have an IRS audit or your GI doc runs out of anesthesia just before your colonoscopy…).
Inflammation running wild in your body is bad enough. It can lead to things like fatigue and muscle loss in the immediate future and things like heart disease and cancer in the long run.
But when it happens in your brain? A brand-new list of not-so-fun stuff.
You see—the microglial cells in the brain are generally protected from what happens in the rest of the body by the blood-brain-barrier (BBB). Like the lining of the gut, the BBB is designed to protect the brain for much of what happens in the rest of the body.
It is, after all, your brain and should be guarded like the password to your online $1,000,000 savings account (because we all have one…).
But this communication between the Kupffer cells and the microglial cells bypasses the BBB, setting up your brain for inflammation.
And what does brain inflammation do, exactly?
I’m glad you asked. Here’s the short list:
- Fatigue (because you weren’t tired enough from the systemic inflammation already happening)
- Brain fog
- Memory issues
- Attention issues (to include ADHD and Autistic Spectrum Disorders)
- Headaches (migraines and others)
- Seizures
- Weight gain
- Depression
- Anxiety
- Schizophrenia
- In the long run–cognitive loss, Alzheimer’s dementia and Parkinson’s disease
Sounds like a pretty long list, huh?
Probably cuts across much of what you experience on a daily basis. If not personally than definitely in someone you love and care about.
And all of this can start in the gut.
Makes you begin to question the wisdom of using medications to treat conditions like migraine headaches, fibromyalgia, depression, anxiety and fatigue (just in case you hadn’t already).
Medications are so incredibly, woefully, sadly, depressingly inadequate at fixing the actual problem. There are NO MEDICATIONS that can heal problems when they start in the gut, and with small intestinal bacterial overgrowth in particular.
So, what can you do about this monster known as SIBO?
You’ll have to wait until part three (and the final part) of this rather lengthy article.