Five Ways Your Digestion Goes Wrong and How To Fix It

It’s normal to take a healthy gut for granted. But, when things go wrong with your digestion, it can be a bit troubling. And if you’re training for an important competition or simply need to be on your best physical and mental game, bad digestion is a big problem.

Then there are those with the chronically unhealthy gut. They feel terrible most of the time, but find ways of dealing with digestive troubles.
This is a mistake because it sets you up for massive health problems including malnutrition, increased disease risk, and poor body composition and metabolism. The sad truth is you’ll never be all you can be with a poorly functioning gut.

Here are five ways digestion goes wrong and how to fix it.

#1: Too much inflammatory gut bacteria

The microflora (or bacteria living in our guts) is a hot topic right now in metabolic science due to the fact that recent evidence indicates that gut bacteria affect all of the following:

  1. How much fat we store
  2. How we balance levels of glucose in the blood, and
  3. How we respond to hormones that make us feel hungry or full.

In fact, gut bacteria do a lot more than just make us fat or lean. They play a role in the absorption of nutrients and compounds into your bloodstream. When you have abundant, healthy bacteria in your gut, your body is able to effectively absorb nutrients from the food you eat, but if you have more inflammatory “bad” bacteria in your gut, pathogens and toxins are absorbed, but beneficial nutrients may not be.

Common symptoms of poor gut bacteria include all of the following:

  • Getting sick frequently and difficulty recovering from training.
  • Constipation and problems with digestion.
  • Neurological problems and feeling like you have a foggy brain.
  • Difficulty losing body fat or putting on muscle, or worse, gaining body fat.

What to do about it:

To solve an inflammatory gut, you need to both eat in a way that promotes the growth of protective bacteria, and stop doing things that promote the growth of bad bacteria.

First, antibiotics and use of other prescription drugs and NSAIDs kill your beneficial bacteria. Avoid all drugs that aren’t medically necessary.
Second, eat plenty of probiotic foods and consider taking a probiotic supplement. Probiotic foods are those that have been fermented, such as high-quality yogurt, sauerkraut, Korean kim chi, kefir, miso, kombucha tea, and pickled vegetables.

Third, eat a varied diet that is high in protein, fruits, and vegetables. Add resistant starch to your diet because it encourages the growth of beneficial bacteria. Get it from raw unmodified potato starch, green bananas, oats, peas, maize, and raw potatoes. It’s also available in cooked and cooled potatoes, and cooked and cooled white rice.

#2: Eating the wrong foods for your unique gut

Bad digestion is not just about your gut bacteria. Another way it goes wrong is when you eat foods that your digestive system is not able to handle for some reason.

Factors that cause us to be intolerant of certain foods include genetics and stress. Unfortunately, it’s common to find you are intolerant of multiple foods once your gut health goes bad. This is because the body releases a protein called zonulin in response to foods that it’s not able to digest properly.

Zonulin increases the permeability of the cell layer that lines the intestines and prevents pathogens from passing into the bloodstream. When the gut becomes permeable or “leaky” dangerous compounds passes into the bloodstream. The result is inflammation, brain fog, immune activation, the development of allergies, lack of recovery from training, and metabolic problems.

What to do about it:

Identify foods you are intolerant of and avoid them like the plague.

Common foods that people are intolerant of due to genetics include gluten, wheat, tree nuts, peanuts, shellfish, lactose, eggs, and soy.

But, you can develop food intolerances to anything (even strawberries or coffee for example) and people with poor guts are more at risk of random intolerances because the gut will have been “leaking” for a while.

#3: Not effectively breaking down food before it hits the intestine

Your intestines don’t deal well with incompletely digested food. When large food particles hit your intestines, you aren’t getting the advantage of the nutrition, and you’re going to have digestive troubles.

Why does incompletely digested food make it out of the stomach?
Two reasons: You aren’t chewing enough and/or you have low stomach acid so that even if you are chewing, food is passing out of the stomach incompletely digested.

Low stomach acid is more common than people realize because it’s caused by aging, stress, and inflammation. It’s often misdiagnosed as too much stomach acid because when partly digested food starts to ferment, it will back up into the esophagus, and doctors commonly think this is acid reflux.

What to do about it:

Studies show you should be chewing each bite at least 15 times and maybe as much as 40 (seriously!) to properly breakdown food and get the greatest release of hunger-reducing hormones. Chances are, you need to work on your chewing skills.

Taking digestive enzymes can improve stomach acid and for many people this will solve the problem. However, low stomach acid could be due to low thyroid function, so if this is a possibility, it’s important to get your thyroid checked.

#4: Too much stress—both physical and mental

If you’re under a lot of stress, whether physical or mental, you’re going to have digestive issues. Stress raises cortisol and when cortisol is chronically elevated, it drives the release of histamine, a compound that jacks up your immune system.

Histamine also increases gastric acid secretion, leading to bloating and the release of other compounds that cause the gut to leak. It also triggers neurotransmitters that stimulate the central nervous system and raise your stress response.

Now, exercise that allows for adequate recovery is not a problem here—it can actually reduce cortisol and improve your stress hormone response by balancing it with better androgen release. But, too much training paired with lack of recovery due to “real” life stress can lead to chronically elevated cortisol.

In addition, the common solution for trainees who aren’t recovering, or are achy and sore, is to turn to ibuprofen or other NSAIDs. Don’t do it. A recent study found that when trained men took 800 mg of ibuprofen and then did a hard cycle workout, they had increased intestinal injury. Researchers conclude that using NSAIDs is not harmless and should be discouraged.

What to do about it:

If you have a highly stressful life, opt for two to four intense workouts a week (no longer than hour), preferably strength training, and focus on recovery—nutrition, sleep, hydration, deep breathing.

If you’re not too stressed out, more frequent workouts may be beneficial, but make sure exercise doesn’t become a chore.If you’re doing two-a-day workouts, only use them for a short period to accomplish a specific goal.
In all cases, take special care of your gut: Avoid drugs, NSAIDs, and get plenty of probiotics and high-quality nutrition.

#5: Eating the wrong foods before asking your body perform at a high level

There are some foods that you simply shouldn’t eat before asking for peak performance from your body. This is because when you start to train, digestion will slow as blood is diverted away from the gut to your working muscles. This can lead to cramping, discomfort, or digestive distress.

Here’s what to avoid before training:

  • Sports drinks that contain sugar in any form whether it’s high-fructose corn syrup, maltodextrin, or sucrose.
  • Foods that are high in fructose because they reduce the body’s use of fat for fuel and can cause problems in the gut during training. Fermentable fruits such as apples and pears are not ideal.
  • Foods that are fermented in the gut are generally not well tolerated during training. These include wheat, most grains, beans, and for some people, dairy.
  • Proteins that contain problematic nutrients such as beans, milk (whey protein is generally not a problem because high-quality sources will be lactose free), and fatty animal products.
  • Beans contain a type of carb called α-galactosides, which we don’t digest but the gut bacteria will. Therefore, when you eat them, you feed the beneficial gut bacteria, but you also may have gut issues in the process.
  • Milk contains lactose, which is not easily digested by some people.
  • Some animal protein sources like bacon, cheese, and fatty meats contain large amounts of saturated fat, which take a longer time to digest. But, if they suit you, go for it.


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