Digestion & Building Lean Muscle

by Dr. David Minkoff March 21, 2023 7 min read

Athletic Woman climbing rope while using PerfectAmino

Your digestive tract’s ability to fully digest and absorb protein determines, in large part, your body's ability to build muscle and lose body fat.

When protein isn’t properly digested, this triggers a sequence of actions, involving our immune system, which leads to inflammation in the body and higher levels of cortisol, the hormone that prevents fat loss and breaks down muscle.

But also, without full digestion, our body receives less of the protein we consume in a form it can actually use.

So we get less protein for muscle, properly balanced hormones, and overall health and energy, while at the same time we’re eating more of it that goes to waste.

Beyond this, improper digestion leads to not only heart burn, acid reflux, GERD, and gas and bloating, but also allows for harmful bacteria, parasites, and fungi to take root, further causing us trouble.

Understanding exactly how digestion works then, and how to keep it, or get it working properly, is very important.


When you consume food, you chew it, swallow it, and it goes into your stomach.

Here we see mostly protein digestion, with fats and carbs mainly digested in the small intestine.

When protein makes its way into your stomach, it releases two main things: hydrochloric acid, or stomach acid, and an enzyme called pepsin.

This stomach acid does a few things: it helps break down proteins and minerals necessary for later protein synthesis in the body; and it kills bacteria, fungi, parasites, and viruses coming in with your food and water.

Now, this protein you ate is made of hundreds or thousands of individual amino acids, all bonded together in long chains like a beaded thread, and then coiled up like a rope, with the coils also bonded together to hold it all together as a "protein."

So first, the stomach acid breaks the bonds holding the coils together, so now it’s one long chain. Then the pepsin starts breaking the bonds that hold the overall chain together. It doesn’t break all of them, but it breaks most.

Then, by the end of this, instead of each protein molecule being a long chain of hundreds or thousands of amino acids, it’s now broken up into many much smaller chains of maybe 20 to 40 amino acids each.

While this is happening, the level of stomach acid is also rising. And by the time these amino acid chains are broken up, the stomach acid should have reached a pH level of about 1 or 2 — very acidic. The stomach can handle this level of acid because of a mucous lining it has along its walls.

But it needs to get to a pH of 1 or 2 because this is the trigger that signals the valve between the stomach and small intestine to open and let the food through.

If the stomach acid didn’t get this acidic, then the food would stay in the stomach much longer and go rancid. Then it would start bubbling up and burn the esophagus, which isn’t made to handle this acid. This is heartburn and acid reflux, when there’s not enough stomach acid, not when there’s too much.

So we want it very acidic. If it’s not, then you get heartburn, but also, you get proteins that aren’t broken down enough. 

From here, the food moves into the small intestine where more enzymes come in, further breaking these short amino acid chains up until they’re individual, free-floating — no more beaded threads, just beads.

Other enzymes also start breaking down the fats and carbohydrates, and all of these broken down pieces start moving through the intestinal wall, into blood vessels that take them to the liver.

The liver then filters all of this, looking for any toxins, which it tags so the kidneys know to get rid of them, and then lets it all out into the bloodstream.

But this protein breakdown is important here. The amino acid chains must be fully broken down into individual amino acids for a few reasons.

First, if they are fully broken down, then the body can use them to build new proteins and collagen in the forms it needs for muscle, bone, hormones, enzymes, etc.

If they’re not fully broken down, the body can’t use them at all.

In this case, they continue through the digestive system and leave the body as waste, or they’re absorbed into the bloodstream and cause inflammation in the body.

This is because of those bacteria, fungi, parasites, and viruses I mentioned coming in with your food, also known as foreign invaders — because they are your enemy.


Your small intestine is surrounded by three walls.

The first is an inner lining about one cell in thickness, which sees the broken down nutrients and lets them through.

The third wall is all the blood vessels surrounding the intestine, which take these nutrients to the liver.

But the second wall, between these two, is made of immune tissue. Lymph tissue, to be exact.

This is why you’ve heard that about 80% of your immune system is in your gut. 

When food comes into the small intestine, this lymph tissue sends out immune cells to check for any foreign invaders. And when the immune cells find some, they send antibodies to surround and destroy them.

This is an immune response. And there’s always some inflammation during an immune response.

So if there were a lot of bacteria, as in salmonella poisoning, you might get a bellyache as an immune response.

But your Immune cells have a very exact way of knowing what is a foreign invader, and what’s not.

These bacteria, fungi, viruses, and parasites have protein coatings on them. Protein shells.

But any protein the body needs is already broken down into individual amino acids at this point, right? So the immune cells see these whole protein structures (bacteria, parasites, etc.) and know they must be foreign invaders.

So the antibodies either attack and kill these invaders, or some may make it into the bloodstream , in which case they land somewhere in the body and the immune cells go there to kill them.

And when this happens we feel inflammation at the spot where they landed due to the immune response.

But the immune cells also remember the exact protein structure of these invaders, so they remember them for the future.

They do this so they don’t mistake the bodys own protein structures for harmful bacteria, and attack them (that’s what an auto-immune disease is — when the body mistakes itself for harmful invaders and attacks itself).

But look at this... if your digestive system didn’t fully break down all your protein into individual amino acids… and some of the partial amino acid chains got out into the bloodstream… it knows they aren’t individual aminos or bodily protein structures, and so assumes they’re harmful bacteria.

So they launch an immune response — against partially broken down proteins.

And immune responses cause inflammation.

Now, if this happens on a daily basis, because you have too little stomach acid, then these partially broken down proteins are continually being released into the bloodstream, causing a continually created inflammation in the body wherever these partial proteins land.

This then creates an extra load on your immune system, which is needed for muscle building and overall health.

And the raised levels of inflammation mean increased levels of cortisol. 

Also, if we have too little stomach acid, harmful bacteria continually make their way into our small intestine without being killed in the stomach.

Here they can take root and grow. It’s not acidic, it’s dark and it’s warm.

They start to consume some of the food you eat.

What do they give you in return? Gas and bloating, as well as bio-toxins that further fuel immune responses, increasing inflammation and cortisol.

But now, not only are you losing some of the protein you ate due to it not being fully broken down… you’re also losing it to these bacteria who eat some of it, and to cortisol released due to inflammation, which breaks down muscle and increases fat storage.

This may seem small.

It's not.

It affects our hormones, energy levels, hunger cravings, ability to recover, mood, and our ability to gain and lose muscle and fat.

If we don’t get all the food that we’re consuming because it’s not broken down enough, or it’s being consumed by bacteria and parasites, then we’ll still be hungry even if we eat a lot.

We’ll have cravings created by these bad bacteria, especially for fast-acting sugar, which can raise fat storage, and we’ll have less amino acids for building muscle, making hormones that direct our body to build muscle, and for enzymes that break down our fat.

These chemicals are made, perform their function, and are then gone. They need to be constantly replaced inside the body.

So we need these proteins fully broken down and we need these bacteria killed off.

This is one reason PerfectAmino is so effective. It’s already fully broken down so that, no matter the state of your digestive tract, you’re getting all of that protein, and without the trouble caused by partial proteins.

Most people have some degree of reduced digestive acid these days. In fact, it’s one of the largest causes of muscle loss as we get older — lowered digestive ability.

If you experience indigestion, heartburn, GERD, or gas and bloating, beyond taking PerfectAmino, I highly recommend you get our Digestive Enzymes to ensure your body is fully breaking down proteins, killing harmful bacteria, and giving your body what it needs to function and thrive.

And if you’re doing a lean bulk, trying to consume high amounts of whole protein, it becomes necessary.

I know that was long, and we touched on several points, but it truly is key to just about every aspect of health in your body.

I hope it helps.

*These statements have not been evaluated by the Food and Drug Administration. These products are not intended to diagnose, treat, cure, or prevent any disease.