• Allison Fahrenbach

Is Your Protein Intake Wrecking Your Gut Health

Updated: Jan 5

Diets high in protein (particularly meat) might be problematic in terms of gut health, especially when carbohydrate intake is low

Protein consumption is somewhat of a hot button topic. Many medical professionals warn about the potential danger of consuming a high protein diet, yet the popularity of high protein diets continues to prevail.

By now, most of you reading this know that I am someone who- as a coach, and someone living with UC- goes to the gut first. I always look at health with a gut focused approach.

So when it comes to protein consumption, especially high protein diets, I think it's incredibly important to take a look at the impact of excessively high protein consumption on gut health.


Because impaired gut health is impaired immune health. Impaired immune health opens the doorway for inflammation. And inflammation can be a barrier to your goals, whether weight loss, muscle gain, health or performance.

Before I get into why high protein diets can negatively impact the health of your gut, I think it’s important to discuss what protein is, why it is important, and what the recommended daily amounts of protein are.

Importance of Protein in the Diet

How and why is protein important? Protein is comprised of amino acids, which are the building blocks of tissues including muscles, hair, skin, blood vessels and nails. Protein plays a critical role in body mechanism; it is crucial for energy, for building and repairing muscle, to process nutrients and to enhance immune system function. Additionally, it is responsible for the production of enzymes and hormones that help the body to function properly. It is involved in almost every body function, from protecting against foreign particles to transporting important molecules.

Protein is essential to health, which is why it's important to make sure you get enough.

But how much protein is “enough?”

And can you eat “too much” protein?

In short, yes and yes, but the science surrounding how much protein you should eat is nothing short of contradicting. I'll go through the numbers in a moment, but my personal response when someone asks me how much protein they should consume always is "it depends."

Context is crucial when it comes to determining how much protein you should consume.

Everything from age, gender, activity level, health, total daily caloric intake, microbiome balance and digestive capability, as well as other variables can impact the amount of protein that's optimal for you.

In most cases, the recommended daily amount of protein for adults is calculated based on body weight. Protein intake can also be determined as a percentage of daily calories as well.

But for most adults with minimal physical activity, experts recommend consuming a minimum daily average of 0.8 grams of protein per kilogram (kg) of body weight. If you strength train consistently throughout the week then the recommendations change to 1.2 to 1.7 grams per kg of body weight each day.

Elderly populations have their own set of recommendations as well, anywhere from 1-1.3g per kg of body weight.

In general, most experts believe that healthy adults can safely tolerate eating 2g of protein per kg of body weight per day over the long term.

When it comes to how much protein is "too much", it really depends upon how much protein you can healthfully digest, not how much "harms the kidneys" which has been disproved here and here. It's been said that some people, including elite athletes, may be able to eat as much as 3.5 g per kg of body weight without any side effects.

Digested Protein vs. Undigested Protein

What do I mean by "how much protein you can healthfully digest"?

Well, when you take in protein beyond what your body individually needs to grow and repair tissue, it will be used as an energy source, as fuel.

The problem is that protein is not an ideal fuel. Protein molecules are large, and complex and their digestion requires more work then digesting fat or carbs.

What this means is that your digestive system is constantly overworked. This is why some people feel tired or lethargic on high protein diets.

(For more on protein digestion check out this and this.)

What happens with the excess protein your body doesn’t require? Well, protein is broken apart in the stomach by acid and gastric pepsin, further hydrolyzed by pancreatic proteases (enzymes), and then degraded in the small intestine where it is taken up into the bloodstream as individual amino acids, to be used by the body.

However, this process does not always work seamlessly.

For three distinct reasons, protein survives past the small intestine and enters the large intestine and/or colon, undigested.

Causes of Improper Protein Digestion

What are the three main reasons for improper protein digestion?

  1. High protein diets. The consumption of high protein diets leads to more protein escaping digestion. This additional protein will be transported to the large intestine.

  2. Low or impaired digestive capability (low proteolytic capacity), which increases the survival of intact proteins. (By low proteolytic capacity I mean the breakdown of proteins into smaller polypeptides or amino acids.) This could be due to myriad of factors, like low stomach acid, insufficient enzymes, etc.

  3. Consuming lots of difficult-to-digest proteins. Some proteins are hard to digest, further increasing the likelihood of the protein surviving (intact) past the small intestine. I'll get into this further down.

What happens when this undigested protein arrives in the colon?

Well, it ferments, causing the proliferation or colonization of bad bacteria. The bacteria in the colon will use the leftover undigested proteins and amino acids as an energy source. This results in several potentially harmful by-products being released into the gut lumen.

As undigested protein sits in the colon the microbes utilize the extra energy for resident protein fermentation (called putrefaction), harvesting bacterial species such as Clostridium perfringens, Desulfovibrio, Bacillus, and Staphylococcus.

These are considered bad bacteria.

The putrefaction of these microbial species produce metabolic byproducts such as ammonia, sulfides, phenols, indoles, and biogenic amines. These byproducts are what further contribute to degraded gut and colonic health.

They lead to reduced epithelial cell viability ( the cells ability to survive and work properly), which leads to: Increased intestinal permeability , DNA damage in cells, inflammation, and inhibited colonocyte cellular respiration and proliferation (repair/regrowth)

The overconsumption and/or indigestibility of protein leads to the production of putrefactive metabolites that may impair optimal gut health and function. All that fermenting protein can cause gas, bloating, constipation, motility dysfunction, and dysbiosis.

Okay, but how does this play into body composition or health goals?

Well, for starters, an inflamed gut is often the catalyst for ill health. Over 70% of your immune system is in your gut so if it’s overrun with inflammation, you are crippling your body’s immune health. And in no way does "leaky gut", or dysbiosis (a proliferation of bad bacteria), constipation, motility dysfunction or chronic inflammation set you up for success when it comes to losing weight or building and maintaining lean body mass.

All of the work you put in at the gym and in your diet will serve you much better if your protein intake is appropriate (not excessive), your digestion is optimal, and you’re limiting the low grade inflammation and the manifestation of bad bacteria in your body.

How to Improve Your Protein Digestion

So what can you do to optimize your protein digestion, and to ensure that the amount of protein you consume helps your body but not at the expense of damaged gut health?

1. Lower your protein intake. Take a moderate approach to protein and experiment to find what works for you. If you've been consuming an aggressively high protein diet for an extended period of time it can help to back off and give your body a break.

I personally cycle my protein intake across the week, and several times throughout the year I spend a few weeks consuming a consistently low protein intake.

I has not only benefited my digestion but also has improved my body's sensitivity to protein when I do consume a higher intake.

It is also worth mentioning that eating protein beyond what's needed for muscle protein synthesis does not accelerate muscle growth. I know a lot of bodybuilders or strength athletes eat well above and beyond their weight in protein a day in attempts to gain muscle. Excess calories from protein don't contribute to fat accumulation as easily as carbs or fats but they also don't increase the rate of muscle growth. The body has built in self limiting mechanisms, meaning there is no way to accelerate muscle gains faster then what your genetics allow unless you use steroids.

2. Consume easy to digest proteins. For example certain proteins- like red meat- are far harder on the digestive system then others. Fish and seafood for example, is much easier on the digestive system then mammal flesh so consuming less meat and rotating in some fish can help.

It can also help to add in some lower acid forming proteins such as tempeh or lentils, and incorporate some bioavailable plant sources of protein such as pea and rice.

Hydrolyzed whey is also easy to digest. So are eggs and egg whites.

Another easy tip is to combine protein with alkaline forming foods such as vegetables to make the protein easier for your body to digest.

3. Increase your fiber intake. Decreased intake of dietary carbohydrates and dietary fibers changes populations of gut bacteria and decreases the production of beneficial fermentation products such as the short chain fatty acid butyrate. High protein diets easily deplete the healthy flora in the gut if you fail to consume enough pre-biotics and fiber. There’s nothing for your healthy bacteria to thrive on.

Also, increasing fiber intake has been shown to decrease putrefaction in the colon. By adding additional fiber into a high protein diet, there’s evidence that the amount of harmful metabolites can be reduced.

4. Supplement with digestive enzymes if needed and make sure your stomach acid is not low. In order to properly digest protein your body needs sufficient stomach acid, or HCl (hydrochloric acid) and enzymes, which break down food.

If HCL is low, or if you have insufficient enzymes present, food doesn't break down properly, and will pass through the small intestine undigested.

5. Make relaxation a priority. Stress has been known to trigger heartburn, weak stomach acid, and therefore poor protein digestion.

Digestive troubles arise when stress hormones shut down the digestive tract. A surge of fight-or-flight hormones means that your stomach isn’t producing the acid it needs to turn on enzymes.

It also means that the small intestine has slowed down, allowing food to stagnate.

Prayer, a moment of mindful silence, or taking a few deep inhales and exhales are simple ways to create the shift prior to eating that the body needs to set stress aside and prepare for digestion.

Turn off the television. Avoid eating in your car or while standing. As much as possible, give yourself time to sit, eat slowly and enjoy your food.

6. Prepare protein properly to increase digestibility and avoid oxidization. The type of protein you eat matters, but so does how you cook and/or prepare it.

Overall, moderate temperatures and short heating times increase digestibility. On the other hand high temperatures and long heating times result in chemical changes that make proteins insoluble, reducing digestibility. So to increase the digestibility of your protein heat protein sources enough to lightly cook them (ensuring they’re “done”) but do not overcook or oxidize. Or you can cook them “low and slow”, like in a crockpot.

Fermentation processes of nearly all protein sources improves the overall digestibility of the protein, so consider occasionally rotating your normal protein sources with proteins that have been fermented, such as miso and tempeh (fermented soybeans), kefir, and/or a fermented vegan protein powder.

If you are ready to explore what protein sources are best for your body, or if you need help figuring out how much protein is best for you, and your goals, I'd love to help! Learn more here!

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