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    Home»Health»What Happens to Your Gut Health and Digestion When You Eat More Protein
    Health

    What Happens to Your Gut Health and Digestion When You Eat More Protein

    Justin M. LarsonBy Justin M. LarsonNovember 14, 2025No Comments4 Mins Read
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    Protein can affect your gut and digestion in many ways. While it promotes gut health, protein can also cause undesirable effects like gas and bloating.

    Eating protein can benefit your gut in the following ways: 

    • Promotes good gut bacteria: Your gut has a mix of microorganisms, like bacteria, which is collectively referred to as the microbiome. Evidence suggests protein, especially of plant sources, may promote an increase in beneficial butyrate-producing bacteria in the gut.
    • Helps in the release of good metabolites: Excess and undigested proteins in the large intestine can be converted into short-chain fatty acids (SCFAs). SCFAs are metabolites, substances that can sometimes benefit your gut. SCFAs can provide energy to colon cells, strengthen the gut barrier, boost metabolism, and may help lower inflammation.
    • Repairs your gut’s barrier: Your body breaks protein down into amino acids needed for tissue growth and repair. Essential amino acids can help repair the cells that line your gut, supporting your gut barrier.
    • Has anti-inflammatory effects: Amino acids like glutamine, glycine, and cysteine can help reduce gut inflammation by blocking proteins that promote inflammation, thereby helping improve digestive system conditions like inflammatory bowel disease (IBD).

    While protein can benefit the digestive system, there are some potential downsides to consider:

    • Plays a role in the release of bad metabolites: Not all metabolites are good. Undigested protein or the breakdown of certain amino acids can cause gut bacteria to produce harmful metabolites, such as ammonia and hydrogen sulfide. These metabolites can cause adverse effects on your gut layer and are linked to inflammatory disorders like diabetes, cancer, and obesity. 
    • Can transform your gut microbiome: Excess protein intake can disrupt your gut’s natural balance. It is linked to a decrease in the presence of helpful microbes like Bifidobacterium and Rothia and an increase in harmful bacteria such as Bacteroides fragilis, which tend to cause disease when the gut barrier is impaired. 
    • May increase infection risk: When there are more harmful bacteria in the gut than good, the microbiome gets imbalanced. This can make you prone to frequent infections. It can also result in loss of gut barrier function, which is linked to conditions like Parkinson’s disease, type 2 diabetes, and obesity.
    • May lead to gastrointestinal issues: Your body may not fully digest fiber from plant-based proteins, such as legumes. This can cause diarrhea and increased gas production, leading to bloating, especially when you don’t drink enough fluid. Additionally, people with protein intolerance may experience bloating, nausea, or stomach pain after consuming protein.

    Several factors can influence whether you will experience benefits, adverse effects, or both from eating protein:

    • Protein source: This is an important factor. Animal-based proteins, such as meat, fish, and eggs, provide essential amino acids in high amounts, which is good for the gut microbiota. But they are typically low in fiber, which is also vital for gut health. Plant-based proteins, on the other hand, typically contain fewer of the essential amino acids and cannot be completely digested because they contain fiber. Fiber from plant-based protein may help improve colon health, promote a more diverse microbiota, and improve the gut barrier.  
    • Processing method used: Different processing methods can impact protein properties, the way your body absorbs them, and the extent to which their nutrients can be broken down. Proteins processed into supplements, shakes, and bars may contain other ingredients, such as inulin and erythritol, which may be harder for your body to digest and may cause bloating and gas.
    • The amount you eat: Eating high amounts of protein can have both good and harmful effects, as excess undigested protein in the colon can be fermented into beneficial metabolites, such as SCFAs, or harmful metabolites, such as ammonia and sulfides.  

    When in doubt, consider consulting a healthcare professional, such as a registered dietitian, especially if you have a medical condition. They can help you make the right dietary choices for your individual needs. 



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