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How Does the Paleo Diet Affect Your Gut Microbiome?

How Does the Paleo Diet Affect Your Gut Microbiome?

How Does the Paleo Diet Affect Your Gut Microbiome?

The paleo diet, also known as the ‘caveman’ or ‘stone age’ diet, was developed with the purpose of returning humans to the fundamentals of eating. 

The essence of the paleo diet is to consume what ancestral hunter-gatherers ate over 10,000 years ago during the Paleolithic era. There is a high priority placed on eating whole, unprocessed, and high-protein foods.

Key health claims of this diet include substantial weight loss, increased glucose sensitivity, and improved overall health. However, it’s important to consider all positive and negative effects on the body and its essential systems, including the gut microbiome, before adopting a long-term paleo diet. 

What is the Paleo Diet and How Does it Work?

In the paleo diet, the whole foods that are eaten are meant to mirror foods consumed by early humans before the evolution of present-day agriculture.

By avoiding processed foods common in the Western diet, this paleolithic meal pattern claims to improve overall health with a high-protein, low-carb AMDR (Acceptable Macronutrient Distribution Range) distribution of calories.

Foods to avoid on this diet include those high in refined sugars and dairy, as well as processed foods, fatty meats, starchy vegetables, and legumes. Instead, you will consume unprocessed foods that are low in natural sugars.

Examples of such foods include the following: 

  • Lean meats
  • Seafood
  • Eggs
  • Non-starchy vegetables
  • Fresh foods
  • Nuts and seeds
  • Plant-based oils

Advantages of the paleo diet include protection against diseases and ailments of modern civilization, primarily obesity and its comorbidities. This high-protein diet stimulates weight loss via increased satiety and a reduction in hunger cues. It also supports heart health and blood sugar control.

But like most diets, paleo has potential risks. Not only is it very expensive and unsuitable for those with a vegan lifestyle, but this highly restrictive diet has several negative consequences. Most important of which are nutrient deficiencies of key vitamins and minerals. These micronutrients are essential for keeping the body and organ systems running properly, including the digestive system.

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The Paleo Diet and the Gut Microbiome

The paleo diet can greatly influence your digestive system's health and the gut microbiome in both positive and negative ways.

Utilize this high-protein diet for short to moderate periods of time has been shown to maintain a stable environment in the gut. Specifically, it supports healthy microbial competition and aids in modulating positive bacterial interactions.

However, using this restrictive diet for longer than one year has been connected to micronutrient deficiencies and alterations in the gut microbiome. It has also been connected to the increased growth of pathogenic bacteria in the gut. Ultimately, these negative effects in the gut may help contribute to the development of chronic illnesses.

Benefits of the Paleo Diet on the Gut Microbiome

Limits processed foods in the diet

Highly processed foods with large amounts of added sugars, sodium, and trans fats, as well as preservatives and other chemicals, are common in the Western diet. However, these foods stimulate chronic inflammation, causing damage to the gastrointestinal tract and reduce microbial diversity. They have also been shown to promote the growth of microbes in the gut that increase inflammation.

Consuming whole and unprocessed foods can eliminate these damaging additives from entering the body. In turn, the risk of developing damage and disease associated with your diet is minimized.

Minimizes free radical damage

The paleo diet promotes increased consumption of foods high in antioxidants, including fresh fruits, non-starchy vegetables, nuts, and unsaturated plant-based oils. Antioxidants protect cells from oxidation and free radical damage, which naturally occurs when your body breaks down food or is exposed to harmful substances.

Antioxidants proactively work against free radicals by ‘deactivating’ these molecules before they can cause cellular damage. This prevents chronic inflammation as well as age-related disease development.

Limits food known to cause gut sensitivity

Foods that contain gluten, wheat, and dairy are known to cause irritation in the gut for nearly 20% of the total population. The paleo diet eliminates many of these foods associated with common allergies and intolerances, which can reduce chronic inflammation of the gut. This minimizes stress in the intestinal tract related to diet and can reduce the development of gut diseases.

Negative Effects of the Paleo Diet on the Gut Microbiome

Micronutrient deficiencies

The total exclusion of specific food groups, like dairy and legumes, can cause essential vitamins and nutrients to go missing from the daily diet. The most common micronutrient deficiencies associated with a long-term paleo diet are calcium and vitamin D.

Missing these essential nutrients not only affects bone strength, but also the function of your gut bacteria. Calcium provides a prebiotic-like effect to feed bacteria in the gut, while vitamin D supports diversification of the microflora, which assists the body in hormone production and immune protection from pathogens.

Decreased gut microbiome diversity and richness

While a short-term paleo diet can contribute to a higher degree of microbiome biodiversity, this restrictive diet can cause several unfavorable changes to the composition of the gut microbiota when used for longer than one year.

Long-term paleo diets reduce the modulation of gut bacteria interactions and healthy competition amongst intestinal microbes, which promotes instability in your digestive ecosystem. The richness of microflora is also lost, which decreases the colonies of beneficial gut bacteria associated with fermenting carbohydrates and dietary fiber, such as Bifidobacterium and Roseburia.

Increased growth of pathogenic bacteria

Limiting certain food groups found in the paleo diet, such as whole wheats, grains, and legumes, decrease the richness and diversity of beneficial bacteria in the gut. A reduction of beneficial bacteria reduces how efficiently the digestive system can fight against pathogens, allowing colonies of harmful microbes to flourish in the intestines.

Reduced diversity gives rise to microbes like Hungatella in the digestive system, which produces high amounts of trimethylamine N-oxide, an organic compound that narrows the arteries and leads to the development of cardiovascular disease.

So, is Going Paleo a Good Idea for Your Gut Health?

Following a whole-food-based paleo diet for less than a year will most likely be harmless to the health of your gut and microbiome. However, the positive and negative consequences should be fully considered before adopting a paleo diet for longer than a year.

If you do decide that going paleo is right for you, you must be proactive about taking care of your gut microbiome. Fortify your intestinal ecosystem by consuming paleo-friendly foods that are high in fiber and micronutrients. This means prioritizing unprocessed vegetables, fresh fruits, nuts, and seeds. Also, consider adding high-quality supplements, like BIOHM's PrebioticProbiotic, or Super Greens, or Super Reds powder, to your daily routine. This can help to keep your microbiome rich and diversified, so that bacteria can function efficiently to keep your gut balanced.


About the Authors:

Dr Mahmoud Ghannoum, Ph.D, EMBA, FAAM, FIDSA is widely considered the leading microbiome researcher in the world. He is the scientist who named the mycobiome, and is the founder of BIOHM, the first company to engineer products and tests to address the total microbiome of both bacteria and fungi, allowing consumers to maintain total digestive health. Ghannoum is responsible for making the breakthrough discovery that bad bacteria and bad fungus work together to create digestive plaque (a discovery covered globally by outlets such as CBS News, Scientific American, Forbes and USA Today). During his career, he has published several books on fungus and over 400 peer-reviewed scientific papers. His work has been cited almost 24,000 times by other scientists, and Stanford University named him as one of the top 0.1% of most cited scientists over the last decade.

Allison Lansman, RDN, LD is a freelance writer and owner of The Freelance RD Nutrition Writing Services. She is passionate about creating exciting, research-based nutrition blog posts with her professional background as a dietitian. Allie prioritizes creating articles all readers can understand and incorporate into their daily lives. 

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