Microbial Diversity! You’ve probably heard the term, but what does it mean and how important is it, really? Well, if your health matters, this topic should matter as well.

The gut plays a significant role in our immune system and overall health. In fact, much of our immunity resides in or derives from our gut. Estimates suggest that up to 70-80% of the body’s immune body is located in the gut-associated lymphoid tissue (GALT), which includes structures like the gut-associated lymphoid follicles, Peyer’s patches, mesenteric lymph nodes, and so on.

The question is, “Why our gut?” To answer that, we need to think about what is in our gut. The answer to that is lots of bacteria and other microbes. They exist in something that we call our microbiome (a community of microorganisms (such as bacteria, fungi, and viruses) that inhabit a particular environment).

The gut microbiome, which is comprised of trillions of microorganisms, interacts closely with the immune system, influencing its development, function, and response to pathogens. However, problems typically arise when diversity is hindered or compromised by factors such as poor diet, excessive use of antibiotics, chronic stress, lack of physical activity, and insufficient sleep – pretty much everything that makes up a modern existence. The thing to keep in mind is that when diversity is high, and the microbiome is robust, we are generally healthier and get numerous immune system benefits. For example…

Immune Regulation: The gut microbiome helps regulate the immune system by promoting the development of immune cells and maintaining a balance between pro-inflammatory and anti-inflammatory responses. Certain beneficial bacteria produce short-chain fatty acids (SCFAs), which have anti-inflammatory effects and help regulate immune cell activity.

Pathogen Exclusion: A diverse microbiome competes with harmful pathogens for resources and space within the gut, helping prevent the colonization and proliferation of pathogenic bacteria and viruses. This competitive exclusion mechanism helps protect us against infections and maintain gut barrier integrity.

Tolerance Development: Exposure to diverse microbial species early in life helps train the immune system to distinguish between harmless antigens and harmful pathogens. This process, known as immune tolerance, is crucial for preventing inappropriate immune responses, such as allergies and autoimmune diseases.

Production of Immunomodulatory Molecules: Some gut bacteria produce immunomodulatory molecules, such as polysaccharides and metabolites, that can directly influence immune cell function and signaling pathways. These molecules can help regulate immune responses and maintain immune homeostasis.

Enhanced Antimicrobial Defense: Certain beneficial bacteria in the gut produce antimicrobial peptides and other compounds that help defend against invading pathogens. The gut microbiome’s defense mechanisms are strengthened, further supporting immune function.

Sounds awesome, right? But what does all that really mean? Well, it means that when it comes to digestive health, the gut microbiome reigns supreme as a vital player in our immune function. In fact, research has repeatedly shown that a rich and diverse microbiome is associated with numerous health benefits, and this includes reduced inflammation, improved digestion, and even protection against chronic diseases such as obesity, diabetes, and autoimmune disorders. However, while all of that sounds great, the problem is that plenty of things in our modern world keep diversity low.

An Often Overlooked Issue

Indeed, achieving and maintaining microbial diversity can be challenging. This is especially true when considering dietary factors that help or hurt the delicate balance of gut bacteria. For example, one often overlooked factor is the presence of anti-nutrients. Many are simply unaware that these compounds can interfere with nutrient absorption and digestion and potentially cause inflammation and gut irritation. Most of that spells bad news for our gut and, by extension, ourselves.

Granted, some will argue the merits of moderation regarding their consumption. However, when considering our physiology, we must remember that we cannot and should not eat everything that is presented to us. In particular, numerous vegetables and grains are known to contain higher levels of anti-nutrients such as lectins, phytates, and oxalates. These are typically not good, and we discover new issues about these all the time. Similarly, refined carbohydrates, which are typically grains, tend to feed bad bacteria, which isn’t good no matter how you cut it.

And while we now know that anti-nutrients hinder or block the uptake of certain nutrients, what is often overlooked in this discussion is that they also impair gut health and exacerbate existing digestive issues. Hence, I would argue that avoiding such compounds might be a good idea, especially for healing and rebalancing the microbiome of individuals with inflamed or otherwise compromised guts (most people). The clues are there, and I can prove it.

Imagine getting intestinal surgery. Your gut would be temporarily compromised as it tried to heal. So, what would a nutritionally competent surgeon recommend in this situation? According to science, a strong recommendation includes the avoidance of vegetables after intestinal surgeries or when managing bowel dysfunction because these foods have the potential to interfere with the healing process. And that should make sense if you think about it. But is it possible that the same holds true for the rest of us who are also trying to heal our gut from a lifestyle that results in inflamed or otherwise compromised intestines?

Let me pose this another way. If someone asked you whether or not you would like to eat something that is not conducive to healing, can inflame your guts, and is likely to either hinder or block the uptake of vital nutrients, would you eat it? We should probably act accordingly.

The good news is that you’re not missing out on anything if you choose this path – other than the bad stuff, of course. By focusing on a diet rich in animal products and fruits, we can provide ourselves ample nourishment while minimizing exposure to anti-nutrients or inflammation. The truth is that animal products offer an abundance of high-quality protein and essential nutrients without the potential irritants, and fruits provide us with a wealth of vitamins, minerals, antioxidants, and prebiotic fibers that support gut health and promote microbial diversity.

It seems to me that if we avoid harsh, inflammatory, and somewhat toxic foods, we can nourish our gut microbiome back to health while reducing the risk of inflammation and digestive discomfort. Of course, you also avoid nitrate accumulation and heavy metal absorption to a large degree, but that’s probably a different article. And granted, food isn’t the whole picture. In addition to choosing foods that support gut health, it’s also essential to be mindful of overall dietary habits and lifestyle factors that can influence the microbiome. Of course, I should also mention that stress management, adequate sleep, regular exercise, and proper hydration are all critical components of a holistic approach to gut health. Act accordingly.

However, at the end of the day, we need to understand that embracing microbial diversity through dietary choices and lifestyle habits is paramount for maintaining optimal gut health and overall well-being. Logically and physiologically speaking, by prioritizing nutrient-dense foods such as animal products and fruits while avoiding harsh anti-nutrients, we can cultivate a thriving gut ecosystem that supports digestion, immunity, and vitality.

Now, if you have followed my work, you may be familiar with “Nature’s Intent.” This nutritional philosophy advocates for a physiologically sound diet rooted in the principles of true omnivorous selection. However, I want you to ask yourself why omnivorous foods are constantly being demonized in the mainstream. Similarly, I want you to ask yourself whether such a diet can really provide the gut-nourishing foods that we need for a healthy and microbial-diverse gut.

Let’s break it down and simplify! What really nourishes our gut? Generally speaking, we need an abundance of fatty acids, probiotics, and prebiotics. Of course, it might also be wise to include plenty of protein, polyphenols, amino acids, vitamins, and minerals such as D, A, Zinc, Magnesium, and plenty of healthy fats. So, where do we get these nutrients in abundance? Let’s take a look!

Animal Products:

• Grass-fed Beef: Contains beneficial nutrients and fatty acids that support gut health.
• Pasture-raised Chicken and Turkey: These are typically high-quality protein sources without the potential anti-nutrient content found in some plant-based proteins.
• Wild-caught Fish: Salmon, mackerel, sardines, and trout are rich in omega-3 fatty acids, which are linked to a healthy gut microbiome.
• Pasture-raised Eggs: Excellent sources of protein and essential nutrients like choline, which support gut health.
• Full-fat Yogurt & Kefir: Yogurt and Kefir are awesome! Choose varieties with live and active cultures for probiotic benefits.
• Grass-fed Cheese: Provides beneficial probiotics and nutrients like calcium.
  
• NOTE: Animal products are naturally rich in essential vitamins and minerals such as D, A, Zinc, and Magnesium. More importantly, they are typically more bioavailable than other sources.

Fruits:

• Berries: Blueberries, strawberries, raspberries, and blackberries are rich in antioxidants and prebiotics such as polyphenols, fructooligosaccharides (FOS), and pectin.
• Apples: Packed with pectin, polyphenols, and fructooligosaccharides (FOS).
• Bananas: Rich in prebiotic fiber (fructooligosaccharides (FOS) and inulin), especially in slightly green bananas.
• Oranges: High in vitamin C, pectin, and polyphenols.
• Mangoes: Provide vitamins, minerals, enzymes, polyphenols, and pectin.
• Pineapple: Aside from fructooligosaccharides (FOS), these contain bromelain, an enzyme that supports digestion and various other functions.
• Papaya: Papaya contains an enzyme called papain, which helps break down proteins and aids in digestion, making it particularly useful for relieving digestive discomfort and improving nutrient absorption. It’s also filled with prebiotic fibers as well.
• Avocado: Rich in monounsaturated fats and fiber that supports a healthy gut microbiome. Although they are not typically classified as traditional prebiotics, they are actually a bit of a powerhouse on multiple fronts.
• Etc.: the list goes on and on.
  
• NOTE: a prebiotic is a type of non-digestible fiber that selectively stimulates the growth and activity of beneficial bacteria in the gut, thereby promoting overall gut health.

Other Foods:

• Coconut: Coconut products like coconut oil, coconut milk, and shredded coconut contain medium-chain triglycerides (MCTs) that support gut health in various ways.
• Nuts and Seeds: Almonds, walnuts, chia seeds, and flaxseeds provide healthy fats, fiber, and protein.
• Etc.

Beverages:

• Herbal Teas: Chamomile, peppermint, and ginger teas are soothing to the digestive system.
• Coffee: Coffee beans are actually the seeds of a fruit (drupe). Coffee stimulates the muscles in the digestive tract, promoting peristalsis, which can help prevent constipation and support regular bowel movements. It can also increase the production of gastric acid in the stomach, aiding in the breakdown of food and enhancing the digestive process. Best of all, coffee is rich in polyphenols, which can support the growth of beneficial gut bacteria and contribute to overall gut health.
• Water: Of course, stay hydrated with plain water throughout the day to support overall health and digestion.

So, as you can see, by incorporating these animal products, fruits, and other foods into your diet, you absolutely can promote a diverse and healthy gut microbiome while also avoiding the question marks regarding harsh anti-nutrient vegetables. Just remember to focus on whole, minimally processed foods and listen to your body’s signals to determine what works best for you. If you want to learn more about the true omnivorous lifestyle and why it’s so beneficial for so many, I would encourage you to read “Nature’s Intent.”

Dr. Robertson is a health researcher and educator, not a physician. The information provided here is not medical advice, a professional diagnosis, opinion, treatment, or service to you or any other individual. The information provided is for educational and anecdotal purposes only and is not a substitute for medical or professional care. You should not use the information in place of a visit, call consultation, or the advice of your physician or other healthcare providers. Dr. Robertson is not liable or responsible for any advice, course of treatment, diagnosis, or additional information, services, or product you obtain or utilize. IF YOU BELIEVE YOU HAVE A MEDICAL EMERGENCY, YOU SHOULD IMMEDIATELY CALL 911 OR YOUR PHYSICIAN.