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Do you find yourself bloated and gassy after eating foods like chickpeas, lentils, garlic, onions, raw broccoli, or cauliflower? Have you noticed negative immune responses to plant foods, leaving you inflamed, sluggish, and dealing with unpleasant-smelling gas?
So, what’s actually going on here? The typical solution is an elimination diet, which often leads us to restrict a broad range of foods. Many end up on low-carbohydrate diets, focusing mainly on animal proteins and maybe a few leafy greens. Some go even further, choosing an all-meat, carnivore approach.
While these dietary changes may bring relief and even hint at healing, we should be careful not to conclude “all plants are bad” or “plants don’t work for me.” No culture in history has relied solely on meat year-round when plants were available. Instead, this is about balance. As omnivores, we are designed to eat a variety of foods, yet modern times have brought unique challenges with fiber digestion. Why?
It’s easy to label foods as “good” or “bad” based on how our body reacts to them. However, we must move beyond individual experiences or echo chambers to address root causes, grounded in scientific understanding. With the exception of highly processed, pesticide-laden, and refined foods—which might best be considered "food-like products”—many foods shouldn’t be dismissed outright.
To truly understand our digestive relationship with plants, we need to examine how we break down carbohydrates and fiber. The phrase “plants don’t work well for me” may imply a flaw in our genetics. But let’s be clear: our ancestors ate what was available. It wasn’t about avoiding certain foods; it was about survival.
This brings us back to our question: why are we struggling more than ever to digest plants? Many people, particularly in North America, are turning to keto and carnivore protocols to address digestive issues. While we could dive deep into the impact of pesticides, additives, and food processing, our focus here is on the bacterial genome—specifically, how the bacteria in our gut help break down plant fibers, support both our small and large intestines, and contribute to the production of short-chain fatty acids like butyrate.
This article sheds light on how our gut bacteria are central to digestion. To gain the full benefits of the food we eat, we need to remove dysbiotic bacteria and nurture beneficial strains, particularly the crucial Bifidobacteria.
Ultimately, our message is about BALANCE. Humans are seasonal eaters; we evolved to eat what was plentiful during different times of the year. In summer, we didn’t count carbs as we enjoyed berries, wild honey, and tubers. We used what was available with the least energy expenditure—it was simply survival, a balance of hunting and gathering.
To fully understand fiber digestion, we need to explore the micro-verse within us. Our microbiome houses billions of microorganisms, some beneficial (commensal) and others more parasitic. These bacteria are in constant communication—not only with each other but also with our mitochondria and even the human genome itself. They exert a vast genetic influence and, alongside our mitochondrial and human genomes, form one of the three key genomic systems within the body.
The bulk of our microbiome resides in the colon, where we find essential subspecies like Bifidobacteria. This bacterial genus is vital for producing B vitamins, activating longevity proteins (sirtuins), preventing pathogenic invasions, producing antioxidants, synthesizing conjugated linoleic acid (which promotes lean body mass), supporting immune function, and breaking down non-digestible carbohydrates (fiber).
Research underscores the powerful role of Bifidobacterium in gut health. Studies show that a decrease in Bifidobacterium species is linked with antibiotic-associated diarrhea, IBS, IBD, obesity, allergies, and other conditions. [1] Key functions of Bifidobacterium include B vitamin and antioxidant production, immune system maturation, gut barrier preservation, and protection against pathogens by lowering luminal pH and blocking harmful bacteria from adhering to the intestinal lining.[2]
Exploring bifidobacterial subspecies reveals immense healing potential, which is why Bifidobacteria is often considered our “master bacteria.” These bacteria reflect the true “processing power” of our microbiome, influencing not only digestion but also anti-aging processes, fat metabolism, and disease prevention.
Research reveals that our microbiome contains about 300 times more genes than the human genome, making each of us an ecosystem teeming with an estimated trillion microscopic organisms. [3] So, what does this mean for breaking down plant fibers?
Complex carbohydrates and fibers are primarily broken down by enzymes known as glycoside hydrolases (GHs), which hydrolyze glycosidic bonds in complex sugars. GHs are essentially the biochemical “power tools” for breaking down complex carbs. However, the human genome encodes only a small number of GHs—around 8 to 17 genes directly tied to carbohydrate digestion [4][5]. This means that many dietary fibers remain undigested until they reach the colon, where microbiota like Bifidobacteria step in to complete the digestive process.
When it comes to Bifidobacteria, research shows significant diversity in GH enzymes. For instance, B. scardovii has around 126 GH genes, while B. indicum has about 25 GH genes. Altogether, the bifidobacterial genome encompasses GH enzymes from 57 different GH families [6]. This vast enzymatic arsenal is central to fiber digestion, underscoring the critical role of our microbiome in handling plant matter.
This is why conditions like lactose intolerance can be reversible. While genetics play a role, we can train our microbiome to produce lactase enzymes, reactivating our ability to digest dairy through bacterial pathways. Similarly, optimizing our microbiome’s bacterial strains can help us better digest foods like beans, legumes, grains, and cruciferous vegetables. Without the right bacteria, our bodies may struggle to break down plants effectively. Rather than demonizing plants, the focus should be on nurturing a healthy, balanced microbiome.
When it comes to plant anti-nutrients—such as oxalates, histamines, and lectins—the problem isn’t these compounds themselves, but rather a lack of the right gut bacteria to break them down effectively. [7] Avoiding plants simply because they contain anti-nutrients doesn’t address the root cause. Our goal shouldn't be to eliminate these foods permanently, but rather to train our gut to digest them with ease once again.
Research reveals that high levels of Bifidobacteria in the gut can rapidly degrade oxalates, histamines, and lectins, especially as the immune system is rebalanced. Unfortunately, modern factors like pesticides, chemicals in water, refined foods, and antibiotics deplete Bifidobacteria populations. Restoring a healthy balance involves promoting Bifidobacteria with supportive elements like HMO prebiotics, resistant starch, polyphenols, and beta-glucans to name a few.
Avoiding certain foods indefinitely misses the point. Blaming specific foods for our issues distracts from addressing the underlying problem. The claim that “plants are toxic due to anti-nutrients and should be avoided in favor of only meat” is, in my view, an unproductive argument. Humans are seasonal eaters, and when I went through a phase of demonizing plants, I found myself struggling more. Restricting plants only increased my stress and led to no lasting solutions.
When we’re exposed to pesticides, overprescribed antibiotics, processed foods, and chemicals in our water, it’s no surprise that anti-nutrients may cause issues. All of these factors deplete the gut bacteria needed to break down compounds like oxalates [8]. Once I learned about the importance of the microbiome and the role of beneficial bacteria, I could finally let go of controlling every dietary input, which led to real progress.
This isn’t to say oxalates, histamines, and lectins are never problematic—they can be. But the real solution lies in restoring gut health. Improving levels of Bifidobacteria through HMOs and other prebiotics can make oxalate intolerance fade away. Demonizing plants, especially those that have nourished humans for millennia, only shifts focus from the true issue: the gut microbiome’s health. Pesticides, depleted soil, and disrupted gut bacteria—not plants themselves—are what make plant anti-nutrients problematic.
Many modern factors contribute to our depleted microbiomes, especially Bifidobacteria, a master bacteria crucial for degrading anti-nutrients. From birth, gut health can be impacted by factors like C-sections, lack of breastfeeding, antibiotic overuse, minimal exposure to diverse bacteria, and processed foods. These conditions can set the stage for a microbiome lacking resilience and diversity.
“At birth, levels of Bifidobacteria are at their highest, especially for babies born naturally. Lower levels are often seen in C-section births, and reduced Bifidobacteria has been associated with diseases like obesity, diabetes, and allergies. Solid foods further shape gut bacteria, leading to a stable adult microbiota.” [9] (Image source: Gut Bifidobacteria Populations in Human Health and Aging, Frontiers in Microbiology, August 2016)
I used to believe that plant lectins and other anti-nutrients were “bad” and that avoiding them would improve my health. But as my list of "foods to avoid" grew longer, I realized I wasn’t addressing the actual issue. My gut bacteria were out of balance, not the foods themselves. Whole foods aren’t simply “good” or “bad”; they’re context-dependent.
Interestingly, not all lectins are toxic. For example, chickpea lectins have been shown to inhibit breast cancer [10], legume lectins can help prevent cancer [11], and legume lectins have shown potential benefits in managing Type 2 diabetes and even supporting HIV treatment [12][13]. Some legume lectins have also been shown to kill cancer cells in mice. Properly cooking and cooling beans increases their resistant starch content, transforming them into a powerful gut and immune superfood.
So why do some people have adverse reactions to plant lectins? A compromised gut mucosal lining and insufficient Bifidobacteria levels are likely contributors. Bifidobacteria help maintain immune balance through a process called “immune exclusion,” where specific lectins are identified and managed. A helpful way to restore this balance is through Human Milk Oligosaccharides (HMOs), which bind to lectins, repopulate Bifidobacteria, and strengthen the gut lining. When Bifidobacteria levels are healthy, reactions to plant anti-nutrients significantly decrease. While there’s more to explore in terms of gut health, boosting Bifidobacteria with HMOs is an effective place to start.
To understand fiber digestion, let's begin in the large intestine, home to about 70% of our total microbiome. The large intestine is essential for breaking down indigestible food (chyme) and absorbing vital nutrients like vitamins, electrolytes, and minerals [14].
Our microbiome predominantly resides in the colon, housing trillions of bacteria that play essential roles in health. The sheer difference between bacterial counts—10^8 versus 10^11—indicates the colon’s significant bacterial load, with nearly 100 billion more bacteria than other gut regions. (Image source: “Bifidobacteria and Butyrate-Producing Colon Bacteria: Importance and Strategies for Their Stimulation in the Human Gut,” Frontiers in Microbiology, 2016) [14].
Colon cells, or “colonocytes,” play a crucial role in this ecosystem, and their main energy source is the short-chain fatty acid butyrate. Bacteria that digest non-digestible fibers produce butyrate along with other SCFAs (short-chain fatty acids) like acetate and propionate. Butyrate is essential for colonocyte energy and supports intestinal homeostasis through its anti-inflammatory properties, impacting processes like cell proliferation and gene expression [15].
Butyrate not only fuels colonocytes but also shapes a low-oxygen, acidic environment that is ideal for anaerobic bacteria, including beneficial Bifidobacteria. However, in an inflamed gut, butyrate transporters become impaired. Inflammatory markers such as TNF-alpha and IL-6 (linked with conditions like IBD) can block butyrate absorption, leaving colonocytes undernourished and the colon prone to higher oxygen levels, which favor aerobic (and often pathogenic) bacteria over beneficial anaerobes [15]. Reducing inflammation, targeting harmful bacteria, and promoting the growth of beneficial strains like Bifidobacteria become essential in restoring gut health.
Butyrate, a crucial short-chain fatty acid, is produced in the gut by bacteria and has extensive health benefits. There are two main pathways for butyrate production:
The acetate salvage pathway provides antioxidant support and maintains an ideal acidic balance in the colon. Without sufficient antioxidants, the colon can become overly alkaline—a condition linked to cancer risks. Ammonia, while useful for mucus production and epithelial cell proliferation in moderate amounts, can contribute to an over-alkalized environment if excessive and not balanced with antioxidants, as seen in diets focused solely on animal proteins.
By visualizing the different pathways, we can see that carbohydrate residues from plant-based fibers are essential for sustaining a balanced SCFA production, optimal colon health, and an acidic environment favorable to beneficial bacteria. (Image source: O'Keefe SJ. Diet, microorganisms and their metabolites, and colon cancer. Nature Reviews Gastroenterology & Hepatology, 2016) [16].
In sum, fiber fermentation provides a unique set of benefits that protein fermentation alone cannot, reinforcing the need for a balanced diet rich in plant fibers to maintain a healthy, low-oxygen, and acidic gut environment.
Different bacteria thrive in specific areas of the gut, and these areas are supported by varying pH levels along the digestive tract. As we move from the stomach through the intestines, the pH gradually changes, supporting different microbial populations. In the small intestine, pH shifts from around 6 to 7.4 as it reaches the ileum. It then drops to about 5.7 in the cecum, only to increase again through the colon, reaching 6.7 by the rectum [17].
A slightly acidic environment in the colon supports microbial balance. The common claim that the entire body needs to be alkaline is misleading. In reality, each area of the gut and body functions best at specific pH levels. Both acidic and alkaline foods have roles in our diet and support beneficial bacteria when balanced correctly. Our goal should be maintaining colonic homeostasis through a balanced diet that supports the right bacterial populations.
Image Source: Front. Pharmacol., April 2020, Volume 11 - "Advances in Oral Drug Delivery for Regional Targeting in the Gastrointestinal Tract.” [18]
In the proximal colon, for instance, a more acidic pH results from short-chain fatty acids produced during carbohydrate fermentation. With high meat intake, however, ammonia and hydrogen sulfide—byproducts known for their toxicity—can become problematic [19]. A diet heavy in animal protein can raise ammonia and hydrogen sulfide levels, which increase gut alkalinity over time, potentially contributing to colon cancer risk.
Studies show that high-protein diets increase fecal concentrations of amino acid-derived metabolites, such as branched-chain fatty acids, phenolic compounds, hydrogen sulfide, and ammonia. High ammonia levels raise pH in the large intestine, as seen in rats after just two days of a high-protein diet [19]. In humans, dietary changes that increase ammonia typically result in higher pH in the colon, especially the rectum. In contrast, non-digestible carbohydrates help lower fecal pH, underscoring the importance of including both plant fibers and animal proteins in our diet.
This evidence suggests that prolonged high-protein, low-fiber diets are not ideal. This isn't to criticize carnivore diets specifically but rather to emphasize the need for balance and seasonally varied eating. Animal proteins are healing and bioavailable, but the gut thrives on a combination of animal proteins and plant fibers. If digesting plants is currently challenging, this is a sign to address the root cause and improve gut resilience.
The small intestine’s lining consists primarily of cells known as enterocytes, which feature microvilli—finger-like projections that increase the surface area for nutrient absorption [20]. These enterocytes play a crucial role not only in nutrient absorption but also in maintaining gut integrity and immune function. They help regulate the gut lining and direct immune responses by identifying potentially harmful antigens. Supporting these cells with the right nutrients is essential for a robust immune defense.
When excess immune signals like TNF-alpha, IL-6, IL-1b, and IL-12 target the gut, enterocyte health can suffer, leading to conditions like Crohn’s disease and ulcerative colitis. To protect and nourish enterocytes, we need to ensure they’re getting their primary fuel: glutamine.
While the colon thrives on butyrate, enterocytes in the small intestine rely on glutamine as their primary fuel source. Glutamine is the most abundant non-essential amino acid in the body, but under stress, it becomes conditionally essential. As the preferred fuel for enterocytes, glutamine helps maintain their structure and function, particularly during times of stress [21].
Glutamine plays several roles in intestinal health, including supporting enterocyte proliferation, regulating tight junction proteins, suppressing inflammatory pathways, and protecting cells from apoptosis and stress. Under prolonged metabolic stress—from conditions like trauma, sepsis, or inflammatory bowel disease—glutamine supplementation has shown positive outcomes for gut health [22].
Research shows that glutamine absorption improves when taken with amino acids like glycine, arginine, and tryptophan. These combinations can significantly reduce inflammation associated with IBD and help stabilize glutamine availability for enterocyte support [23][24].
Meat—especially organic, wild-caught seafood, organic chicken, grass-fed beef, and organ meats—provides an ideal combination of glutamine, glycine, tryptophan, and arginine in a highly bioavailable form. These foods efficiently fuel the enterocytes of the small intestine, while plant fibers nourish the colon’s microbiome. Together, these sources support two essential functions of the gut, affirming our evolutionary omnivorous diet.
In summary, while plants provide fiber to fuel beneficial bacteria in the colon, animal proteins nourish the cells of the small intestine, creating a synergistic foundation for gut health.
Human Milk Oligosaccharides (HMOs) are specialized sugars naturally found in human breast milk and are known for their profound ability to support beneficial gut bacteria, especially Bifidobacteria. While infants receive these sugars naturally during breastfeeding, advancements in health science have made it possible to isolate and use HMOs in supplements, which can help adults, too, maintain a balanced and robust microbiome.
HMOs act as “bifidogenic” prebiotics, meaning they selectively fuel Bifidobacteria, the “master bacteria” in the gut. Bifidobacteria not only play a protective role by crowding out pathogens but also support other beneficial microbes through cross-feeding. When HMOs enter the digestive system, they pass through the stomach and small intestine without being digested, making their way to the colon, where they serve as a direct food source for Bifidobacteria. This process strengthens the gut lining by stimulating the gene FUT2 and MUC2, which promotes the production of mucins that reinforce the gut barrier and support immune defense [25].
For those with lactose intolerance, HMOs can even help in rebalancing the microbiome and restoring tolerance, as a healthier gut microbiome can improve digestion overall.
While HMOs set the stage for a healthy microbiome, maintaining robust Bifidobacteria levels long-term involves a diet rich in diverse plant fibers. These include polyphenols, cellulose, hemi-cellulose, beta-glucans, and inulin-type fructans—all essential for sustaining beneficial bacteria and supporting gut health.
By combining HMOs with these diverse plant fibers, we provide Bifidobacteria with a continuous source of nutrients to support the gut lining, improve immunity, and boost overall gut health. This strategic approach to gut health can protect against dysbiosis (an imbalance of gut microbes) and prevent infections, including C. difficile overgrowth.
A balanced diet abundant in prebiotic fibers creates an environment that sustains Bifidobacteria and promotes overall gut health. Whether you’re recovering from antibiotic use or looking to boost your microbiome resilience, a mix of HMOs and fiber-rich foods like apples, oats, berries, and leafy greens can nurture beneficial bacteria and help prevent infections.
Author: Brandon Moase, Nutritionist from The Nutritional Paradigm
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