Diet and the Gut Microbiome

by Dr. Haylee Nye

Did you know that changing from an animal-based diet to a plant-based diet can alter your gut microbiome in at little as 24 hours? What we eat can greatly change the state of our health, starting with shifting the microbiome. Studies have shown that bacterial diversity, or lack thereof, can either support the immune system or aggravate it. So, what kind of diet can give us the greatest chance at enhancing that microbiome and preventing issues like diabetes, autoimmune disease, and heart disease?


Majority of studies have found that protein consumption correlates with overall microbiome diversity. Pea protein has been found to increase short chain fatty acids (SCFA), which are considered anti-inflammatory and important in protecting the gut wall from damage. However, too much animal protein with a low carbohydrate diet is associated with increased risk of cardiovascular disease, cancer, and diabetes. Plant-derived proteins such as legumes, nuts, seeds, and vegetables are associated with better health outcomes.


A diet rich in saturated fat increases certain bacteria in the microbiome that activates the inflammatory signals in the immune system. This negatively effects insulin sensitivity and leads to increased risk of heart disease and other inflammatory diseases. On the other hand, a diet rich in unsaturated fats such as olive oil, avocado, salmon increases gut species such as lactobacillus and bifidobacteria, which fight inflammation and reduces risk for heart disease.


This macronutrient is the most well-studied for the ability to modify the gut microbiome. Carbs exists in two varieties: digestible and non-digestible or insoluble fiber.

Insoluble fiber is not absorbed in the small intestine, but travels to the large intestine and the good bacteria can feed on this fiber. Prebiotics are a kind of non-digestible fiber, which include soybeans, inulin, raw oats, and fructooligosaccharides (FOS), often found with probiotics. A diet low in fiber reduces SCFA production and bacterial abundance. A diet rich in whole grain increases fiber fermentation (SCFA), which leads to an increase in bifodobacteria and lactobacilli. This positive ‘gut reaction’ reduces inflammation and risk for diabetes and heart disease.

A note about artificial sweeteners

Artificial sweeteners have been shown alter the gut microbiome and induce glucose intolerance, also known as insulin resistance! Mice fed with saccharin (found in diet soda) had reduced lactobacillus species, while mice fed with real sugar increased lactobacillus. Due to these finding, artificial sweeteners are unhealthier to consume than natural sugars.


Fermented foods such as yogurt, sauerkraut (or other veggies), kimchi, miso, kefir, and natto increase good cholesterol, decrease triglycerides, decrease inflammation markers such as C-reactive protein (hsCRP), and improve insulin sensitivity. In addition, probiotic capsules that contain lactobacillus and bifidobacteria reduces pathogenic bacteria in the gut and can prevent traveler’s diarrhea. Specific high dose probiotic strains are used to treat inflammatory conditions such as Crohn’s Disease, ulcerative colitis, asthma, rheumatoid arthritis, and multiple sclerosis.


Many diets have been studied to evaluate to effect on the microbiome: omnivore, vegan, vegetarian, gluten-free, and Mediterranean. The consensus was that a reduction in polysaccharides, or insoluble fiber, reduces gut diversity and increases risk for disease. In addition, too much red meat can also reduce gut diversity. Research has concluded that the Mediterranean diet was the most beneficial at increasing SCFAs, the healthy fuel that feeds our gut wall and immune system.

“Mediterranean diet is highly regarded as a healthy balanced diet. It is distinguished by beneficial fatty acid profile that is rich in both monounsaturated and polyunsaturated fatty acids, high levels of polyphenols and other antioxidants, high intake of fiber, and other low glycemic carbohydrates, and relatively greater vegetable intake than animal protein intake. Specifically, olive oil, assorted fruits, vegetables, cereals, legumes, and nuts; moderate consumption of fish, poultry and red wine; and a lower intake of dairy products, red meat, processed meat and sweets characterize the traditional Mediterranean diet.”


The gut microbiome has a profound impact on our health. In the past decade, our gut microbes have been shown to play a large role in disease, including heart disease, diabetes, obesity, and mood disorders. The hopeful news is that we can modulate our microbiome in as little as 24 hours with right diet and supplementation. Increasing non-digestible fiber such as whole grains and vegetables will impact the good bacteria and allow the little bugs to thrive so we can thrive!


Singh, Rasnik K., et al. “Influence of diet on the gut microbiome and implications for human health.” Journal of Translational Medicine 15.1 (2017): 73.