Research has indicated that plant-based diets can cause shifts in the composition of the microbiome and have beneficial effects on gut health. In turn, this can lead to a lower risk of pathological conditions and diseases. 

The gut microbiome is the collection of all microbes in the colon, including bacteria, fungi, protozoa and viruses. These organisms have unique relationships with their hosts. Recent research has indicated that the microbiome plays a large role in human health – including disease prevention, digestion and neural function. 

“The microbiome is not only a direct determinant of gut health, but also the health of our skin and other organ systems,” said Dr. Rasnik Singh, a dermatology chief resident at Henry Ford Hospital and author of a review discussing the influence of diet on the microbiome and implications for human health. “Increasing evidence suggests that we really are what we eat.”

Studies have suggested that plant-based diets increase the diversity of the microbiome. Having a diverse microbiome has been said to make the gut more resilient and capable of protecting against foreign pathogens. 

Different species of microbes occupy unique niches and perform distinctive functions; for example, Bacteroides fragilis is capable of activating very specific immune responses that play important roles in the development and regulation of the immune system.

Because these microbiotas each have their own roles, there is not enough room for invading bacteria to compete and survive. A less diverse microbiome allows for invading species to occupy open niches within the microbiome and potentially cause disease.

“A diverse microbiota is crucial for optimal health. In fact, studies have shown that decreases in microbial diversity is associated with obesity, type 2 diabetes, and other systemic inflammatory conditions,” Singh said. 

A 2012 study found a positive association between microbial diversity and fruit and vegetable intake. Similarly, researchers found there to be a negative correlation between microbial diversity and body mass index. 

Vegan and vegetarian diets, which are high in fiber, are known to lower the abundance of certain disease-causing organisms.

For example, studies have shown that the quantity of Enterobacteriaceae, a family of pathogenic and inflammatory bacteria, is lower in plant-based diets than omnivorous diets. The high fiber in vegan and vegetarian diets decreases the pH in the colon, which makes it more difficult for Enterobacteriaceae to survive, thus reducing the risk of disease. 

Another important marker of gut health is the Firmicutes to Bacteroidetes ratio. Firmicutes and Bacteroidetes are the most dominant groups within the gut microbiome, accounting for about 90% of the total microbial count. This ratio is important because it can indicate several pathological conditions, namely obesity. 

In obese individuals, the relative proportion of Firmicutes to Bacteroidetes was increased compared with those with a normal BMI. 

One 2010 study compared the diets of children in Burkina Faso to the diets of children in Italy in order to determine the effect of diet on gut health. The Italian children typically consumed a diet that was high in animal protein, sugar, starch and fat, and low in fiber, while the typical diet of children in Burkina Faso was characterized by a diet low in fat and animal protein and rich in starch, fiber and plant protein.The study concluded that the more plant-based diets of the children in Burkina Faso was associated with increased counts of Bacteroidetes, which may help prevent obesity.

“Plant-based diets seem to encourage the growth of beneficial bacteria…which in turn impacts the relative abundance of important gut substrates such as short-chain fatty acids,” Singh said.  

Diet is also known to affect the enterotypes of the microbiome. Enterotypes are clusters of bacterial communities in the gut that allow researchers to identify common microbial traits amongst people. There are three main enterotypes observed in human microbiomes: Prevotella, Bacteroides and Ruminococcus. 

Several studies have shown that Prevotella is significantly richer in vegan and vegetarian diets than omnivorous diets. In mice, increased levels of Prevotella are associated with improved glucose metabolism, however, not enough research has been conducted on humans to confirm that it has the same effect.

Bacteroides, on the other hand, are shown to be more abundant in diets that are rich in animal protein. Bacteroides can be pathogenic (disease-causing) and promote inflammation. However, they can also be beneficial to the human host, playing a role in carbohydrate metabolism and intestinal bacteria nutrition.

Ruminococcus is the third main enterotype and is associated with long-term fruit and vegetable consumption. These organisms specialize in breaking down complex carbohydrates and are known to lower arterial stiffness, which can affect cardiac performance and is associated with an increased risk of cardiovascular diseases.  

Studies have shown that diets high in animal protein may increase the chance of developing cardiovascular diseases by influencing the gut microbiome. When someone consumes red meat, their body produces a substance called trimethylamine-N-oxide (TMAO) through several metabolic pathways within the intestinal microbiome. TMAO has been shown to promote atherosclerosis, a disease of the arteries characterized by the buildup of fat on their inner walls.

Vegans and vegetarians are much less likely to produce TMAO through these microbiotic pathways, which in turn prevents risk of atherosclerosis. 

Vegan gut microbiota may also protect against inflammatory diseases according to several studies. One study found that four specific fecal enzymes, associated with toxic and inflammatory products were decreased amongst those who adhered to a plant-based diet compared to those who adhered to a more omnivorous diet. Similarly, there is a negative correlation between vegan gut microbiota and hyperthyroidism.

“A balanced plant-based diet may be most beneficial for gut health in their association with probiotics, antioxidants, and healthy gut substrates,” Singh said.

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