A new study, published in the European Journal of Clinical Nutrition, demonstrated a connection between diet, and stool pH and bacterial levels in adults.1 The researchers studied stool samples from vegetarians, vegans, and omnivores. They found lower levels of potentially pathogenic bacteria, like E. coli, in people consuming the vegan or vegetarian diets. What they also found, in conjunction, was a decrease in stool pH level with decreases in consumption of animal proteins. Those on the omnivore diet had a stool pH of 6.9; those on the vegetarian diet (which included dairy and eggs) had a stool pH of 6.6; and those on a vegan diet (no animal proteins) had a stool pH of 6.3.

The higher pH in the omnivore diet is explained in part by an increase in the production of alkaline metabolites by enhanced growth of the protein-digesting putrefactive bacteria in the gut. That’s right—a diet high in animal protein promotes increased putrefying activity of gut bacteria, raising the pH of stool and making products like putracene, cadaverine, and nitrosamine, which could lead to colon cancer. Diets lower in animal protein and—this is key—higher in fiber promote gut bacterial activity that produces more acid via production of the beneficial short-chain fatty acids (SCFAs) butyrate, propionate, and acetate, promoting a more acidic environment in the gut.

The change in pH levels explains why potentially pathogenic bacteria were increased in the higher pH (more alkaline) stools of people consuming an omnivorous diet. Lower pH ranges do not support the growth of potential pathogens, which thrive in the higher pH range over 6.5.2,3 So I say, stay alive under 6.5!

Here is a major point. The lower pH may be mainly a biomarker indicating the production of the SCFAs, particularly butyrate. Butyrate is a major fuel for the colonocytes, and is critical for optimum colon health. Butyrate also affects nuclear transcription in a positive way. In other words, when colonic cells are under attack from absorption of free radicals from fecal material (more likely to happen with chronic constipation), the nucleus, under stress, sends a message to the cell: either commit suicide (apoptosis) or produce more damaged cells (cancer).  Butyrate is more likely to promote apoptosis, preventing cancerous cells and allowing new cells to come in and maintain a healthy colon lining.

However, we must always remember everything is a question of balance.  All of the SCFAs including butyrate come from the fermentation of soluble fiber from plants by commensal bacteria. Too much fermentation with too low of a pH (or too much acid) can damage the colonic lining creating increased permeability problems leading to numerous problems including immune imbalances which can have total body effects.

The researchers also found a decrease in levels of Bifidobacteria and Bacteroides in the people on a vegan diet. This is in contrast to other studies that have found increases in Bifidobacteria, and seems an anomalous finding, since high-fiber diets support the growth of Bifidobacteria, while suppressing the growth of potential pathogens. Perhaps a closer look at the diets would be in order. Many vegetarians and vegans eat high amounts of refined carbohydrates, and too much fats and oils which do not promote healthy Bifidobacteria levels.

The researchers state, “In addition to age, gender and diet, factors such as microbial interaction, food transit through different intestinal compartments with different bacterial colonization density, availability of nutrients, colonic supply, sulphate and bile acids, and bacterial adaptation may all be involved in the composition and activity of colonic microflora. This may help in understanding the lower abundance of Bifidobacteria and Bacteroides species in vegans and vegetarians, which was not linked to stool pH.”

At any rate, all diets—vegan, vegetarian, and omnivore—will benefit by adding probiotic-rich foods along with supplements to help replenish levels of the beneficial Bifidobacteria and Lactobacilli. These bacteria, along with a high-fiber diet high in vegetables and fruits, help to lower the pH in the intestines by producing the nourishing SCFAs.

Incidentally, this topic can confuse the message of the benefits of a high-alkaline diet. You may have heard that a diet high in animal protein, sugar, and refined carbohydrates creates acidity in the body. Yes, these foods do lower urine and salivary pH levels, which are thought to be associated with bone mineralization, a process that helps neutralize acidity by pulling alkaline minerals from bone.  Chronic low grade acidity (metabolic acidosis) also causes excess loss of calcium, magnesium and potassium in the urine. Diets high in vegetables and fruits, on the other hand, produce more alkaline urine and saliva levels, which is associated with reduced bone loss and reduced loss of minerals in the urine.4 These variabilities in optimum pH in different areas show the body’s ability to change based on local environment and physiologic and biochemical requirements.

The bottom line is, healthy pH levels, whether in the colon or systemic, are found when you eat a high-fiber diet, high in vegetables and fruits, healthy proteins, and healthy fats. Complement this with foods and supplements high in beneficial bacteria, omega-3 fatty acids, and digestive enzymes, and you will be supporting optimal health (which begins in the digestive system).


  1.  J. Zimmer, et al., “A vegan or vegetarian diet substantially alters the human colonic faecal microbiota.” Eur J Clin Nutr. 2012 Jan;66(1):53-60.
  2. J. Adler, “A method for measuring chemotaxis and use of the method to determine optimum conditions for chemotaxis by Escherichia coli.” J Gen Microbiol. 1973 Jan;74(1):77-91.
  3. G.R. Gibson, et al., “Prebiotics and resistance to gastrointestinal infections.” Br J Nutr. 2005 Apr;93 Suppl 1:S31-4.
  4. B. Dawson-Hughes, et al., “Treatment with potassium bicarbonate lowers calcium excretion and bone resorption in older men and women.” J Clin Endocrinol Metab. 2009 Jan;94(1):96-102.