Are probiotics essential for optimal gut health?

Probiotics are often being recommended to deal with a variety of digestive health complaints today. I have been intrigued for many years of the role of the digestive system; it’s functions and ultimately how bacteria can contribute to improved or decreased health. Recently, the last two newsletters from Ray Peat PhD have quoted studies, where animals that were born into sterile environments had improved metabolic rates. He also alluded to the increased lifespan of animals with higher metabolic rate in his book, Generative Energy. Probiotics have been touted for many years to assist with optimal gut function but like many products these days have swiftly been elevated to cult status, with their miraculous, cure all capacity suggested by those that sell them. But what does the science say? A summary of The Cochrane database provides plenty of research that shows that probiotics do have a positive impact in the short term, decreasing acute diarrheal like symptoms; however it’s impact on issues such as IBS remain inconclusive and controversial.

The gut flora and microbial mass is suggested to weigh up to 7kgs, second only in weight to the skin as the largest mass found in the human body. There exist over four hundred different species of bacteria with a predominance of anaerobic bacteria found mostly in the lower bowel. The problem with anaerobic bacteria is that the by-product of these species is the production of lactic acid and other metabolites that are damaging to cellular function.

Bacteria are often classified as pathogenic or disease causing or ‘friendly’ whose role can assist in production of Vitamin K2, biotin and B vitamins amongst other compounds. Bacteria can also increase the production of nitric oxide and endotoxin ( a compound well known to disrupt the mucosal barrier and enzymatic process of the bowel) is known to increase it further. An intriguing question would be whether an increase of certain bacteria predominate when we have a lower intake of certain foods

It is clear that metabolites from all bacteria do pose a challenge to cellular function and certainly when there is an overgrowth or dysbiosis they produce increased compounds that can create health issues dependant on the host’s immune and metabolic status. Probiotics like other supplements are often recommended long term but even the so-called friendly bacteria have the capacity to cause metabolic disturbances. Some species of lactobacilli in excess, cause a condition called D-Lactate acidosis, which disrupts metabolism and has significant impact on mood, digestion and energy. I can recall a three-year-old client who presented with anger and constipation ( 1 bowel movement per week) whose mother thought she was doing the right thing by feeding plenty of fermented foods and yoghurts with natural bacteria. Within a week of removing these foods the issues had stopped.

Chis Masterjohn PhD suggests, ‘Not every fermented food is good for every person, and some people don't tolerate fermented foods well at all. I think this is largely mediated by the biogenic amine content.’

A common diagnosis clients have been told is one of fructose or carbohydrate malabsorption. When carbohydrate in the diet is high in the absence of a healthy bowel this may be an issue. However if Lactobacillus levels have not been checked, we cannot rule out the possibility of fermentation of carbohydrate due to the action of increased Lactobacilli.

E.E. Metchnikoff’s view that disease starts in the colon is a widely accepted statement. Reducing the amount of bacterial agents in the bowel and increasing protective factors such as decreased adrenalin and improved thyroid function can complete elevating the biological status of a person. A stressed digestive system that does fails to produce adequate stomach acid (Achlorhydria or hypochlorhydria) often increases the amount of bacteria in the lumen of the bowel. Partially undigested food accumulates and elevates lipopolysaccharides from increased endotoxin, damaging the bowel. An increase in adrenaline and decreased thyroid hormone can contribute to decreased stomach acid production via stress pathways. Helicobacter pylori, bacteria that buries into the stomach wall may also contribute to this issue.

High protein diets have the capacity to increase bacterial action in the bowel and a metabolite of tryptophan degradation is indole. This increases ammonia and is problematic to the function of the bowel. This is often the reason for practitioners often suggesting an alkalinising type of diet. Alkaline environments pose just as much a problem as acidic environments. To decrease the bacterial actions of tryptophan, increasing the amount of gelatin like substances may be more beneficial than trying to restrict protein. The amino acids glycine, arginine and proline, found in gelatin do not have the carcinogenic properties associated with tryptophan, which is high when consuming muscle meats alone. Metchnikoff's theory of putrefactive dysbiosis  would fit better here but fermentive dysbiosis of grains and carbohydrates is prevalent in the poor performing bowel also.

Whilst antibiotics have gotten a bad rep over the last twenty years there can still be much use for them especially when there are stubborn gastrointestinal infections. Antibiotics seems to also work well in reducing the impact of endotoxemia

Testing the bowel can be completed with a CDSA (comprehensive stool analysis) or to accurately assess metabolite an organic acid urine analysis. These tests often cost £250-400 and present a considerable expense to clients. I personally think these tests should be completed after you have tried to optimise the bowel with optimal foods that digest well and support hormonal function. A caveat to that would be, when a client presents with parasitic infections or autoimmune type systems that may need further investigation

To summarise, I think probiotics can be useful in the short term to people with acute problems, primarily due to restricting proliferation of problematic bacteria but in many cases long term use is unwarranted and may even contribute to health issues.



  1. Lord, R.S and Bralley, J.A. Laboratory Evaluations for Integrative and Functional Medicine. Metametrix Institute. 2nd 2008.
  2. Peat, R. Generative Energy. Restoring the Wholeness of Life. 1994.
  3. Chris Masterjohns Blog
  4. .;jsessionid=5315A28A4390280DD5D4257508AD7AC0.f04t02
  6. Ray Peat Newsletters: Directing Epigenetic Adaptation/Imprinting and Aging