bacterial overgrowth

Why you really shouldn’t be giving up sugar in the New Year.

It’s that time of year again, the silly season is upon us and plenty of people using inaccurate words such as detox are thrown around like Christmas wrapping paper. For many, the New Year is associated with dietary restrictions, born out of a period of over consumption from the festivities. May of those decisions such as stopping sugar or in particular fruit, as part of the so-called ‘detox ‘ is probably one the poorer choices that people do during this period of fad dieting. So it’s time to put the record straight on how to detox, or more appropriately how to maintain detoxification processes efficiently.

Detoxification and its suggested three phases, like most of the processes in the body is energy/nutrient/hormone dependant. Therefore the ability to detoxify efficiently is regulated by the amount of energy available and influenced greatly by how well your hormones function. The thyroid gland for example, is key to maintaining energy and this means energy for the liver to function. Detoxification is just one of the many functions of the liver, which also include glucose production and storage and the maintenance of adequate cholesterol.

The CDR or cell danger response suggests an evolutionary response to insults that affect the human body (and in particular cellular function) from a variety of sources. These can include:

  • Viral
  • Bacteriological
  • Chemical
  • Parasites
  • Electromagnetic stress
  • Physical and psychological trauma.

The net effects of the CDR can be suggested as a protective mechanism that stiffens cell membranes, perhaps to protect other cells, a decrease in processing of many nutrients and other compounds such as metals, and a decrease in metabolism. Whether this down regulation of function is protective or a result of the damage inflicted remains to be answered. Increased oxidative stress to how the body’s cells function can decrease the ability to generate energy using oxygen. Cellular respiration (ability to use oxygen to provide energy) using oxygen and carbohydrate remains the most efficient system for generating energy. Increased stress decreases the ability to utilise carbohydrate as a fuel. Other compounding factors with the CDR are a change to the gut bacteria, which can increase the fermentation of carbohydrates. So called beneficial bacteria such as Lactobacilli can produce lactic acid that disrupts the cells of the digestive system and increase the amount of gut damaging endotoxin.

For many the over indulgence will increase factors such as endotoxin, making them feel low, irritable and poor energy and sleep. An increase to neuro- transmitters such as serotonin and histamine, will exacerbate these issues and decrease sleep quality. The New Years resolution brings about a restriction of calories and eating less, burdening the digestive system less. People often make the assumption (one of many) that cutting out sugar has caused this miracle change but it may simply be the decrease in food itself. Perhaps it’s the lack of calories and the increase in adrenaline, much like the runners high, which makes people feel great?

For some, the equation of increased movement with less calories that is often employed at this time of year will have a good effect. For many others, and in particular, those who have a cell damage response, that is being resolved, this equation seems to have little effect. The decrease in available energy, to a cell that struggles to maintain adequate energy output, will find the move more, eat less, scenario a challenge.

Ketogenic diets often have great short-term effects for weight loss. In the long term a ketogenic remains a stressed energy state requiring the need for more cortisol, a decrease in carbon dioxide (decreasing the amount of available oxygen for use) and a less efficient form of energy production. Those who have a large amount of weight to lose, potentially expose the metabolic system to increased stress by oxidising fatty acids.

The stressed body requires carbohydrate. Low blood sugar states require a balance of carbohydrate (with fat and protein), to maintain optimal detoxification you need carbohydrate. Unfortunately with the fear mongering on social media you can often observe the following.

  1. Sugar feeds and causes cancer.
  2. Sugar is addictive

Here’s the thing. There is not any scientific proof to validate those statements. The primary fuel for any cell is glucose, even in cancer cells, if sugar is not available, it will generate energy from protein. Otto Warburg’s research has often been misinterpreted to suit inaccurate memes. Damage to the respiratory function of the cell is often the source of mutagenic aspects of cellular/mitochondrial (energy producing cells) that potentiates the growth of cancer.

The sugar is addictive study; well if you look closely at the study you will see that sugar activates the same reward centre of the brain such as sex, exercise and receiving gifts. The science of addiction is beyond the scope of my expertise, however if you have someone that cannot regulate energetic processes that well, they may seek out adequate energy, with sources of easily processed carbohydrates. It would appear that insulin sensitivity becomes an issue when there is an excess of energy.

Are you eating too much? Or is it simply that you cannot process the energy available? Well, if you eating less and moving more but weight, energy, sleep, libido or emotional balance aren’t improving. Then you know which one it is.

I am not suggesting here is that you should over eat sugar and carbohydrates. Much like, I wouldn’t NUTRITIONsuggest overeating broccoli, or drinking too much water.

Either way removing the protective capacity of carbohydrates to create balance is probably not the way to go.

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