Chronic infection – Life is an arms race – how to tackle with natural remedies

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You and I are a free lunch; indeed, we are a nutritious Petri dish, on which microbes can and do flourish! There is a battle, an arms race, going on inside our bodies every second of the day. This is a race we can never hope to "win". We can only hope to stay sufficiently ahead of the game for as long as possible so that we stay feeling well. This arms race is a "numbers game" – our body must use its "resources" to keep the numbers of the bad guys [the harmful microbes] down to a sufficiently low level so that we do indeed stay feeling well. That this constant battle is going on is clear – within minutes of death, when our bodies cease fighting this arms race, we rapidly decompose – the bad guys win and they win quickly. The business of fighting back against the microbes uses a great deal of energy – we know this too because if you give a normal person influenza, they immediately develop fatigue as the body diverts its reserves and "resources" into fighting infection.

In my writing, including on this website, see Overview of CFS/ME Protocol and also in my book, "The Energy Equation" and my other books too, I discuss the Energy Equation in detail. However, in brief, the Energy Equation can be very simply expressed. Fatigue is the subjective symptom experienced when energy demand exceeds energy delivery.

I have written in detail about how one can improve energy delivery [via interventions such as the mitochondrial supplement package] and also how one can reduce energy demand [via, for example, the use of EPD, to reduce the immunological “hole” in certain patients]. Here we have another, and very common, example of an Immunological Hole in the ‘energy bucket’. Having a chronic infection and/or microbial overload kicks a large "immunological hole" in the energy bucket, . This hole is there all the time causing a permanent drain on one's energy and has the potential to become larger, if left untreated. The combined job of physician and patient is to reduce the size of this hole to an absolute minimum.

This "hole" could well be the tipping point for some patients – that is to say, the chronic infection or microbial overload may push a particular patient's own individual Energy Equation into the red and make them feel really very ill. Likewise, dealing with this chronic infection and/or microbial overload could dramatically improve the patient’s well-being.

I have talked about the "resources" or reserves that the body has at its disposal to fight these chronic infections and /or microbial overloads. Here I have to consider what I will call the "normal" state of affairs, that is the way things have been in this arms race for the majority of our time on this planet, and then the "abnormal" state of affairs, that is the changes brought about in this arms race by the introduction of Modern Western diets. The introduction of these Modern Western diets has significantly tipped the balance of power in this arms race in the favour of the bad guys.

These bad guys are a difficult enemy and persistence and patience will be required to keep ahead in the arms race:

"Butch Cassidy: How many are following us?
Sundance Kid: All of 'em.
Butch Cassidy: All of 'em. What's the matter with those guys?
Butch Cassidy: Ah, you're wasting your time. They can't track us over rocks.
Sundance Kid: Tell them that.
Butch Cassidy: [after looking for himself] Who are those guys?"

The normal state of affairs

We can never sterilise the body - we have to put up with a certain level of bacteria, yeasts, viruses and sometimes parasites. We have been doing this for millions of years - so much so that our DNA is at least 8% viral. We have done a deal with the virus – we will give you a comfortable home if you leave us alone. This is the policy of pacifism! Trillions of microbes live in the gut. Indeed, if one totalled up all the cells in the body including gut flora then you and I are 90% bacteria. The strategy is twofold, both to keep the numbers of the bad guys down and also to fill the gut with friendly, less demanding microbes (largely bacteria, but also some yeast) which have an additional number of helpful functions such as:

  • They have their own viruses called phages which kill unfriendly bacteria. Indeed 15% of stool dry weight is made up of these bacterial viruses. Clearly there is a balanced predator-prey ecology within the gut. Predator-prey models are extensively studied within the discipline of Mathematical Ecology and Biology and generally there exist two equilibria points – one where there are no predator and no prey [the death of both predator and prey!] and another where predator and prey co-exist in a steady state equilibrium – this is the balance that we are looking for! For those who may be interested, please see Volterra Equation and in particular look for the subsection "population equilibrium".
  • They ferment foods to produce energy for the body. The most important of the friendly microbes for this function are the bacteroides. These are anaerobic bacteria in the large bowel which ferment vegetable fibre to short chain fatty acids. These short chain fatty acids nourish the lining of the bowel and, to a lesser extent, our bodies.
  • They produce essential nutrients such as vitamin K and biotin. These are essential because they cannot be synthesised in the body.
  • They help to programme the immune system. See Reprogramming the Immune System for when this 'goes wrong'
  • There are probably other benefits of these organisms yet to be identified.

However, these friendly gut microbes are miniscule compared with human cells and all too easily spill over from the gut into the blood stream and this can lead to very undesirable effects. We know both that these microbes spill over from the gut and that they may cause undesirable effects from several pieces of evidence:  

  1. Metchnikoff (See Wikipedia page on Metchnikoff), who first described probiotics and developed Kefir. Metchnikoff conducted an experiment where he drank Kefir, collected his own urine and grew identical microbes from his urine.
  2. Simply brushing one’s teeth can cause a bacteraemia (i.e. bacteria in the bloodstream) - this is why dentists insist on antibiotics for patients with heart valve lesions prior to any dental work.
  3. Nishihara has shown that fermenting microbes in the gut can be present in the brain with the potential to ferment neurotransmitters and cause psychiatric disease. See "Disclosure of the major causes of mental illness— mitochondrial deterioration in brain neurons via opportunistic infection" by Katsunari Nishihara
  4. Albert et al have shown the presence in joints of microbes which drive arthritis (hence arthritis can be cured with antibiotics). See their article Antibiotic treatment in patients with chronic low back pain and vertebral bone edema (Modic type 1 changes): a double-blind randomized clinical controlled trial of efficacy.
  5. Interstitial cystitis or allergic bladder is a condition that I believe results from allergy to gut flora and responds well to the treatment of such.

These are all, as I have said, very undesirable effects, but in the past the impact of these effects was not significant because of the diet that previous generations consumed.

The evolutionarily correct diet is zero carbohydrates (on a day to day basis) with an autumn bonanza of fruit and other natural harvests. This autumn bonanza temporarily switched on metabolic syndrome and weight gain and allowed us to survive the winter. We survived the winter on fat from fat reserves and fatty meat and fish. The important point about fat is that microbes cannot utilise it. How do I know this? I can leave a bottle of olive oil in my kitchen at room temperature for months and it does not go off. Ditto a lump of lard or butter in my fridge.  Fat is what the body should run on. It is deposited where most work is done - notably the brain (which uses 20% of all the energy consumed in the body), the bone marrow (for blood creation) and round the gut (90% of the immune system is gut associated). Fat is an important defence against microbes because microbes cannot ferment fat. So fat is an important part of our previous defence against all the nasty effects I have noted above.  But………

The modern abnormal state of affairs

We have a massive problem with Western diets because they are high in carbohydrates (grains, root vegetables, sugar, fruit sugar, pulses). These foodstuffs, unlike fats, are readily fermented by microbes. Given the right substrate, microbes can double their numbers every twenty minutes!

If the digestive tract is working perfectly then these microbes are killed by stomach acid, pancreatic enzymes and bile salts. However, there are several factors which result in faulty sterilisation of the upper gut and put us at risk of fermenting gut:

  1. Hypochlorhydria – caused by a leaky gut from allergy, infections (viral or food poisoning, H pylori). There could be a genetic predisposition here.
  2. Poor energy delivery - so we cannot make the acid or enzymes necessary for normal gut function. This is a central issue in CFS/ME.
  3. Nutritional deficiencies – so the body does not have the raw materials for normal gut function
  4. Ageing – all the above factors come into play – indeed we know this - most older people will tell me that they can no longer eat large meals because it overwhelms their ability to digest – they ferment instead and this is uncomfortable.

So, the combination of the gut not working properly (and therefore not killing the microbes) and the Western diet (too high in carbohydrates, leading to microbe fermentation) leads to a problem with microbes both inside the gut and also a problem with microbes outside the gut. Before I describe how to deal with these twin problems of microbes inside and outside the gut, we should first look at the symptoms which would lead the physician to the conclusion that the patient is suffering from a chronic infection and / or a microbe overload.

The clinical picture of chronic infection/microbial overload

This presents with all the symptoms of immune activation as the body tries to reduce the numbers of microbes, viz:

General symptoms

  • Fatigue – this is an essential symptom to enforce rest so that the immune system has the energy available to fight.
  • Malaise and “illness behaviour” - this is a physiological response to being ill - see Wikipedia Article on Sickness Behaviour
  • Fever – most microbes are killed by heat.

Local symptoms

  • Mucus and catarrh – this physically washes out microbes
  • Runny eyes -  ditto
  • Cough and sneeze – physically blasts out microbes in the airways
  • Airways narrowing, wheeze, asthma - results in the air we breathe becoming more turbulent so microbes are thrown against and stick to the mucous lining of the airways to be coughed up and swallowed.
  • Vomiting – an essential defence against food poisoning and microbes inhaled (which are coughed up and swallowed)
  • Diarrhoea – ditto
  • Colic - ditto
  • Cystitis – empty the bladder of urine and therefore microbes

Now, we can consider the twin problems of microbes inside the gut and microbes outside the gut and how to deal with them.

How to reduce the work of the immune system: reduce microbes in the gut

We do this by reducing the numbers of [bad] microbes that the immune system has to deal with and also by encouraging the friendly ones. There is a two pronged approach – firstly, starve the little wretches out and secondly, kill them. This means putting in place all the treatments to tackle the upper fermenting gut. See Treatment of the fermenting gut. Perhaps the most important treatment is the ketogenic diet. See Ketogenic diet - a connection between mitochondria and diet. See also

How to reduce the work of the immune system: reduce microbes that are outside the gut but inside the body

This is more difficult because the body needs some sugar in the blood stream to function and microbes can happily ferment this. These are not at sufficient levels to cause overt infection such as septicaemia or abscess, but are present in sufficient numbers to drive a destructive low grade inflammation. I think of this as microbial allergy. We need other methods to kill these microbes. Established options and suggestions are as follows:

  1. Antibiotics, antifungals, antivirals – these are of proven benefit but resistant strains may emerge and side effects are possible.
  2. Intravenous vitamin C (but this can be difficult to administer and is expensive)
  3. Heat (pyrotherapy) – sauna regimes are of proven benefit, but this therapy is often not tolerated in severe CFS
  4. See My book "The Infection Game - life is an arms race" for lots more detail
  5. Light – discussed in detail below.

Light Therapy

To the Ancient Greeks and Romans, the sun was Apollo’s fiery chariot making its way across the sky, bringing life-giving light to the planet. Apollo was the god of medicine and healing as well as of sun and light.

Ultraviolet ["UV"] light kills all microbes. How do I know that? It is already used to sterilise water for drinking and swimming pools. Sunshine was the main treatment for TB in pre-antibiotic era. Please see these links for an interesting history of this treatment - Science Museum HOW DOES ULTRAVIOLET LIGHT AFFECT OUR HEALTH? and Treatment of TB patients . I suspect the reason we love sunbathing is because light penetrates the skin and kills these microbes, thereby reducing our infectious burden. This means we spend less energy on the immune system, leaving more energy for other things. More energy is available for a mental and physical life! In addition, sunshine is a good treatment for infectious skin conditions such as acne and eczema.

The Romans had a word especially for sunbathing - apricus - "having lots of sunshine; warmed by the sun" - from which we have the verb, "to apricate" ('to sunbathe or bask in the sun' - intransitive - 'to expose to sunlight' - transitive).

Light as a treatment for infection has been used for years for serious infections. The patient was treated by removing a pint of blood, irradiating it, then returning it to the body. The problem with this treatment is, again, that it is high tech and expensive. However, equally good results can be obtained by intranasal light. This makes perfect sense – the nasal mucosa is thin and so light can easily get to the blood stream. The nose is well perfused with blood and so it is easily radiated. But most importantly the results obtained with intranasal light are as good as with intravenous treatment. Indeed, it may be that intranasal light impacts directly on the brain and this could be helpful for any patient with brain pathology and/or fermenting brain.  See Vielight for details of the Vielight device and research.

I am asking myself what is the mechanism of action? I suspect the mechanism is that the light kills microbes and that this both makes the blood less sticky (and so it flows better) and also reduces the work of the immune system.

Remember Dr Les Simpson from New Zealand, who described rouleaux formation [stacks of red blood cells] in the red cells of CFS patients? Rouleaux is a marker of infection. Simpson showed that red cells in CFS sufferers stick together in clumps. This would have a dire effect on blood supply because blood would not flow through tiny capillaries and so fuel and oxygen delivery would be seriously impaired. Clearly, this would impact adversely on energy delivery mechanisms. (Simpson suggested treatment with essential fatty acids - I prescribe these routinely in CFS see my Basic Package of supplements).

See here for Les Simpson's work:

As you can see from the pictures and videos, light restores normal circulation by unclogging these red cells. See Youtube video Vielight - Blood Disaggregation These results are obtained after just 25 minutes of light therapy. My guess is that these red cells are sticky because of the presence of microbes in the blood – the idea here is that light kills these microbes.

Other observations on light therapy

TB sufferers treated with sunshine could not immediately tolerate full body exposure. Special trolleys were designed which could be pushed out onto balconies so initially just the feet were exposed, then legs, trunk and finally the whole body. Too much sun too soon made them ill – this could possibly be a Herxheimer reaction?

Dr Horowitz comments that 50% of his Lyme patients were intolerant of sunshine- again possibly a Herxheimer reaction?

Doxycycline, often used to treat Lyme disease, can cause light sensitivity – again perhaps the mechanism of this is a Herx reaction?

The Vielight device (or Bionase - much less expensive)

The device that supplies this light is  Vielight 633 Red (Systemic PBM)  Ten million have been sold, mostly in Russia and China. The conditions for which there is an excellent evidence base for positive responses include high blood pressure, high LDL cholesterol, diabetes, atherosclerosis, asthma, stroke, cancer, immune system deficiencies, infections, rheumatoid arthritis, fibromyalgia and psoriasis. All these conditions can be explained by fermenting gut and allergy/infection to microbes spilling over from the gut.

This device uses near infrared light - interestingly there is some evidence that this "kick starts" mitochondria to produce more ATP - the energy molecule. See Infrared Light Therapy Runs Ahead of Science. Many thanks to Hannah Moss for linking me to this piece -- New Scientist Article "Burst of light speeds up healing by turbocharging our cells" This article states that "The effect on cells of near-infrared light, which has a wavelength of 670 nanometres, was first reported 40 years ago. The light causes mitochondria, the cell's powerhouses, to produce more ATP, a compound that provides the cell's energy." So, given that the devices noted operate at similar wavelengths, this is further evidence of benefit. In addition, it explains why we all feel better for sunbathing!

We have just found a very similar device which emits light at a very similar frequency (630 as opposed to 633 for the Red (Qi-Light) device from Vielight) which should work just as well but is much cheaper. See Bionase Revolutionary medical device

You can see instructions for use here - How to use Bionase and there is a YouTube here Bionase YouTube

I am excited by this idea – it makes perfect sense, is biologically plausible, free from side effects and can be done at home with no medical input.

Remember – there is no point killing the wretches in the blood if you are feeding them in the gut!! YOU MUST ALSO DO THE DIET. And remember that here, the PK diet is essential.

As ever, I look forward to feedback from my patients! And here is such feedback below!

November 2020 Patient Feedback

I have received this feedback from a patient:

Your site recommends the Bionase and Vielight devices. The Bionase made no noticeable difference but I suspected it was not strong enough, so I tried the most powerful devices I could find, the Redlightman red device and Redlightman infrared device light devices from Red Light Man ( which are the two most powerful devices from this site and these had exactly the same effects as antifungals (and also cured a paronychia finger nail infection when the NHS suggestions didn’t work). The Bionase device is two X 4-8 MW/cm2. The Vielight device you link to is 5 or 7.6 MW/cm2. The red and infrared light devices are 1200 MW/cm2, i.e. 75-150 X more powerful than Bionase and 158-240 X more powerful than the Vielight you link to (Vielight offers some slightly more powerful devices, but these are still nowhere near as powerful as the Red Light Man devices). While the Bionase has an advantage in that it is intranasal and so can direct light across a thin barrier inside the nose, this advantage is dwarfed by the mega power of the Red Light Man devices, although these devices cannot be placed close to the skin for long because of the heat so in practice the power will be less than 1200 MW/cm2, but still much more powerful than the Bionase or Vielight. At the end of the section on red light on your website you say “As ever, I look forward to feedback from my patients!”, so I hope that this is helpful. My recommendation is that you put in links to the Red Light Man devices on your site. The red light device that emits light at four wavelengths (610, 630, 660, and 680nm) and its power is 1100mw/cm2 at 0cm, 450mw/cm2 at 5cm, 180mw/cm2 at 10cm. The infrared light device has two wavelengths (760 and 830nm) and power of 1200mw/cm2 at 0cm, 500mw/cm2 at 5cm 200mw/cm2 at 10cm (the Bionase is 630 nm and the Vielight to which you link is 633 nm)

January 2018 Patient Feedback

I have recently received an email from a mother of one of my patients concerning Light [UV] Therapy.

She writes:

Oskar Bernhard used heliotherapy ( sun therapy) at Samadan hospital at Bad Durrheim in the Black Forest in World War 1. Then at the request of the health department of the 14th German Army Corps, he started a sun Clinic at Kindersolbad. His success at healing wounds was notable. Please see:

Prior to Dr Bernhard's work, Dr Auguste Rollier opened a sun Clinic in Leysin in Switzerland in 1903. For every 1000 feet above sea level, the UV increases by 4%. Therefore this sun Clinic at 5000 feet, increased UV by 20%. He had the patients gradually exposed to the sun, with the early morning sun on their backs.

Dr Rollier treated 1129 patients who either had non-infectious (closed TB) tuberculosis or septic infections.

  • 652 were children
  • 477 were adults

Of these 1129 patients,

  • 804 had closed TB (703 healed),
  • 325 had septic infections (242 healed).

Of the rest of the 1129 patients,

  • 73 of the 804 improved
  • 39 of the 325 improved
  • 22 of the 804 remained stationary
  • 19 of the 325 remained stationary
  • 6 of the 804 died
  • 25 of the 325 died

Very impressive results, pre-antibiotics.


For more on the theory of photobiomodulation, with full references, please see Vielight link on the theory of Biomodulation

Also please see Novothor locations where you will find details of photobiomodulation machines in the UK and elsewhere.

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Postscript - Groundhog Regimes

I have developed general strategies for good health, and for dealing with both acute and chronic infections. Please see:

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