Hygiene hypothesis - good bugs and bad bugs

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Many people die because of infection (terminal illness often results from pneumonia or septicaemia) as the immune system eventually fails or is overwhelmed.

Infections also often become chronic and lead to other problems "down the line" - cancer, dementia, heart disease.

One must stay ahead of the game.

It is always a numbers game, indeed an “arms race” in which micro-organisms are striving to eat us and we are striving to keep them at bay.

Please see

and these related articles:

Having a robust immune system

So it is critical for our health and longevity to have a robust immune system which is able to deal efficiently with attacks from "bad bugs" and does not allow for low grade chronic infections to set in as a result of an "unfinished job" fighting an infection. Any low grade infection will slowly, but continuously, erode the efficacy of the immune system and when a major acute infection comes, the system is likely to be overwhelmed by it.

We also know that excessive cleanliness predisposes to allergy and poor immune function. So, for example, the first born child is more likely to be allergic than younger siblings because mother is overly hygienic with the first and is too overworked to be bothered with subsequent babies! We need some exposure to friendly bacteria in food and water, and from playing outdoors to correctly program the immune system. (Please see Reprogramming the Immune System – where conventional and complementary medicine can come together)

We are constantly exposed to microbes in our daily lives. It is important to do things which will help our immune system protect us and when an infection develops, help the immune system kill all the "bad bugs" to avoid low grade chronic infection.

The first line of defence against microbes is natural barriers such as skin, gut wall and other mucosal membranes. Their effectiveness largely depends on acid. The stomach may be extremely acid – down to pH 2, skin is pH 4.5 – many microbes are simply killed by this acid environment. pH 7 is neutral.

Problem areas


Broken skin clearly needs to be kept clean to prevent microbes accessing the body easily! Intact skin should be acidic as this encourages the friendly bacteria which physically displace unfriendly bacteria and yeast. Just putting water on skin will instantly raise the pH by simple dilution of natural acids from sebum.

What to do: if there is broken skin, do not wash unless there is obvious grime! If there is obvious grime then, after washing, use coconut oil cream with some ascorbic acid (vitamin C) stirred in to restore normal skin pH. Vitamin C is also an anti-oxidant, and will penetrate the skin and protect against pro-oxidant stress from, for example, sunshine, which may result in age spots and sun damage. See Minerals and vitamins in creams

Coconut oil contains caprylic acid, which nourishes the friendly bacteria and encourages their growth. Caprylic acid is also mildly antifungal. This, together with ascorbic acid and minerals, is the best deodorant or rather odorant preventive! This is because body odour arises from unfriendly bacteria fermenting sweat on the skin and so killing the unfriendly bacteria, whilst at the same time encouraging the friendly bacteria, is a good tactic to reduce body odour!

I do not advocate antiseptic sterilising wipes, disinfectants and medicated soaps. These temporarily get rid of microbes indiscriminately and the skin is rapidly recolonised by good and bad microbes.


Topical nail infections with fungi are common in people eating western diets. Topical neem oil often works well. (See below.)


The problem with Western diets is they are high in refined carbohydrate which encourages unfriendly bacteria in the mouth, particularly streptococcus mutans, which cause tooth decay. In his classic book, (Amazon.co.uk Link for Weston Price's book "Nutrition and Physical Degeneration") Weston Price demonstrates the perfect dentition of indigenous people eating primitive diets – perfectly formed teeth and no dental decay right into old age! The normal pH of saliva is slightly acid – the mouth should not be made too acid because acid dissolves teeth! Indeed streptococcus mutans causes tooth decay because sugars are fermented to acids.

1.What to do: eat a paleo-ketogenic diet - please see -

2.Use neem toothpaste and mouth wash. (see My online shop's neem mouthwash) Neem is extremely safe and excellent at killing streptococcus mutans. Many people comment their teeth feel smooth after using neem regularly and that dental plaque disappears. The major cause of tooth loss however is gum disease and this can be prevented by good nutrition (diets and supplements), with neem a very helpful addition.


Again Western diets high in refined carbohydrate have much to answer for! Such a diet lends itself to a fermenting upper gut. The treatment is Fermentation in the gut and CFS

Again an acid stomach is highly protective against fermentation because this acid sterilises food. See Heartburn - at last I have sussed out why this is such a common problem

Neem may be helpful – it is active against most yeast and aerobes which are common causes of upper gut fermentation, but does not upset the anaerobes in the lower gut. A suggested dose would be 500mgs capsule of neem leaf (also contains tumeric) with food.

Ears and Nose

The ears and nose again benefit from an acid environment so the above coconut cream mixes can be applied to the insides of the lower nostril and ears.

The Perineum

This is the area of the body where there are openings through which infection could enter – namely the urethra, anus and the vagina. There is a natural movement of secretions outwards which naturally wash microbes away. Again, an acid environment encourages the friendly non-colonising microbes. Coconut oil cream, with ascorbic acid and possibly minerals, applied locally would be helpful!

Sexually transmitted diseases

This is a major route for infections and a major cause of disease. It is an inevitable risk for a species that reproduces the way we do. Obviously there is no risk between virgin couples but love, lust and desire are major complicating factors!

What to do: this is no place for a lecture on standards of behaviour – the above says all! Prevention is always better than cure.

All the above should be done in conjunction with The general approach to maintaining and restoring good health


This is a very useful antimicrobial. For details see Neem and Health on the website of the Neem Foundation.

Neem is of proven benefit topically for skin and mouth infections, but the real joy is the fact it is inexpensive and remarkably safe and well tolerated. For any physician the starting point is ‘First, do no harm’! There are clearly some CFSs for whom chronic low grade infection is a major problem. Indeed, I wonder to what extent CFS represents an inappropriate activation against otherwise benign microbes. See Valacyclovir in the treatment of post viral fatigue syndrome and Chronic viral presence in CFS/ME

One can be allergic to anything under the sun (including the sun) and fungal and bacterial allergy is well established. Why not viral allergy? Indeed, it may be that part of the ageing process is inappropriate reactions against microbes – arthritis and asthma, for example, have well documented ‘allergy against microbe’ causes.

I have always struggled to know what best to do with chronic low grade infections. The problem is that the treatments - which may be antibiotics, antifungals or antivirals – have the potential to make things worse. Indeed, we know from Acumen research that all these medications can get stuck on to mitochondria, membranes and DNA thereby blocking normal cell biochemistry.

So a safe broad spectrum antimicrobial with thousands of years’ experience of use and safety has much to be recommended! Neem comes either as the leaf or bark extract or a combination. The bark is the stronger, so for any treatment I would suggest neem multi (mainly leaf) initially and if tolerated or if the anti-viral properties are needed, use neem antiviral (90% bark)

A suggested dose would be 500mgs daily, increasing perhaps to 500mgs three times daily with food. As with any anti-microbial, die off reactions are common so start low and build up slow!

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