In biology, a pathogen in the oldest and broadest sense, is anything that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ. The four most common types of pathogen are bacteria, viruses,fungi and parasites. Your immune system comes into contact with pathogens on a daily basis. It will usually eliminate the pathogens, generally without you even knowing about it. Sometimes, you will be unwell whilst your immune system deals with the problem eg a common cold, food poisoning etc. You will be ill for a short while and then you recover.

In the case of chronic conditions, your immune system is unable to deal with pathogens that are causing the problem. This could be because your immune system is compromised, overwhelmed or for some reason does not recognise the pathogen as a threat to your wellbeing. Chronic conditions tend to last for a long time – often for the rest of your life. By identifying and eliminating the pathogens which are at the root of your health condition, your symptoms will disappear. If the pathogen is no longer there then it can’t cause any problems. The pathogens we find tend to be remnants or weaker versions of the virus, bacteria etc – not the full blown version. The remnants of malaria, for example, tend to give fatigue, night sweats and stiff muscles whereas full-blown malaria would almost certainly require treatment in a hospital.

This page does not attempt to provide detailed information about the common forms of pathogens – a simple internet search will yield all the information you could want!. The aim is to provide some basic information and illustrate the ways in which pathogens can impact your health.


Bacteria are microscopic one-celled creatures that can live inside or outside of the the body. There are millions of bacteria living in your body, particularly in the digestive system. These are part of the natural flora and fauna of the gut and are necessary for the proper digestion of food. However, some bacteria cause harm by their very nature eg salmonella and e-coli.

Bacteria tend to be at the root of may digestive problems. 80% of people with digestive issues have helicobacter pylori, for example.

Bacteria are also commonly involved in urinary issues and skin issues.

Rod-shaped bacteria
such as e-coli. E-coli causes abdominal
cramps, diarrhea, nausea, fatigue and fever


Viruses are multi-celled, sub-microscopic in size and can only reproduce inside another living organism. Viruses often live in the central nervous system and typically cause symptoms such as headaches, fatigue, achy/painful arms and legs.

Chronic conditions such as ME, chronic fatigue syndrome and fibromyalgia usually have a number of viruses as a common factor, such as Epstein Barr and hepatitis.

Other common viruses include influenza, herpes, chicken pox and human papiloma virus.

Illustration of an influenza
virus (H1N1) particle.


A fungus is any member of the group of eukaryotic organisms that include microorganisms such as yeast and moulds. They are often an underlying cause of skin issues such as psoriasis and exzema, as well as urinary infections and respiratory issues.

One of the most commonly found fungus is candida – or one of its many strains. Candida forms part of the natural flora and fauna of our digestive system and is only harmful if it passes to other areas of the body or if you suffer from “overgrowth”. Candida causes a wide range of symptoms including headaches, urinary issues, joint pain, digestive issues, fatigue, “brain fog” and nail infections.

Other common fungals are pseudomonas aeruginosa and aspergillus which primarily cause respiratory issues and trichophytons which affect the skin.

Candida albicans is detected in 40-60% of adults and can become pathogenic in immunocompromised persons. It causes the infection candidiasis. It’s one of the most common hospital acquired infections.


A parasite is an organism that lives within or on a host. The host is another organism. The parasite uses the host’s resources to fuel its life cycle and to maintain itself.

Parasites vary widely. Around 70% are not visible to the human eye, such as the malarial parasite, but some worm parasites can reach over 30 meters in length.

The giardia lamblia parasite is most
commonly associated with diarrhea,
stomach cramps and nausea

Parasites which commonly cause ill health include hookworms, scabies, amoeba and toxoplasma gondii. They are often associated with digestive issues as well as skin issues.