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The use of DNA technology has brought major changes to microbiology allowing more accurate investigation and identification of a variety of pathogens in a range of health conditions from cancer, auto-immune disease to chronic fatigue and fibromyalgia. Molecular studies have given insight into the effect such pathogens induce in disease states and the mechanisms involved. Organisms such as Mycoplasma, Chlamydia and Borrelia species have been found to be capable of inducing inflammatory mediators such as cytokines and chemokines in many tissues including gut wall, glial and neuronal cells. Providing anti-inflammatory treatment is useful but is only half the picture and is not treating the causal infection. As antibiotic resistance increases world-wide, there is a need to find adequate antimicrobial solutions amongst the pharmacopeia of natural herbal medicines. Statistics gathered over the past decade on the presence of Mycoplasma, Chlamydia and Borrelia species in chronically ill patients show a high level of infection in many inflammatory illnesses previously not considered as a result of pathogenic bacteria. Treatment of these infections in the majority of cases ameliorates symptoms. Testing has been performed through Nested PCR and Real-time PCR with external verification though sequencing.