The mainstream, but antiquated, view about chronic disease is best expressed by a certain physician thusly: “Of our thousand bacterial species, I only have to worry about a couple dozen” while a 2002 Nature paper concludes, “Multicellular organisms live, by and large, harmoniously with microbes.1
However, there is substantial evidence that chronic diseases are caused by pathogens as opposed to other causes. This evidence includes:
In addition, it seems highly likely that supposedly non-infectious chronic diseases are in fact caused by pathogens when one considers their clinical features, histology, treatment response, microbe populations, presence of co-infections, the ease with which co-infections proliferate, and the failure of systematic lifestyle interventions.
According to the Marshall Pathogenesis, humans accumulate a plethora of pathogenic bacteria during their lifetimes, and it is the genetic mutations which result from active infection that play a major role in what is commonly thought of as “genetic susceptibility.”
Besides the absence of proof implicating human genes as the major causative factor, there is a range of evidence - including strong epidemiological and compelling evolutionary evidence - suggesting that pathogens cause chronic diseases.
Epidemiological evidence including case clustering in time or location supports a pathogenic cause for disease.
One useful way to determine if a disease is caused by faulty human genes is look towards the central principle of evolutionary biology: evolutionary fitness. Evolutionary fitness is defined as the extent to which an organism is adapted to or able to produce offspring in a particular environment. The fitness concept can be applied to the problem of disease causation to distinguish evolutionarily feasible hypotheses of causation from marginally feasible or untenable ones.52 53
If the common inflammatory diseases (including autoimmune diseases) were genetic, the only way they would manage not to be weeded out of the population would be if they conferred some sort of beneficial survival trait not related to the disease.
To date, no such benefits have been identified in any chronic disease, schizophrenia being a good example.54 Schizophrenics have a high suicide rate, few children, and a high rate of abnormality in their children.55 56 Schizophrenic mothers are more likely than non-schizophrenics to have stillborn babies and children with congenital malformations.57 On the contrary, incidence of the disease is only escalating suggesting that bacteria are passed from generation to generation. This would mean schizophrenic mothers and fathers would be less likely to pass on a theoretical schizophrenic gene to their offspring.
Biology and law typically don't have much in common, but one useful metaphor for considering the validity of a proposed pathogenesis for chronic disease is to compare the search for the cause of disease to that of a trial for homicide. Two key pieces of evidence in any such trial are opportunity and motive. Basically, could the defendant have done it, and was it in his interests to do so?
Bacteria have both motive and opportunity.
Unlike toxins, environmental causes, human genetics or many of the other major proposed causes for chronic disease, bacteria are driven by a biological imperative, namely the evolutionary impetus to promote their genes through aggressive reproduction. Of course, the same cannot be said for other potential causes, especially human genes. In fact, it's decidedly in the interests of humans not to pass on genes, which limit reproductive fitness, in some cases drastically so.
Pathogenicity is, in a sense, a highly skilled trade, and only a tiny minority of all the numberless tons of microbes on the earth has ever involved itself in it; most bacteria are busy with their own business, browsing and recycling the rest of life. Indeed, pathogenicity often seems to me a sort of biological accident in which signals are misdirected by the microbe or misinterpreted by the host.—Lewis Thomas, The Medusa and the Snail
Sterile in health
Characteristic of medically important bacteria's outer surface is a rigid cell wall containing peptidoglycan –Review of Medical Microbiology and Immunology, 2008