Not long ago, scientists believed they had located all bacteria capable of causing human disease, But DNA discoveries in the last decade have led the NIH Human Microbiome Project to now estimate that as many as 90% of cells in the body are bacterial in origin. Many of these bacteria, which have yet to be named and characterized, have been implicated in the progression of autoimmune disease.

In a paper published in Autoimmunity Reviews, the ARF team, under the guidance of Professor Trevor Marshall of Murdoch University, Western Australia, has explained how Homo sapiens must now be viewed as a superorganism in which a plethora of bacterial genomes - a metagenome - work in concert with our own. Marshall and team contend that the human genome can no longer be studied in isolation.

"When analyzing a genetic pathway, we must study how bacterial and human genes interact, in order to fully understand any process related to the human superorganism," states Marshall. "Especially since some of these pathways contribute to the pathogenesis of autoimmune disease."

For example, the team notes that the single gene ACE has an impact on myocardial infarction, renal tubular dysgenesis, Alzheimer's, the progression of SARS, diabetes mellitus, and sarcoidosis, yet recently ACE has been shown to be affected by the common species Lactobacillus and Bifidobacteria. Found in yogurt, these species are often considered to be innocuous or "friendly."

"No one would argue that these species aren't present in the human body, yet there has been inadequate study of how these 'friendly' species affect disease," states Amy Proal, the paper's lead author.

"What we thought were autoantibodies generated against the body itself can now be understood as antibodies directed against the hidden bacteria," states Marshall. "In autoimmune disease, the immune system is not attacking itself. It is protecting the body from pathogens."

To validate their lab discoveries, Marshall's team has been conducting an observational clinical trial of more than 500 autoimmune patients and reported at the recent 6th International Congress on Autoimmunity that antibacterial therapies targeted at these hidden microbes are capable of reversing autoimmune disease processes.

dx.doi/10.1016/j.autrev.2009.02.016