I have two friends that suffer from RA or rheumatoid arthritis. It is a scary and painful autoimmune disease where the body attacks the joints. Current treatments include immune suppressing drugs which slow the progression of the damage, but have some fairly intimidating side effects. The cause of RA is not known, but a supportable hypothesis is brewing.

That hypothesis is that RA is caused by dysfunction in the digestive microbiome.

Now this is not exactly a new theory. The following article dates back a few years and outlines nicely why this hypothesis is consistent with the history of the disease. It also points out the danger of trying to figure out which microbes are a problem by yourself, since oral immunization (eating) with a strain of salmonella seemed protective against RA whereas Lactobacillus bifidus (found in many probiotics) seemed to aggravate the immune systems of sterile mice.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3275101/

But they are working on figuring out which strains can help and which ones hurt
http://www.ncbi.nlm.nih.gov/pubmed/24355439
http://www.ncbi.nlm.nih.gov/pubmed/24192039

These studies linked gingivitis (I kid you not) with RA…again the issue is that the microbes somewhere in the digestive tract are out of balance and if the host is susceptible, problems ensue.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3668087/
http://www.ncbi.nlm.nih.gov/pubmed/24807405
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990988/

In the following studies they used mice with what is basically a mouse form of RA and found not only that the antibiotics were causing the mouse problems, but also that correcting the microbiome seemed helpful

http://www.ncbi.nlm.nih.gov/pubmed/24911078
http://www.ncbi.nlm.nih.gov/pubmed/24873878

So to summarize, there may be a genetic component, but the actual trigger that causes someone to get RA may well be some sort of digestive tract dysbiosis involving too much of certain “bad” bacteria and a shortage of protective bacteria.

That said, the identities of the protective bacteria seem elusive.

There is nothing here to tell you that a cure is right around the corner. We have not yet found the treasure.

But we just might have found the map.