sorry for the late reply. the microbiome is the name given to the community of bacteria that live in the gut - otherwise known as gut bacteria, commensal flora, microflora or microbiota. there is a great review article from Nature about the relationship between gut bacteria and humans that introduces the concept of the 'superorganism' - http://www.nature.com/mi/journal/v3/n5/full/mi201020a.html
since around half of the species in the gut are not culturable, new metagenomic DNA based techniques are being used to identify and quantify the various species of bacteria that live in our guts. experiments on mice are finding out what effects different species of gut bacteria and community composition have on the immune system. in AS there are elevated levels of Th17 helper cells. in genetically identical mice from two different laboratories, one group had much higher Th17 levels than the other and this was found to be due to their different gut bacteria.
many researchers now consider it highly likely that the inflammation in AS originates in the gut and then spreads to the joints as the majority of AS patients have gut inflammation and ileocolitis upon endoscopy. in patients with IBD (crohn's & UC), it has been found that they have an altered gut microbiome with an overgrowth of certain species and an overall loss of species diversity. the question is whether this the altered microbiome is a cause of or result of the disease. some evidence suggests it could be the cause. in both crohn's & UC, antibiotic use increases the risk of disease in a dose dependent relationship. in patients with UC, fecal transplants have lead to long lasting remissions up to 13 years. this suggests that by altering the microbiome you can change from an inflammatory diseased state back to a healthy equilibrium. in mice fecal transplants have been shown to dramatically alter the microbiome and increase species diversity.
in the future, treatments that specifically target aspects of the immune system, alter gene expression or other methods may be able to completely eliminate AS symptoms but if an altered micriobiome turns out to play an important role then it could still be leaving the root cause untreated. as new research is discovering, the microbiome plays a huge role in proper immune function, nutrient metabolism, protection from enteric pathogens, and even neurological function via the gut-brain axis. that is why i think it is the most promising avenue for a cure at this stage but it still remains to be established whether AS patients have an altered microbiome. one study showed that there was no significant differences in AS patients at the phylum-level when measuring Bacteroides, Eubacterium–Clostridium and Bifidobacterium. the study did not however measure important phyla such as Firmicutes, Provotella and Ruminococcus and the techniques used were not able to measure bacterial diversity such as the ones that have been used to test the microbiome of IBD patients. i think this is definitely on area of research (among many) that is worth keeping an eye on. it may turn out that we are merely dysfunctional superorganisms
rather than genetic mutants