My understanding of the immune reaction to common gut bacteria is that the bacteria are presented to the immune system as a result of the weakening of the mucous membrane barrier allowing bacteria to reach the underlying tissue which triggers an immune reaction. This is usually referred to as increased gut permeability and the known causes are: a gut infection, stress, non-steroidal anti-inflammatories and alcohol. There are other candidates like food lectins, specifically wheat and bean lectins have been shown to reduce the depth of crypts in the gut and continued use might cause permeability. Once the immune system is triggered, inflammation is started and inflammation itself increases gut permeability, amplifying the effect. Certain of the gut bacteria are opportunistic pathogens - they infect sites of damage. That is why you get Bactroides fragilis and Escheria coli in fistula cultures. Bactroides is an interesting case. It is known to cause abscesses and is associated with fistulas, but not exclusively. It is also one of the most antibiotic resistant bacteria going. Antibiotics which completely eliminate Lactobacillus sp. only reduce Bactroides by 50 - 60%. Moreover, I have seen reports of Bactroides showing resistance to all of the antibiotics used to treat infections from it. Moerover, it secretes a polysaccheride that is so efficient at shutting down the immune system that it has been proposed as a treatment for Crohn's inflammation. This one is a survivor. More to the point, it is one of the species that was identified as being a target of the immune globulins associated with Crohn's. Now there are two possible ways to deal with the sensitivity to bactroides and company. One is to restore the integrity of the mucous membranes in the gut. The usual treatment with immune suppressors will possibly do that if you don't continually defeat it by doing things that cause gut permeability. The other is to remove the bacteria that cause the problem. That is nearly impossible for Bactroides and possibly others (it seems that only about
25% of gut bacteria are characterized). It is essentially what is being attempted when cipro or flagyl are prescribed. The strange thing about
all this medical protocol is that most of what is being attempted is done better by other bacteria. Lactobacillus casei, which is wiped out by antibiotics, can safely reduce inflammation. Several Lactobacillus species attach to the gut wall and form an effective barrier between the gut and its contents. Bifidobacter breve has been shown to competitively displace Bactroides fragilis from the ileum if it supported by whey (the trials used filtered, cell-free whey from the culturing of Bifidobacter breve, but there was no suggestion that this would be the only form of whey that would work). Other unidentified bacteria were credited with displacing Bactroides from the colon during these same whey trials. The only reason that I can see that doctors are not all prescribing something like this is the push for a new drug that can be patented. In fact, I saw a proposal to genetically modify existing bacteria (patentable) to improve their working. I would not touch a modified bacteria with a ten foot pole. Researchers are only just beginning to understand the complexity of the gut's immune system. They are finding that factors that they had defined as upregulators of some immune agent can in fact either regulate it up or down and maybe do other things besides. Changing a bacteria that has evolved with the human gut for millennia is a recipe for disaster. If the bacterial evolution gets it wrong, the host dies and the bacteria perishes. If the researcher gets it wrong, he still makes a fortune - you die. Sorry for the long rant.
