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There is a major problem in accessing the effect of the balance of
intestinal flora.
 (Unless there are recent developments of which I am not aware)  there are
currently no tests available to test the relative QUANTITIES of the various
microorganisms resident in the intestines.  Currently available tests can
detect the PRESENCE of various microorganisms.    But, because many of
these are often present in insignificant amounts,  the significance (or
lack thereof) of their presence must be judged based on the overall
available information ("clinical presentation")*.   In addition,  the
particular strain of a species present may be more important to know than
which species  (many species that are generally non virulent have some
highly virulent strains (for example the E-coli that caused the infamous
Jack-in-the-Box incident)).   I would think that an antibody titer test
could be developed to quantify the various important species and/or strains
but this would probably be very expensive and useful only for research.
In addition, it would not be useful for the real nasties (like Lyme
disease) that have antigenic variation.
 
Another problems is the question of how do you define "normal"?   As we
have found with cholesterol, knowing what the statistical distribution of
values is for a given metabolite or microorganism does NOT tell us what is
healthy!    (Especially in such an UNhealthy society!)   Presumably this
might be determined by determining the distribution for a sample of HEALTHY
people.
 
As a student, years ago, I worked on development of a technique that could
rapidly determine the QUANTITATIVE  composition of SOME of the intestinal
(and other) micro flora   (those that were distinguishable by microscopic
examination).    This project was abandoned for reasons that were not
stated  (I suspect that it was because the automated method we were working
on promised to be TOO cheap (not enough profit) and could be done in a
doctor's office, without the necessity for sending it out to a lab.     At
any rate, no one seems to be very interested in developing methods to
quantify the intestinal (or other) micro flora.       Maybe because our
current pharmaceutical approach tends to wreck the balance anyway.
 
Pardon my cynicism - I can't help observing that most of the best work on
vitamins and nutrients was done in the Soviet Union - Probably because they
weren't interested in making a profit - just obtaining the most benefits at
the lowest costs.    (You can't patent a naturally occurring nutrient
((How you can patent a naturally occurring gene is beyond me))).   And
after seeing how Celiac Disease, Lyme Disease, Hemochromatosis are ALL
grossly under diagnosed (in the range of 90% or more undiagnosed) in the
United States,  how major and fundamental discoveries are largely ignored
for many years (the fundamental role of iron in infection - thoroughly
researched in the early 80's and still grossly under appreciated,  the
importance of fever as a defense mechanism) and how the diagnosis of some
diseases (especially Lyme) is controlled much more by politics than by
science, one really has to wonder just what is wrong with the
administrative structure of medicine.      Perhaps it (like ANY other human
endeavor) needs a lot of informed OUTSIDE input.
 
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* This is not as simple as it may seem.   For example, many microorganisms
that are ordinarily innocuous may be highly virulent in the presence of
iron overload  (vibrio fulnificus, for example, is potentially fatal in
iron overload while usually harmless in those with normal iron status).