Your gut is a complex ecosystem which normally contains hundreds of different species of bacteria ( http://www.answers.com/topic/intestinal-flora-2 ). Your gut flora is different from everyone else's. It would be tedious, expensive and not very helpful to test you for hundreds or even thousands of species of bacterial flora. I would be wary of any test which purports to tell you about the health of your gut flora. What's "normal" for someone else may not be normal for you.

Furthermore, as Acton pointed out in a previous thread, it is nearly impossible to permanently change your gut flora with agents such as probiotics ( http://paleohacks.com/questions/1435/what-is-the-best-way-to-re-populate-the-gut-with-beneficial-flora#axzz13Is7ZZdR ).

If you are not having any symptoms, I wouldn't worry about the organisms in your gut. However, if you're having symptoms such as diarrhea, constipation, cramps, bloating, etc., you can be tested for bacterial pathogens, parasites, food allergies or celiac disease.

You can fix your gut flora by treating your underlying condition (infection, allergy, celiac, poor diet, etc). But you usually cannot cure your underlying condition by treating your bowel flora.

Are there any kind of medical tests to determine which bacteria do you have and which do you lack.

Yes. This kind of testing is done in a number of ways. Older tests are based mainly on culturing. The cultured colonies are subjected to a variety of morphological and biochemical tests. Modern tests use molecular technology such as polymerase chain reaction (PCR) which uses DNA to identify species of bacteria.

One company that offers PCR testing is Metametrix. They call their test "GI Effects Complete Profile -- Stool." Here's a sample report from their test:

Metametrix sample test report

As you can see from the sample, Metametrix tells you the relative quantities of a variety of bacteria. They include both aerobic and anaerobic types.

How much does this cost? Metametrix doesn't publish a price for this test, but the IBS Treatment Center, which is a reseller of PCR gut flora testing, charges $350. I don't know whether IBS uses Metametrix or some other lab.

IBS Treatment Center test description

Diagnos-Techs, which was recommended in another answer, apparently uses older-culture based techniques. (I say apparently because I can't find a description of their methods on their website.) Here's a sample report from them. As you can see, they look at fewer species of bacteria and they don't tell you the quantities of each one:

Diagnos-Techs sample test report

If you want to know more about the various techniques used for identifying gut flora, here's an article from the scientific literature:

O'Sullivan DJ. Methods of Analysis of the Intestinal Microflora. Curr Issues Intest Microbiol. 2000 1(2):39-50.

The one thing I can think of is food allergies. More gut damage = more allergies.

Yes there are. The one I like the best is from diagnos techs. Not sure if I'm spelling that right but they do a great job. I use this testing all the time in my naturopathic practice.

if your gut flora is off it can change your mental state; brain fog, depression, irritability, fatigue.

your health and your mind state depends on your gut.

One thing I wonder about is if your gut flora is traditionally established as a result of exposure to fecal bacteria during birth, doesn't that mean that you would permanently destroy that colony with a single round of antibiotics? I mean, how would you be able to reestablish colonies of hundreds of species of bacteria, some of which are anaerobic? I'm not sure that you pick them up as you go since they would for the most part be destroyed by stomach acid.