The gastrointestinal tract is actually a dynamic organ system, in other words, more than just waste system. More than 70% of the immune system resides in the gut. Dr. Leo Galland is a MD who treats M.E. patients and has many great articles at mdheal.org. He states that when ME patients come to him, the first place he looks is in the gut and he is looking for pathogens. The GI tract would be the most suspectible to infection and Galland believes that is why there is a majority of the immune system is there.
The gut is a very diverse organ which has a plethora of organisms residing in it (e.g. bacteria, yeast, and many other organisms), this is known as the microbiota. The gut is also a symbiotic environment (unless you are sick) which means all that diversity co-exists and has mutual relationships. When an organism becomes dominant and it is a pathogen, then the immune system will kick in to control the situation. Activation of the immune system generates all kinds of issues such as higher oxidative stress etc. Immune activation in the gut also leads to "leaky gut" which creates more inflammation, inflammation leads to other issues (taxes a number of systems).
It can be sometimes difficult to find out what the gut is dealing with, so testing may be hit or miss. There are some stool culture tests you can do but some of these become analysis paralysis, sometimes the results can be clear.
Most groupings are bacteria (gram negative and gram positive), yeast/fungal, parasitic which can include protozoa species. For myself, I address it with natural methods. For instance, I would decrease sugars which can feed certain species, I would remove fresh dairy because if you have an infection, you likely have a secondary lactase deficiency. Aged cheeses are ok meaning they have less lactose. I would also increase fresh vegetables which will help cultivate healthy bacteria, I make sure they are sanitized to decrease the risk of other possible pathogens. I might try some kefir which seems to work best, I try apple cider vinegar or other fermented foods which could increase healthy bacteria and colostrum which also acts as prebiotic. You could find that these last items may not work.
I increase natural antibiotics such as garlic, oregano, black seed, drink chai tea (which has many natural antibiotics), coconut oil, curry spices (Sharwood's has about 8 spices that are all antibiotic).
I find that using a wider spectrum of treatment is more effective. The reason for this is that not all pathogens are created equal, meaning that substance A may kill pathogen X, but may not be effective against pathogen Y, so by increasing the spectrum of natural antibiotics, my chances increase. If a substance is effective, then you should see some results by days 7 to 10.
The information should be considered educational and not a diagnosis or a guide to treatment. Please consult your healthcare professional.