"...natural remedies like olive leaf extract and soil based organisms which usually kill anything and everything in there."
I know that many -- possibly even a majority, but certainly many -- pathogens survive herbal treatments. Many folks on these boards end up using prescription Antibiotics
to clear up parasitic infections, if they're truly present (often the ailment is related to something other than bugs, such as IBS, food intolerance, food allergy
, gastro disturbance, fat malabsorption, lactose/mannitol/sorbitol sensitivity, etc.).
"What kind of bacteria is this?"
Might be something completely unrelated to bacteria. Protozoa, flaggelate, virus, worm, etc. Or IBS, etc. (see above).
"...what can I take to kill it???"
No amount of herbs, or advice on taking same, will help you it this is a sorbitol intolerance. Or IBS, etc etc.
"...but I think I now have some other organism infecting my digestive tract as well."
Clearly the time for clinical diagnosis has arrived for you (I assume you haven't done this yet):