Some of the microbes that often invade other organs of the body are rarely found in the stomach. Is the reason for this the presence of HCL?
Yes, but that is not the reason for its presence....
In order to stay alive, humans (like any other organism) need to break down the molecules in their food. This is done in the gastro-intestinal tract, that runs from the mouth to the anus.
Digestion already starts in the mouth, where the enzyme amylase in the saliva starts breaking down polysaccharides.
The rest of the chain can be broken down roughly into two sections: an Acidic section (the stomach) and an Basic (Alkaline ) section: starting with the duodenum via the small intestines and the colon to the rectum and the anus .
The Acidic section is extremely acidic: pH between 1.5 and 3.5, so it's a pretty hostile environment. A lot of macromolecules are already broken down here, either through the presence of HCl itself, and/or thanks to the presence of Pepsin (a protease)
The second section is less hostile. pH varies from around 6 in the duodenum to around 7.4 at the end of the small intestines.
In the last section (the colon, from ileum to rectum ) it wobbles between 5.5 and 6.7. Acidic again, but much less so than in the stomach.
By far most bacteria prefer to stay in the more friendly environment of the intestines/colon/rectum, forming the intestinal flora. Some enter via the backdoor (the anus ), but most of them have to pass the stomach.
In order to survive, different bacteria have developed different strategies. Some have very thick cell walls, enabling them to stay in the stomach and survive long enough to eventually pass on to the duodenum and beyond.
Others form spores that are impervious to the gastric environment and, once arrived in the intestines, "wake up" and come alive in the more friendly intestinal lumen. Best examples of this category: Clostridium Difficile and Clostridium Perfringens .
Special case: Helicobacter Pylori. This, and some others like it, produces an enzyme called Urease. This breaks down Urea (which is present in all our tissues) into Ammonia (
H. Pylori seems to actually like living in the stomach. Drawback is that its presence causes damage of the gastric lining, causing gastric ulcers .....