your gut : a bag and 2 pipes

stomach : small bag on the upper left abdomen. preparation bag.
small intestine : long thin coiled pipe designed for maximum absorption
colon : wide shorter looping (one loop) pipe. recycling plant. loads of bacteria

The digestion system seems likely to play a part in fecal body odor and other metabolic body odors (e.g. secondary trimethylaminuria), so it's probably important we understand it best as possible. This post is about the basic visual and mechanical structure and main purposes. What does the gut look like and do ?

Stomach : a small bag on the upper left hand abdomen. This is where food first ends up. Generally it is held here and turned to mush and then released into the small intestine through the pyloric valve in small controlled amounts. Simple carbs won't stay long, whereas a meal will take a while. Hydrochloric acid is added to it, and some other things to make it easier to digest. The mush is called 'chyme'. Each part of the intestine is separated by valves.

Small intestine : A long thin pipe that coils in an overlapping way. This is the main absorption point. It is designed for maximum absorption of molecules of a certain small size. There are millions of finger-like microvilli on the lining (like a carpet) to make 'catching' the molecules easier. It's this microvilli that is wiped out in full-blown celiac. The pancreas puts digestive enzymes into the pipe early on to break down the food, and bile is also squirted in by the gallbladder to digest fats. The absorbed molecules go into the portal vein and then are taken to the liver for filtering before entering the main circulation. The intestine acts as a barrier so that large molecules cannot get into the portal vein unless broken down. With leaky gut (which is really leaky small intestine), large molecules can get through junctions in the barrier and so are absorbed when they shouldn't be. Because you want maximum absorption here, there is usually very few gut microbes here, especially at the top end, largely because they would compete with you for the food. The small intestine is known as 3 parts ; duodenum, jejunum, ileum. Many feel that when someone has gut candidiasis overgrowth, it's growing at the ileum (for example). However, it's likely that overgrowth of anything in the colon will cause problems too. The small intestine and colon are separated by the ileocecal valve.

Large Intestine/colon : A short, wide pipe that ascends from your appendix area, goes up to your ribcage and across, and down the other side and then loops to the anus. the colon is where most bacteria is, even in a healthy gut. Good flora scavenges from any leftover food/chyme and many produce helpful fatty acids. The protein/sulfur eating bacteria tend to be at the lower left side of the colon (near the end). The chyme becomes feces as water is absorbed and the 'rubbish' is then exited.

It's probably more complicated than that but hopefully this gives you an image in your mind of what the gut mechanically looks like.

What goes wrong ?

Some examples. If anything is wrong with the digestion enzymes such as HCL, pancreatic enzymes, bile etc, you can end up with too much undigested food entering the colon which will likely alter the flora ecology detrimentally. for instance too much protein getting into the colon.

If the tight junctions in your small intestine barrier cells are weakened you can absorb molecules too big that are not intended to be absorbed. These enter the portal vein and are sent to the liver which likely regards these as unexpected molecules.

If conditions aren't right, perhaps microbes can colonize the lower small intestine or further up.

Perhaps the colon microbes can be unnaturally altered and produce toxins. In Secondary TMAU, the diagnosis means there is too much trimethylamine produced. It's currently thought the bacteria that produce this are in the colon, so it means overgrowth of this bacteria. Who knows if this bacteria can grow in the small intestine as well. Presumably no-one is currently looking whereas a Body Odor & Research center likely would be.