Everything "rots" in your colon, and it's not a bad thing at all
The internet is full of vegetarian and vegan websites claiming meat is bad because it "rots" in your colon. This is actually a very old idea, tracing back in the United States to neo-puritan vegetarian movements obsessed with the uncleanliness of the colon. According to folks like John Harvey Kellogg, the colon, like the genitalia, was a source of uncleanliness, so it must be bombarded by as much harsh fiber as possible and regular enemas to keep it "clean."
But his philosophy, which seems quite dysfunctional today, was a reaction to another idea that was popular during this time: that the colon was a useless vestigial remnant used to store garbage before clearance. Taken to its extreme, it led to a brief fancy by surgeons like Sir William Arbuthnot Lane to simply just remove the colons of people who suffered from constipation, believing it was nearly useless anyway. Colon removals are still performed today, but mainly in truly serious cases of damage such as severe inflammatory bowel disease.
Kellogg also believed it was a garbage dispenser, but he thought it was very important to keep it as clear and clean as possible, ideally eliminating after every single meal.
The truth is that the colon is not a garbage dispenser, it is a rich and biodiverse ecosystem in which much of the intestinal microbiota resides. And nature abhors a waste, so if a food makes it into the colon, there will probably be something eager to eat it. I suppose "rot" could be an uncharitable way to view it, as these remnants are degraded by bacteria, producing a variety of harmful, harmless, and beneficial byproducts that can play important roles in human health. If we are going to view things in such a negative light, it's worth thinking about how when you die and your immune system flat-lines forever, this bacteria will be on the front lines for rotting you. But for now, it's our very own internal composting system.
our colon is more like a composting bin than a trash can
Being a rich, full ecosystem, some bacteria in the colon even feed primarily on the byproducts of other bacteria in the colon, which is known as cross-feeding.
These bacteria will consume basically anything that the small intestine does not absorb. In humans compared to other primates, the small intestine is enlarged and the colon is diminished, indicating that humans evolved to consume more foods that are readily absorbed by the small intestine. In other primates, like the gorilla for example, the small intestine is much smaller and the colon is much much larger. Gorillas, who eat a diet of mainly rough leaves and pith that the small intestine would not be able to absorb, get most of their energy (around 60%) from bacterial degradation to short-chain fatty acids (SCFA) in the colon.
Humans can also get energy from SCFA, probably as much as 9%, though this data suffers from the fact that most of it comes from Western populations. Recent studies on more diverse populations shows that other groups of people have very different gut bacterial populations, which might allow them to extract more energy from colonic fermentation. Overall, in humans SCFA are less important as an energy source, but retain an important role in controlling inflammation and gut integrity.
In the opposite circles of the "meat will rot in your colon" crowd, there is the idea that if you remove carbohydrates, particularly complex carbohydrates, from the diet you can avoid some of the more noxious types of fermentation in the colon that may produce flatulence and diarrhea.
This works for some people, but fails for others, particularly over time. This is a testament to the plucky nature of our microbiome. There are plenty of bacteria in the colon more than eager to chomp on excess dietary iron and amino acids, among many other things which are present on low-carb diets as well.
This problem can be exacerbated when the small intestine is damaged, allowing nutrients that should be absorbed mainly by the small intestine into the colon. This seems to be a reason that iron supplementation sometimes fails to improve anemia and instead causes gastrointestinal problems. It is also perhaps the mechanism in which heme iron could lead to inflammation that is connected with colon cancer.
Small intestine dysfunction can also be caused by the overgrowth of bacteria that really belong in the large intestine and colon, known as Small Intestine Bacterial Overgrowth (SIBO).
On the other side, there is a worry that low-carb will lead to inflammation due to lowered SCFA production. Lucas Tafur has written that perhaps these studies did not last long enough for the ecosystem to adjust and cross-feed in order to produce SCFA.
There is also a need for more studies on different people from different cultures in order to fully capture the full capacities of the human microbiome. For example, some people have cellulose-degrading bacteria, others do not. In the future, perhaps a scan of individual gut biomes could help people figure out what diet is best for them.
So yeah, lots of things "rot" in your colon. And that's not a bad thing at all. That's exactly how the colon is supposed to work. It's not supposed to be squeaky clean and scoured with wheat bran, it's supposed to be a jungle. It's controlling the "bad" bacteria and their byproducts, as well as selecting for good bacteria and maintaining the integrity of the gut lining and the "gut brain" (our second brain) that really matters.
If you enjoyed this post, you'd probably like my series on the colon.