SCFA

Everything "rots" in your colon, and it's not a bad thing at all
08/05/2012 - 22:12

 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.

Home is where the gut bacteria is
05/11/2012 - 21:45

 Ugh, I got back from Europe this week and I feel like I have so much catching up to do. Books to review, emails to answer, projects to finish, mad programming skillz to acquire, apartment to spruce up... and somehow every night I go to bed with so much undone. More about my travels later, as there is an interesting new paper out.

I've written about the need to sample gut flora from different cultures before they are "acculturated" to an industrial diet, so I was delighted to see Human gut microbiome viewed across age and geography. The researchers sampled the gut microbiomes of 115 rural villagers from Malawi, 100 Guahibo Amerindians from Amazonia in Venezuela, and 316 people from the greater metropolitan areas of St. Louis, Philadelphia, and Boulder. They found significant differences between the gut bacteria in these three populations. 

Now while you may be familiar with the standard American diet, the diets of the other populations are bit more obscure. The researchers thankfully provided their diet survey in a table in a zip file. 

Some common foods the Guahibo ate (24 hour recall) were

  • Corn arepas/Bollito
  • Cassava cake
  • Soup (what was in the soup though??)
  • Coffee (haha)
  • Sugar (lol) and sometimes sugar cane juice and soda
  • Milk (I wouldn't be surprised if the government is providing this)

Consumption of meat and fish seems rare. Sadly this diet already seem significantly industrialized. 

In Malawi some common foods (recall over a month) include

  • Nsima, Corn porridge, and pigeon peas are the staple foods
  • Sweet potato, banana, cassava, rice
  • Some fruits like oranges, mango, and papaya
  • Greens like pumpkin, mustard, and sweet potato leaves
  • Vegetables like onions and tomatoes
  • Meat from chickens, cows, goats and pigs pretty rarely, though it seemed that some individuals were eating a lot more meat than others, a few were eating it every day
  • Small fish and eggs more common
  • Biscuits/cookies
  • A few people were using vegetable oil

I wish they had used a consistent method for food surveys and provided more information about the diet. Perhaps there needs to be more collaboration in this field with anthropologists?

Each different community of adults had its own particular microbiome signatures, but the Malawaian and Amerindians were less distinct from each other than the Americans were from the two other populations. Interestingly the researchers said that the differences in functions parallel those between carnivorous and herbivorous mammals. Malawaian and Amerindians microbiomes contained more genes for glutamate production, whereas US gut bacteria seemed more focused on degrading it. US gut bacteria also contained more genes for degrading other amino acids like aspartate, proline, ornithine, and lysine, as well as the use of simple sugars. Richer numbers of genes involved in synthesis of biotin and lipoic acid, processing of xenobiotics, and bile salt metabolism, which the researchers thought was related to the higher fat content in the American diet. Malawaian and Amerindian gut bacteria produced more amalyse, which is important for degrading starch. 

Another thing they found, which has also been found in other studies, is that as people in all the cultures aged, their gut bacterial populations changed. In infants, Bifidobacterium dominate, but their presence declines in early childhood. Functionally, infant gut bacteria had more genes involved in making folate, whereas adults had more bacteria with genes for metabolizing dietary folate. Adult gut bacteria also contained more genes for producing B12, vitamin B7, and vitamin B1, as well as processing of arginine, glutamate, aspartate, and lysine. Not surprisingly, infants microbiomes were enriched in enzymes involved in foraging of glycans from breastmilk. 

The authors concluded that "Together, these findings suggest that the microbiota should be considered when assessing the nutritional needs of humans at various stages of development." I think this is another good reason to question the idea that human breastmilk provides some sort of model for how humans should eat. 

Some genes involving glycan processing were more common in the Amerindian and Malawaian baby microbiomes, which the authors thought might be related to differences in glycan content of breastmilk. While all the samples used were from breastfed babies, I would be curious to know whether or not the babies were being exclusively breastfed. Supplementary formula could be an issue in the US and many other cultures use carbohydrate-rich supplementary foods even in young infants. But the researchers say these glycan processing genes decreases during maturity in Malawaian and Amerindian babies as they transition to diets rich in complex plant-derived polysaccharides, whereas they increase with age in US infants as they become exposed to diets rich in easily-absorbed sugars. However, the dietary survey says the Amerindians were eating a lot of sugar every day, so I'm not sure of that.

The Malawaian and Amerindian infant microbiomes were rich in urease gene representation, which was uncommon in both infant and adult American microbiomes. Urease can be used to produce amino acids and recycle nitrogen, which is important when diets are deficient in protein. 

The supplement contains a comparison of breast and formula fed babies show that formula-fed microbiomes were more focused on carbohydrate (fructose, mannose) and amino acid metabolism, with more genes involved in biosynthesis of B12. 

For me this paper raises more questions than it answers. How plastic are these populations? What happens when you feed an American adult an Amerindian diet? Would the gut bacteria be able to shift or is it too late? 

There aren't any studies on this that I know of yet, but I did read a study recently that was very interesting: Modulation of fecal markers relevant to colon cancer risk: a high- starch Chinese diet did not generate expected beneficial changes relative to a Western-type diet. The study didn't look at gut microbiome genes or populations, but it did examine many of the products of the gut microbiome, such as short-chain fatty acids, as well as other colonic markers associated with lower risk of colon cancer. The study basically wanted to see if they could shift these by shifting the diet. Would Australians eating a high-starch "low-income" Chinese diet have the same favorable products and markers that the Chinese had? Unfortunately, after three weeks all the results besides fecal PH were worse! Too bad the study was only three weeks though and the diets actually seem kind of weird, but then again I've never been to Australia:

I guess processed oil has been used for long enough in China that most Chinese people I know, even older people, consider it a traditional food...

Furthermore, how responsive are the gut bacterial populations to cultural change? It seems like the Amerindians are now consuming a significant amount of processed sugar, yet this doesn't seem to be reflected in the gut microbiome. They don't seem to be getting closer to the features of the American gut microbiome that the researchers theorized might be related to sugar consumption. Will this happen over generations? Or are the gut biomes of cultures as resistant to change as those of individuals? It would be interesting to study the gut microbiomes of migrants vs. the original population the migrants came from. Also, I'd be curious about the outlier individuals from the dietary survey, such as the couple of Malawaian individuals who reported consuming meat every day. Does their gut microbiome reflect this? What would happen if you compared American vegetarians with American omnivores?

Also, this adds another layer of complexity when looking at traditional diets. Can you get all the health benefits of a particular culture's diet if you don't have their microbiome? How many health differences between populations are explained by different microbiome heritage rather than diet? 

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