Home is where the gut bacteria is

 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?