Our intestine is home to three pounds of bacteria. We feed them and they feed us. They help us break down proteins, lipids, and carbohydrates from our food into nutrients that we can then absorb. Without them, we would not reap the benefits of the many foods we consume.
As an example, gut microbes contain genes that code for enzymes which break down plant polysaccharides we can then digest. Without our gut microbes, we would not be able to obtain nutrients from these carbohydrates. But where did our gut microbes get these genes in the first place?
From seaweed microbe to gut microbe
In 2010, researchers from Université Pierre et Marie Curie reported that genes used to break down seaweed carbohydrates were transferred from a marine bacterium to a microbe within the Japanese gut microbiome.
This transfer was (relatively) straightforward to decipher because marine algae contain polysaccharides different than those in terrestrial plants. These polysaccharides, such as agar and carrageenan, are not found in terrestrial plants and require different enzymes to break them down. The marine microbe Zobellia galactanivorans that dwells on red algae (also called nori) contains these enzymes, and more.
Upon examining the DNA sequences from Zobellia galactanivorans, the researchers found that the microbe contains five genes that encode for enzymes similar to those known to digest plant polysaccharides. These newly identified enzymes contain the signature pattern that indicates break down of marine polysaccharides but seem to be missing portions used to recognize agar and carrageenan. Instead the enzyme breaks down porphyran, typical of red algae.
To quantify the prevalence of porphyran degrading enzymes (called porphyranases), the researcher searched their sequences against a database containing all publicly available DNA sequences. All hits were found in marine bacterial genomes with the exception of one: the human gut bacterium Bacteroides plebeius which had only been isolated from the microbiome of Japanese individuals.
In their own studies, the researchers then found that out of 13 Japanese volunteers, there were seven potential porphyranases in the microbiomes of four people and six putative agar-degrading enzymes in four people. Out of these 13 individuals, a mother and her infant both had gut microbiomes containing porphyranase and agarase genes, suggesting that the microbes containing these genes are passed down generations.
In contrast, in the gut microbiomes from 18 North American samples, they found no porphyranases or agarose degrading genes in the gut microbiomes.
Seaweed past and present
The exact timing of the transfer of these genes is hard to pin down. The researchers believe this occurred relatively recent in the context of the millions of years of mammalian gut microbiome evolution. The sequences of these genes are relatively similar between that in the gut microbe and the marine microbe. Had the transfer occurred early in human gut microbiome history, these sequences would have diverged much further.
You are probably wondering whether or not this gene transfer can occur more frequently now that sushi and nori have become popular in the Western diet. It is unlikely that gene transfer events like this one occur because there is no selective pressure for these genes to hang around. On average, a day of Japanese cuisine means consuming 14 grams of seaweed; any gut microbes that have acquired porphyranases would more likely thrive with the constant source of porphyran. “The biggest difference in Japan is the quantity of seaweed that is eaten every day. It is far higher than just eating sushi once a week. I don’t think the pressure is high enough to keep the genes in our gut,” Gurvan Michel, an author from paper, told Nature. Furthermore, in the past, red algae were not roasted like it is today meaning that contact with seaweed-associated microbes is less likely today.
Shaping the gut microbiome
Now in 2018, a group of researchers from Stanford showed that when mice were fed porphyran along with a Bacteroides strain capable of using porphyran, they could introduce the strain into the gut microbiome of these mice. This only happens if the introduced strain could use porphyran: introduced strains that could not use porphyran did not colonize the gut.
And more strikingly, they were able to control the amount of the porphyran-digesting bacteria in the gut by varying porphyran intake. For each 10-fold decrease in porphyran administered, they saw a 10-fold decrease in abundance of the Bacteriodes strain.
In the distant future, it may be possible to “reprogram the microbiome” so that our microbiome could be customized to promote beneficial microbes in the gut, ward off disease, or modulate the immune system.
This account of seaweed and microbes shows us that this popular adage is true: you are what you eat.
Congratulations