Scientists at Harvard University have proposed a new model for studying nutrition, human embryonic stem cells. Human embryonic stem cells are unique in their ability to turn into all the cell types in the body, including the various tissue types in the human gut.

Drs. Doug Melton and Danny Ben-Zvi propose in an essay in Cell that human embryonic stem cell derived tissues populated by gut microbiota may be an ideal system for studying the physiology of digestion and nutrition. The authors state that the mechanisms of human nutrition are largely unknown and that it is difficult to model how nutrition affects human health on a biological front. By developing systems of stem cell derived tissues, it may be possible to model the gut in the petri dish or even on a chip. Significant engineering advances have been made to model biological systems on a chip. These chips are devices with specific cell types in chambers that are connected through microfluidic channels to better model the tissues and organs in the human body and how they interact with one another.

Chips could be developed that are made of up cells of the various organs that make up our gastrointestinal tract. These organoids could then be populated by bacteria that make up the microbiota. Food could be passed through the chip and scientists could watch bacteria break down food that is passing through it and see how the microbiota adapts to changes in diet. Various conditions could be tested such as what bacterial strains are best at digesting complex carbohydrates? The authors state that many combinations of bacterial strains should be tested to find what bacteria conduct these tasks most efficiently. To do this in mice would require thousands of animals and this may be too restrictive to conduct such experiments. This however could be done using chips with stem cell derived tissues that make up our GI tract and connected through microfluidic channels to stem cell derived liver and pancreas cells that are important for nutrition and digestion.

Significant biological and engineering challenges still exist before this is a reality, including the ability for specific strains of bacteria to thrive in such an environment. However, if some challenges can be overcome, the authors propose that the complexity of nutrition and digestion could be better dissected using systems of stem cell derived tissues in the dish. This work would complement existing research using model organisms and epidemiological and other human studies to better address the questions that we ask every day about what food we should eat and the effects this has on the human body.

There is a common saying “You are what you eat.” But is this actually true? A lot of attention has been paid to the microbes in our gut and the effects they have on disease and nutrition, but little has been reported on what microbes are in the food that we eat on a daily basis and the impact that this has on our microbiome and the microbial communities in our body. A team of three scientists at the University of California, Davis set out to characterize the microbes that are in three different dietary patterns.

Published in the journal PeerJ, the scientists described the microbial communities in a typical American diet, a USDA recommended diet, and a vegan diet. The American diet consisted of convenience foods like Starbucks, McDonalds, and Stouffer’s frozen food. The USDA recommended diet consisted of foods such as fruits and vegetables, lean meat, dairy, and whole grains. The vegan diet excluded all animal products (at the bottom I have included what exactly was in each diet).

The USDA diet contained by far the most microbes at approximately 1.3 billion per day, while the vegan diet came in second with about 6 million microbes, and the American diet last at 1.4 million microbes. The USDA diet consisted of many live active cultures such as yogurt and cottage cheese which was most likely the reason for the higher number of microbes.

This study did not answer the important question of what happens when we ingest these foods and what impact does diet have on our microbiome. But it opens up the door to many further questions about the impact that our diet has on our microbiome. This study was only a small study and while previous studies have shown that microbial shifts have been seen after a large change in diet, we still do not know how readily the microbes in our food colonize in our gut. While this study suggests that different diets vary in terms of the number and composition of microbes we consume, further studies need to be conducted to better understand its impact as well as other factors such as cooking techniques and processing have on our microbiome.

As a side note, one of the authors of this study, Dr. Jonathan Eisen, writes a very interesting blog himself and if you are interested in the microbiome, I recommend you take a look. Here is his post about this recently published work.

And if you are interested in exactly what was in diets that they studied, here it is:

The American diet consisted of a “large Starbucks Mocha Frapuccino for breakfast, a McDonald’s Big Mac, French fries, and Coca Cola for lunch, Stouffer’s lasagna for dinner, and Oreo cookies for a snack.”

The USDA recommended diet consisted of “cereal with milk and raspberries for breakfast, an apple and yogurt for a morning snack, a turkey sandwich on whole wheat bread with salad (including a hard-boiled egg, grapes, parmesan cheese, and Ceasar dressing) for lunch, carrots, cottage cheese and chocolate chips for an afternoon snack, and chicken, asparagus, peas and spinach on quinoa for dinner.”

And the vegan diet consisted of “oatmeal with banana, peanut butter, and almond milk for breakfast, a protein shake (including vegetable-based protein powder, soy milk, banana and blueberries) for a morning snack, a vegetable and tofu soup (including soba noodles, spinach, carrots, celery and onions in vegetable broth) for lunch, an apple and almonds with tea for an afternoon snack, a Portobello mushroom burger (including Portobello mushroom, avocado, tomato, lettuce, and a whole wheat bun) with steamed broccoli for dinner, and popcorn, hazelnuts and fig bars for an evening snack.”

Can human embryonic stem cells model human nutrition?

What microbes are in the food we eat?