What is the microbiome?
The microbiome is the bacteria that reside within and on our bodies. Often these bacteria do more than just hang out with us. Some bacteria fight off disease, while some cause disease. Others will help us digest foods or reject bad food. For this post, I am going to focus on the gut biome, the bacteria that live in our large and small intestines, because the gut has made for some interesting headlines lately. The “microbiome” refers to all of the bacteria on the body.
The small intestines have a plethora of bacteria that act symbiotically with us to help us digest and process foods. Scientists have been studying the gut biome for many years, but it is only recently that it has garnered public attention. There have been several theories lately that have suggested the gut biome is responsible for everything from food allergies to autoimmune diseases to autism. Furthermore, new diet fads, fecal transplants, and probiotic supplements have emerged as a result of the gut biome hype, many of which are untested or whose claims are unsubstantiated. As is the case with pop-science trends, the microbiome is becoming the poster child for pseudo-scientific claims and grandiose promises.
What does the research show?
Let’s start with some facts because the gut biome does affect our health and well-being. The National Institute of Health is currently working on the Human Microbiome Project. This project seeks to identify and characterize the bacteria (and fungi) that are associated with the human body. Similar to the Human Genome Project, the original plan was to characterize the microbiome of healthy individuals and then to compare it to unhealthy individuals in hopes of understanding the role the microbiome plays in disease. However, those goals may need to be adjusted.
The Human Microbiome studies have revealed two things: 1) no two human microbiomes are alike, and 2) the microbiome is dynamic. Because each person has a unique microbiome, there is not a gold-standard, “healthy” microbiome by which to compare “diseased” microbiomes. Also, because the gut biome changes with diet and environment, it is difficult to determine a particular signature for a person. It’s composition is just too dynamic.
Additionally, the microbiome’s composition (the types of bacteria that make up the biome) are different at different times depending on the individual’s diet and environment. This is especially true with the gut biome. There are hundreds of different species of bacteria that could potentially live in our digestive system, and those species may be in different abundances at different times. Furthermore, sometimes studying two different parts of the same sample will show different results. This is a classic sampling problem. Imagine that you wanted to find the amount of lead in soil in a field. You could collect soil from the top of the ground, which might give you a different lead concentration than if you took soil that was one foot underground or you might get different results if you took samples that were 100 feet away from each other. The gut biome has a similar problem. Apparently, the biome composition is different depending on where in the digestive tract you retrieve the bacteria (e.g., from a fecal sample or from the small intestines).
With these caveats, scientists have still observed some trends. For one, an individual’s gut biome changes after taking antibiotics. This makes sense because antibiotics are meant to kill bacteria. What is unclear is how long the changes persist and how this affects a person’s health.
Scientists also know that the gut biome plays a role in aiding digestion of certain hard-to-digest foods, such as carbohydrates. Furthermore, they have found differences between the gut biomes of obese people and non-obese people and between people with digestive diseases, such as Crohn’s disease. However, whether the different gut biome is the cause or is the result is unclear.
There are several other correlations between the microbiome and physiological effects. The difficulty is whether these are merely correlations or causation. William Hanage has an excellent article in Nature, “Microbiology: Microbiome Science Needs a Healthy Dose of Skepticism” in which he discusses five key questions to help discern the truth from the hype:
- Can experiments detect differences that matter?
- Does the study show causation or just correlation?
- What is the mechanism?
- How much do experiments really reflect reality?
- Could anything else explain the results?
Many studies show that the gut biome is very responsive to diet and environment, which means the differences we see in people with a certain disease (or condition) may be the gut responding to the disease rather than causing it.
The gut biome is a new area of research that may shed some light on digestive disorders and the effects of antibiotics on the body. However, Hanage cautions us to not fall into the same kind of non-discretionary, cure-all thinking that we’ve seen in other new areas of science such as the Human Genome Project, stem cell research, genetic engineering, or nanotechnology. He also remind us not to blame the microbiome for all of our ills: “In pre-scientific times when something happened that people did not understand, they blamed it on spirits. We must resist the urge to transform our microbial passengers into modern-day phantoms.”