Did you know you are a minority in your own body? You have more visitors in your body than you have of your own cells, up to 3 times more. These visitors include bacteria, eukaryotes, viruses, fungi, and even archaea and are collectively referred to as a “microbiome”. In exchange for a warm home and food, the microbiome makes vitamin K, helps break down food, modulates our immune system and supports a healthy mood. So obviously the microbiome is super important for health. Disturbances to the microbiome are implicated in many health conditions:
Heart disease
Irritable bowel syndrome
Inflammatory bowel disease
Depression
Anxiety
Asthma
Acne
Eczema
Obesity
Type 2 diabetes
Psoriasis
Rheumatoid arthritis
This is by no means an exhaustive list. How the microbiome can impact such disparate aspects of the body is not completely understood, but we have a pretty good grasp of several mechanisms: immune modulation, neurotransmitter creation and degradation, and synthesis of nutrients.
Whenever I have a patient with an autoimmune disease, one of the first things we do is a stool test to evaluate her microbiome. Why? Well, somewhere around 80% of our immune system resides in the gut-associated lymphoid tissue (GALT), which is a fancy way of saying the immune system’s home base is in the gut. So because the immune system is the issue, we have to go to the source, therefore we look at the gut.
The immune system’s job is to recognize stuff that isn’t part of you, and to attack and destroy anything it finds and identifies as ‘not you”. If you want to calm down the immune system, as in the case of autoimmune disease, you need to identify what is revving the immune system up. For instance, in rheumatoid arthritis, oral bacteria such as Porphyromonas gingivalis (P. gingivalis), Proteus mirabilis (P. mirabilis), and others like Epstein–Barr virus (EBV) and mycoplasma have all been implicated as causal agents. If you want to get to the root cause of rheumatoid arthritis, you look at the microbiome, and so it goes for any autoimmune condition.
The immune system is constantly surveilling the intestines, sorting through what is food, what is friend and what is foe. When the microbiome is imbalanced and you have bad bacteria, the immune system reacts (as it should), but there is often collateral damage. Much like the stuffy nose you get with a cold, the symptoms are from our own immune system, and not so much the invader. If you’re interested in reading more on this topic, here is a great journal article: http://jem.rupress.org/content/216/1/20
The next big job of the microbiome is to create and degrade neurotransmitters like serotonin and histamine. There are actually lots of serotonin receptors in the GI tract, and it plays an important role in GI motility (pooping daily). But these neurotransmitters also travel up the vagus nerve and can impact brain health, hunger and satiety, and even stress levels. Here’s a cool research article on this: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5859128/ So whenever I have a patient with any sort of seemingly brain issue, I always ask about digestion.
Lastly, the microbiome impacts our nutritional status. We’ve known for a long time that many B vitamins and vitamin K are made by bacteria. But bacteria are also vital for the proper breakdown of carbohydrates. Bacteria make short chain fatty acids (SCFA) from these carbohydrates, which serve as the main fuel source for colon cells. SCFA’s also prevent heart disease, and should there be a cardiac events, it is less damaging. Bacteria also create amino acids like threonine and lysine, which is important for the immune system. So if you don’t have a healthy microbiome, it doesn’t matter how great your diet is, you will still be missing out on key nutrients.
I’m certain we will discover more ways that the microbiome impacts our health, but even with just the three we talked about, there is still a massive impact on our health. One of the best ways to promote a healthy microbiome is to feed them the proper food. Bacteria love fiber, so a diet high in fiber promotes good bacteria. You can also help reinocculate your gut with good bacteria by eating foods with live cultures, playing in the dirt, and having pets!
Sometimes these easy changes are enough to make a big impact on health, but sometimes the microbiome is so disrupted that we need to do a stool analysis to see what is throwing the microbiome off. It could be anything from yeast to pathogenic bacteria to low digestive enzymes. Once you know what the problem is, it is relatively easy to restore the microbiome to a healthy status, which in turn supports your whole body.