Microbiome 101
The microbiome has become a pretty popular buzz word these days. And for good reason! One of very first questions I ask all my patients and clients is always, “How is your digestion?” Research on the microbiome claims it has a seemingly miraculous ability to influence everything from mood and gastrointestinal health to autoimmunity and neurological disease. So what exactly is the microbiome? Around the end of the 20thcentury, scientists started digging more into the idea that we have bacteria (and other microorganisms such as fungi and archaea) that reside in/on us but are not actually harming us (a contrast to the prevailing germ theory which states that specific germs explicitly cause certain diseases); rather, this collective community may actually be of great benefit. The microbiome is the collection of trillions of extremely tiny critters, and all their genetic material, that is inside and on top of (really all around) us. The food we eat, entry into life (cesarean vs vaginal delivery), breast-feeding vs formula feeding, and the environment we surround ourselves in all inform our microbiome.
We have learned that the microbiome is largely responsible for nutrient digestion and absorption, vitamin production (some B’s and K, vital to neurological function and blood coagulation, respectively), immune regulation, toxin degradation and excretion, and several other extremely important elements of human physiology.1 Surprisingly, around 70% of our immune system is actually in our gut! When we ingest fiber in the presence of healthy gut bugs, they break it down into little anti-inflammatory compounds called short chain fatty acids (SCFA). SCFAs are responsible for keeping the lining of our gut (and our brains) nice and healthy (a contrast to the popular term “leaky gut” which implies an interrupted gut lining). SCFAs also help protect against dysbiosis (an alteration in the microbiome where unfavorable strains crowd out beneficial strains) by keeping the pH of our intestines low and unfavorable for pathogens. In addition, our commensal (friendly) bacteria help us produce neurotransmitters such as GABA and serotonin (colloquially known as the calming and happy neurotransmitter, respectively). This is why drugs that affect the brain also often affect the gut, and vice versa. These physiologic components of the microbiome are just the beginning of a larger discussion around the complex gut-brain-axis and the Vagus nerve (the 10th cranial nerve) that is central to afferent (to the brain) communication. Our body is continuously detecting the climate of our microbiome and feeding that information back to our brain in a two-way communication. It is (we are) all connected.
When you really think about it, all this information means we delegated HUGE parts of our intricate physiology to these bugs. It is no wonder that chronic disease is on the rise when we consider how often we bomb these critters with an antibiotic that is non-selective in the bacteria it destroys. Certainly, antibiotics, and the advent of penicillin, have saved millions of lives. But we are now in a situation where we must continuously weigh risk vs benefit, especially in the presence of chronic disease. In fact, researchers from Stanford showed that though some species are able to recover about a month post-antibiotic intervention, some strains failed to recover within 6 months.2 They concluded in a later study that, “antibiotic perturbation may cause a shift to an alternative stable state, the full consequences of which remain unknown.” 3 Unfortunately, antibiotics are not the only microbiome-altering synthetic agents out there. Common drugs, even over the counter medication, can affect your microbiota including laxatives, proton pump inhibitors (medication often used to address symptoms of acid reflux), metformin, and NSAIDs (non-steroidal anti-inflammatories).4,5 Thus, avoid unnecessary exposure for yourself and take medications only when medically indicated. If you are interested in coming off those medications, it is wise to speak with a healthcare provider that can help guide you through this (or a naturopathic physician that can get you feeling so good with lifestyle changes that you don’t need them in the first place).
A quick note: Interconnection with the endocrine system (hormones)
Another related and growing challenge facing individuals in the U.S. is the loss of consistent hormonal homeostasis (or physiologic balance). When our bodies start to adjust to prolonged hormonal imbalances, we can experience all kinds of physical and/or psychological distress. The discussion of hormones is for another time, but for the purpose of today’s discussion, you want to understand that hormone status is directly connected to the microbiome.
An example of this intelligent interconnected network is estrogen, a hormone found in varying amounts in both men and women. Estrogen is first conjugated in the liver, which basically means your liver attaches a little tag so that estrogen can continue to work its way through, and eventually out, of your body. (NOTE: this process itself requires proper levels of nutrients such as B vitamins, zinc, magnesium and relatively low levels of other toxins. This is why even one alcoholic drink per day can plug up this process and increase your estrogen levels.) Your conjugated (“tagged”) estrogen is then eliminated via your stool in the presence of healthy gut flora. If unhealthy gut flora are present, they can produce an enzyme called beta-glucuronidase which deconjugates your estrogen and reactivates it. This reactivated estrogen is now in a perfect position to be reabsorbed (known as “enterohepatic circulation”) by the body, a phenomenon that can create estrogen excess, a relatively common hormonal state that both men and women find themselves in today. So, to recap, the presence of unhealthy bacteria paves the path for you to accumulate more estrogen in your body.
If you are curious about your microbiome, it is best to talk to a provider that is well-versed in it as it is still a relatively new discovery and the unfortunate truth is scientific research tends to dramatically precede clinical action (by ~15 years). Naturopathic physicians are primed for this discussion as we are trained in identifying the root cause of illness, a root that many would argue starts in the gut (for the aforementioned reasons!). You can schedule a time to chat with me by clicking here.
In general, the best way to improve your microbiome is to feed the good bugs by eating a healthy, whole food-based diet with plenty of fiber and filtered water. Similarly, the characteristic “unhealthy” bugs thrive when we consume foods that feed them (ie. sugar, chemically laden, highly processed foods) and allow them to persist.
NOTE: I am a doctor, but I am not your doctor and I do not know any of your medical background or history. This information is meant to be informational/educational and is not intended as medical advice. Please consult with a physician prior to adjusting your treatment regimen.
1. Jandhyala SM, et al., Role of the normal gut microbiota. World J Gastroenterol. 2015;21(29):8836-8847. doi:10.3748/wjg.v21.i29.8787
2. Dethlefsen L, Huse S, Sogin ML, Relman DA. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 2008;6(11):e280. doi:10.1371/journal.pbio.0060280
3. Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A. 2011;108 Suppl 1(Suppl 1):4554-4561. doi:10.1073/pnas.1000087107
4. Vich Vila A, Collij V, Sanna S, et al. Impact of commonly used drugs on the composition and metabolic function of the gut microbiota. Nat Commun. 2020;11(1):1-11. doi:10.1038/s41467-019-14177-z
5. Rogers MAM, Aronoff DM. The influence of non-steroidal anti-inflammatory drugs on the gut microbiome. Clin Microbiol Infect. 2016;22(2):178.e1-178.e9. doi:10.1016/j.cmi.2015.10.003