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The Gut Microbiome

Updated: Jun 10

The term “gut microbiome” or “gut microbiota” was not very commonly used until recently. In 2013, a PubMed search for “gut microbiome” or “gut microbiota” returned 1,472 results. A decade later, the number of results increased tenfold to 14,728. But interest in the gut microbiome has extended outside of the medical and scientific community and has permeated popular science. The topic has even infiltrated TikTok and has its own #guttok hashtag, which unfortunately contains a lot of pseudoscience, such as how to “fix” your gut microbiome overnight, with proof being a less bloated-looking abdomen. 


The importance of a healthy gut microbiome is becoming more apparent as more research is done. So, it is becoming increasingly important to parse out evidence-based information from pop culture pseudoscience. 


The gut microbiome contains a diverse population of bacteria, viruses, and archaea. Most of them are symbiotic, meaning they help the body, and the body helps them. They are involved in our immune system functions, help break down toxins, and are essential to the synthesis of B vitamins and vitamin K. Additionally, these microorganisms help break down more complex carbohydrates. Therefore, what we ingest (or do not), what other diseases we have, and even our genetics play into our gut microbiome. The gut microbiome is often referred to as an organ of its own, but unlike most other organs, the gut microbiome is more of an ecosystem in and of itself that begins growing the moment we are born. 


Infancy and Childhood 

Some bacteria are passed to fetuses in utero, but colonization of the human microbiome truly begins at birth. In a vaginal delivery, an infant is exposed to many types of bacteria when passing through the birth canal. Not only the number of bacteria is compromised, but the diversity is also compromised in cesarean sections where an infant is not passing through the birth canal. Many C-sections are medically necessary for the safety and health of the mother and baby, but scheduled ones have become increasingly common worldwide, though there is no real benefit much of the time. Additionally, after vaginal delivery, a baby is usually swiftly whisked away to be wiped off because they do not come out looking clean. But in fact, the stuff we see on the baby, known as the Vernix Caseosa, that is often considered gross actually has antibacterial, wound-healing, and moisturizer properties


Babies’ microbiomes continue to grow through exposure to new environments and, importantly, breastfeeding. Breast milk contains probiotics and prebiotics that are crucial to keeping the gut microbiome balanced and mediating the effects of harmful bacteria.  


Composition of human breast milk

Image 1: Composition of human breast milk

While research has now made it quite obvious that a newborn needs beneficial bacteria to help keep them safe since they do not have an immune system, it is not as obvious how far these benefits extend into childhood. One study found that one-year-old children with immature gut microbiomes whose mothers had asthma were at an increased risk of developing asthma at 5 years old. Though the reason is not entirely clear, it seems that these children are already susceptible to developing asthma, and those with a more diverse and mature gut microbiome were able to reduce that risk during the first year of life. However, more research is needed to determine whether microbial supplementation would be beneficial for those children who may be in a situation where they are not able to properly form their microbiome, such as prolonged exposure to antibiotics. 


The gut microbiome plays a role in mediating weight through protecting against harmful microbes in the intestines, breaking down complex carbohydrates, and regulating fat absorption. While obesity is the result of many other factors as well, early colonization of the gut microbiome has been shown to play a role in the development of childhood obesity. Meta-analyses have reported a 33% increase in the development of childhood obesity in children born via C-section. Long-term studies following infants at birth are needed to discern how all of these factors interact in the development of the dysregulated gut microbiome and its connection to obesity in childhood. 


Disease Development 

Perhaps unsurprisingly, the gut microbiome is heavily involved in inflammatory bowel diseases, including inflammatory bowel syndrome (IBS), Crohn’s disease (CD), and ulcerative colitis (UC). These chronic conditions are thought “to develop as a result of interactions between environmental, microbial, and immune-mediated factors in a genetically susceptible host.” Many animal studies have shown that altering the microbiome of mice results in inflammation like that of IBD in humans. These studies have also shown that altering the immune system of mice can make them more susceptible to this inflammation and even induce colitis. This relationship between genetic susceptibility and immune-mediated factors is also apparent in humans.

Components of the gut-brain axis

Image 2: Components of the gut-brain axis

One investigation observed that the likelihood of developing inflammatory bowel disease (IBD) in childhood escalated by 2.9 times when antibiotics were administered once or more during the child's initial year of life. 


While research continues into the more obvious areas affected by the gut microbiome, other connections are being explored as well. The gut-brain-axis is a relatively new association but has already impacted how we think about brain health. One potential cause of cognitive decline and movement dysfunction is chronic neuroinflammation, which occurs naturally in aging brains as well, just not to such a degree that everyday functioning is affected. The anti-neuroinflammatory diet consists of foods rich in probiotics, prebiotics, and antioxidants that are minimally processed and low in fat and sugar. These foods work to provide sustenance for the beneficial bacteria in the gut, which in turn help modulate metabolism and inflammation throughout the body and within the brain. Additionally, an anti-neuroinflammatory diet can help with mental health disorders. One meta-analysis study found that individuals who reported eating more inflammatory foods also had an increased risk of depression. These studies highlight the importance of healthy and informed diet choices for not just physical health but mental health as well. 


What to Do with the Information (and Disinformation) About the Gut Microbiome 

For many people, the gut microbiome is an abstract idea, so it does not seem as straightforward as something such as heart health, where we know that fat results in clogged arteries. But if we think of the gut microbiome as its own organ living in its own ecosystem, which interacts with the rest of our body, we can put into perspective the role it plays in our overall health.  


Though research on the gut microbiome has moved very quickly, there is still much to be explored before anyone can make definitive statements about how the gut microbiome is connected to certain diseases. Scientists are currently in the process of characterizing the varieties of bacteria present in the human gut. It will require many years of studying numerous individuals to differentiate the effects of specific bacteria from environmental and genetic factors in the development of diseases. It is improbable that this effort will lead to a universal cure, but it will serve as a guide to inform treatment and lifestyle adjustments.  


In this time where so much is still being discovered, it is perhaps most important to remember that everyone has a different gut microbiome. So, seeing someone online claim that eating or drinking something in particular will eliminate your bloating, or that doing something will “fix” your gut is not guaranteed to work for you or anyone else. The best approach for now is to listen to science, listen to our own bodies, and try to live overall healthy lives. 

Written by: Amanda Wilburn 


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