The Basics of the Human Microbiome

Many of us are aware there is an invisible world of life that resides within us—the human microbiome. While you might be familiar with the idea that your body is home to trillions of microorganisms, you may not realize the true extent of their influence on your health. Today, we’re taking a closer look at what exactly this invisible world contains and sharing some must-know information that will help you make the most of your health.

What is the Human Microbiome?

Let's get started with the basics. The human microbiome is essentially a diverse community of microorganisms—including bacteria, viruses, fungi, and archaea—that dwell within our body. Typically, they can be found in the skin, mouth, respiratory tract, and most prominently, the gastrointestinal tract—aka the gut.

The human body is home to trillions of microorganisms, most of which reside in the gut itself. This vast and intricate community of bacteria, viruses, fungi, and other microorganisms is collectively known as the human microbiome. Far from being insignificant, these tiny inhabitants have a large impact on our health—both mentally and physically. Their most prominent roles are aiding in digestion, bolstering the immune system, and even influencing our mood.

Defining the Microbiome

The term "microbiome" refers to the collective genome of all the microorganisms living in a particular environment. In the context of the human body, it usually refers to the gut microbiome. This ecosystem is incredibly diverse, with each person's microbiome being unique, much like a fingerprint. The gut microbiome is primarily composed of bacteria, and these microorganisms outnumber human cells by about 10 to 1, making them a large part of our biological makeup.

What is the Role of the Gut Microbiome?

Digestion and Nutrient Absorption

Certain foods, particularly complex carbohydrates and fibers, cannot be broken down by our digestive enzymes alone. The bacteria in our gut help ferment these substances, producing short-chain fatty acids and gasses as byproducts. These short-chain fatty acids are essential for maintaining the health of the colon and providing energy to the cells lining the gut.

Immune System Support

Much to the surprise of many, the gut microbiome is closely linked with the immune system. It acts as a barrier against harmful pathogens by competing for space and nutrients, thus preventing pesky infections. On top of this, the microbiome helps train the immune system to distinguish between harmful and harmless substances, which reduces the likelihood of autoimmune responses and allergies.

Mental Health 

Interestingly, the gut microbiome also influences mental health and behavior through the gut-brain axis. This bidirectional communication system connects the gut and the brain via the vagus nerve and various biochemical signaling pathways. Certain gut bacteria produce neurotransmitters like serotonin and dopamine, which can affect mood, anxiety, and stress levels. This connection is so strong that the gut is now referred to as the "second brain."

What Factors Influence the Gut Microbiome?

Diet

Diet is easily one of the most important factors influencing the composition of the gut microbiome. A diet that is rich in fruits, vegetables, whole grains, and fermented foods promotes a healthy microbiome. On the flip side, a diet that’s high in processed foods, sugars, and unhealthy fats can lead to an imbalance—known as dysbiosis—which is linked to a wealth of health issues, including obesity, diabetes, and inflammatory bowel diseases.

Medications

While antibiotics are sometimes essential for treating bacterial infections, they do wreak havoc on the gut microbiome by killing off the healthy, beneficial bacteria. This disruption has the power to lead to short-term side effects like diarrhea and long-term consequences like increased susceptibility to infections and chronic diseases. Other common medications, like Advil and Tylenol, also negatively impact the microbiome.

Lifestyle

Factors like stress, sleep, and physical exertion also impact the gut microbiome. Chronic stress has the ability to alter the composition of gut bacteria, often leading to digestive issues and a generally weakened immune system. Regular exercise, on the other hand, promotes a healthy microbiome. As far as sleep goes, we all know how important getting our 7-9 hours is for our mental function, but it’s actually critical for our gut health as well.

How to Maintain a Healthy Gut Microbiome

Taking Probiotics and Prebiotics Regularly

Probiotics are live beneficial bacteria that can be consumed through fermented foods like yogurt, kefir, sauerkraut, and kimchi, or in supplement form. They can help replenish and maintain a healthy balance of gut bacteria. Prebiotics, on the other hand, are non-digestible fibers that serve as food for the beneficial bacteria in the gut. Foods rich in prebiotics include garlic, onions, leeks, asparagus, bananas, and whole grains.

Eating a Diverse Diet

Doctors have always recommended eating a diverse and balanced diet to maintain proper health, but it’s also essential for supporting a healthy gut microbiome. Incorporating a range of fruits, vegetables, whole grains, lean proteins, and healthy fats promotes microbial diversity and better gut health. The more fruits and veggies you can eat in a day, the better. Each type of plant-powered food offers a unique type of bacteria, creating a more diverse environment within our guts. Be sure to limit the intake of processed foods and sugars as well, as this is equally important.

Exercise and Other Stress Reduction Practices

Regular physical activity has countless benefits for gut health, including promoting microbial diversity and ramping up immune function. Stress management techniques like meditation, yoga, and deep breathing exercises also help maintain a healthy gut by reducing the negative impact of chronic stress on the microbiome.

Final Thoughts

The human microbiome is an ecosystem of sorts—one that directly impacts our mental and physical health. From aiding in digestion to influencing our mood, the trillions of microorganisms within us are indispensable allies that help us feel our best. Knowing how to cultivate a healthy gut microbiome can help us take our power back and improve our health, one day at a time.

Keywords: Gut microbiome, what is the gut microbiome, human microbiome, gut health

References:

Salvadori M, Rosso G. Update on the gut microbiome in health and diseases. World J Methodol. 2024 Mar 20;14(1):89196. doi: 10.5662/wjm.v14.i1.89196. Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10989414/

Bianchetti G, De Maio F, Abeltino A, Serantoni C, Riente A, Santarelli G, Sanguinetti M, Delogu G, Martinoli R, Barbaresi S, Spirito M, Maulucci G. Unraveling the Gut Microbiome-Diet Connection: Exploring the Impact of Digital Precision and Personalized Nutrition on Microbiota Composition and Host Physiology. Nutrients. 2023 Sep 11;15(18):3931. doi: 10.3390/nu15183931. Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10537332/

Chaudhry TS, Senapati SG, Gadam S, Mannam HPSS, Voruganti HV, Abbasi Z, Abhinav T, Challa AB, Pallipamu N, Bheemisetty N, Arunachalam SP. The Impact of Microbiota on the Gut-Brain Axis: Examining the Complex Interplay and Implications. J Clin Med. 2023 Aug 11;12(16):5231. doi: 10.3390/jcm12165231. Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10455396/

Engen PA, Green SJ, Voigt RM, Forsyth CB, Keshavarzian A. The Gastrointestinal Microbiome: Alcohol Effects on the Composition of Intestinal Microbiota. Alcohol Res. 2015;37(2):223-36. Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4590619/

Rogers MAM, Aronoff DM. The influence of non-steroidal anti-inflammatory drugs on the gut microbiome. Clin Microbiol Infect. 2016 Feb;22(2):178.e1-178.e9. doi: 10.1016/j.cmi.2015.10.003. Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4754147/