Redefining the Gut Microbiome

For a long time, we thought of our bodies as solely made up of human cells. But recent discoveries reveal a hidden world within us — a vast ecosystem of trillions of microbial cells. Don’t be alarmed by the word “microbes.” These microscopic organisms, collectively known as the microbiome, are not enemies but essential partners in our health. This blog post dives into the fascinating world of the gut microbiome, exploring its functions, its surprising influence on our overall well-being, and how we can nurture this vital “organ” for optimal health.

What is the microbiome?

The microbiome is a bustling ecosystem of microbes that live on and in you. This ecosystem contains bacteria, viruses, archaea, fungi (yeasts and mold), and protozoa, with over 10 trillion bacterial cells alone. 1

These microorganisms reside in various niches in the body, including our gut, skin, oral cavity, respiratory tract, and genitourinary system. They don’t just live there passively, they play important roles in our health:

  • train the immune system so it functions properly
  • make vitamins
  • improve the skin barrier
  • protect us from pathogens

The gut microbiome: A closer look

When considering the microbiome niches across the body, the gut takes center stage because it houses a large proportion of our microbial counterparts, collectively known as the gut microbiome. So, understandably, many scientific studies have focused on the gut microbiome. From this work, it’s becoming clear how highly important it is, with far-reaching effects on the body beyond the gut.

The gut microbiome consists of microorganisms that play roles essential to our well-being, roles we once had no idea what they were responsible for.

What does the gut microbiome do? 2

  • aids in food digestion
  • digests fiber into beneficial nutrients
  • aids in the absorption of minerals
  • produces metabolites (eg., butyrate and vitamins)
  • helps develop and regulate the immune system
  • prevents pathogens from taking up residence
  • produces neurotransmitters
  • aids in stress regulation

So, it’s not, as we once assumed, just our cells that contribute to keeping us healthy. Our gut microbiome keeps us healthy too. Its role in our bodies is so pivotal that we consider it to be more than just a bunch of microbes.

The gut microbiome as an “organ”

The Encyclopedia Britannica defines an organ as “a group of tissues in a living organism that have been adapted to perform a specific function.” Just as your body has human cells that make up tissues, the microbiome also has microbial cells. In that sense, we believe that the gut microbiome deserves to be viewed as a sort of “organ” in the same way as the brain, heart, or lungs. Heart and lung health are critical to maintaining overall health, so too is the health of the gut microbiome.

Our gut microbiome health matters

Since the gut microbiome is important on the level of “organ” status, we need to take a step back and discuss what “gut microbiome health” actually means. When we say gut microbiome health, imagine an interconnected, diverse ecosystem of bacteria, viruses, archaea, fungi, and protozoa that is in balance. When it’s in balance, we’ve got the right levels of various microbes functioning in ways that lead to gut health and, as we’ll soon discuss, overall health.

However, at times, this complex gut microbiome ecosystem can become out-of-balance and disrupted. Though the composition of healthy and diseased microbiomes can vary, disrupted microbiomes are associated with disease. Abnormal gut microbiomes are linked to conditions such as inflammatory bowel diseases (IBD) (which can manifest as Crohn’s disease and ulcerative colitis) and even colorectal cancer. 2 So, indeed, the gut microbiome impacts the health of the gut, but what about the rest of the body?

The far-reaching impacts of the gut microbiome

Scientific studies increasingly support the idea that the health of the gut microbiome is linked to the health of other systems in the body. There’s a two-way link between the gut and other organs, referred to as an axis. For example, the gut and the brain are linked through the gut-brain axis, meaning what happens in the gut impacts the brain and vice-versa. The same goes for other parts of the body, such as the skin, heart, lungs, pancreas, and liver. Though this field is still emerging, it is likely more evidence will surface to support the gut’s impact on every organ in the body.

Because the health of the gut has far-reaching effects across body sites, the gut microbiome is crucial for overall health, influencing the health of various parts of the body and vice-versa. Though research on these gut axes is still in its infancy, disrupted gut microbiomes have been correlated to conditions related to the brain, skin, heart, and lungs. 3 Changes in the gut microbiome are linked to brain health, emotional and mental well-being, skin vibrancy, and cardiovascular and respiratory health.

Below are a few examples of the gut microbiome axes disease and disorder associations:

  • Gut-brain axis: Autism spectrum disorder, mental health disorders (depression and anxiety), Parkinson’s disease, and Alzheimer’s disease 4
  • Gut-skin axis: Acne, atopic dermatitis, psoriasis, rosacea, and dandruff 5
  • Gut-heart axis: Cardiovascular disease (coronary artery disease, stroke, and peripheral arterial disease) 6
  • Gut-lung axis: Chronic obstructive pulmonary disease (COPD), Asthma, and Cystic fibrosis (CF) 7

These links are bi-directional and multi-directional; therefore, understanding overall health means taking into account the complexities of these relationships. What’s clear, though, is the importance of a balanced and diverse microbiome for overall health.

How to care for your gut microbiome

In light of the importance of the gut microbiome, we can implement a few strategies to promote a balanced and diverse microbiome. “Biotics” play a large role in these strategies, so we’ll start with a few definitions according to the International Scientific Association for Probiotics and Prebiotics (ISAPP):

  • Probiotics: “live microorganisms which when administered in adequate amounts confer a health benefit on the host” 8
  • Prebiotics: “a substrate that is selectively utilized by host microorganisms conferring a health benefit” 9
  • Synbiotics: “a mixture comprising live microorganisms and substrate(s) selectively utilized by host microorganisms that confers a health benefit on the host” 10
  • Postbiotics: “preparation of inanimate microorganisms and/or their components that confers a health benefit on the host” 11

Consuming probiotics, prebiotics, synbiotics, or postbiotics has the potential to nurture the gut microbial ecosystem. Probiotics introduce beneficial microbes to the ecosystem (often transiently, but with benefits, even if they rarely take up residence), prebiotics feed the beneficial microbes already in the microbiome, synbiotics add a combination of probiotics and prebiotics, and postbiotics contribute beneficial “inanimate” microbes and microbial parts to the ecosystem.

These biotics can be found as supplements or in certain foods. Fermented foods are a great source of beneficial bacteria, with some strains even functioning as probiotics, given they are “administered in adequate amounts,” as in yogurt. Fermented vegetables like sauerkraut and kimchi can even be potentially considered synbiotics if they contain the right level of probiotic strains as well as prebiotic substrate due to the presence of the vegetable material. However, validating the synbiotic status of home-fermented foods would require scientific studies on every batch due to their variability. Eating prebiotic-rich food like fruits, vegetables, legumes, nuts, and seeds is a great way to “feed” the beneficial microbes in your gut microbiome. Nurturing the microbiome in the above ways will also naturally lead to an increase in what you’d find in postbiotics supplements.

Besides biotics, these other healthy lifestyle choices can promote the health of your gut microbiome:

  • Getting adequate sleep – disturbed sleep alters the gut microbiome composition 12
  • Reducing stress – stress alters the gut microbiome, leading to a decrease in beneficial microbes and reduced diversity 13
  • Exercising regularly – exercise increases beneficial microbes and diversity 14
  • Limiting antibiotic use – antibiotics kill microorganisms indiscriminately and can cause significant and possibly long-term changes in the gut microbiome, including lowering diversity. 15 So, it’s best to only use antibiotics when they are needed.

Remember, nurturing your gut microbiome goes beyond just what you eat. A combination of healthy dietary habits and lifestyle choices can significantly benefit this vital ecosystem.

The importance of the gut microbiome “organ”

Far from a simple digestive system, our gut is a thriving world teeming with trillions of microorganisms. This intricate ecosystem, known as the gut microbiome, acts like a hidden organ within our digestive tract, tirelessly working to influence our health in countless ways. They aid in digestion, fend off harmful bacteria, and even modulate our mood and brain function. Maintaining a healthy gut microbiome is no longer a distant dream; through dietary choices, mindful habits, and a focus on “biotics,” we can nurture this vital internal world. By taking charge of our gut health, we unlock a path to a more vibrant and resilient existence.

About the Author
Dr. Justine Dees is a freelance science communicator with a PhD in microbiology, she is also the founder of Joyful Microbe, a microbiology resource for educators and enthusiasts, and co-founder of SciComm Society, a science communication resource for scientists. You can learn more about Dr. Dees at her website


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