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The Microbiome in Health and Disease

An Introduction to the Microbiome: The Role of Gut Microbiome in Health and Disease by Hanna Keith Santos

You are not alone, literally, because trillions of microscopic organisms live on and inside your body. The collection of these tiny organisms is called the microbiome.

The microbiome is a vast community of bacteria, protozoa, fungi, and viruses that inhabit the human body. They reside on your skin, mouth, respiratory tract, genitals, and gastrointestinal systems. The most abundant population of microbes, with around 10-100 trillion bacterial cells, occupy the colon walls. 

Recent advances in sequencing and other technologies have enabled researchers to characterize the microbiome in unprecedented detail, revealing some of its diverse and intricate interactions with the human host. The gut microbiome has received much attention because of its critical role in metabolism, immune function, and other physiological processes. This article will further explore the gut microbiome and how it helps maintain our health.

What Makes a Healthy Gut Microbiome

The gut microbiota predominantly comprises 40,000 bacterial species, 98% of which come from the phyla Firmicutes, Actinobacteria, and Bacteroidetes. But the specific composition of the gut microbiome varies from one person to another and can be influenced by genetics, age, diet, and the external environment. 

In truth, there is no single “good” microbiome composition. Instead, a healthy microbiome can come in many forms, shapes, and sizes. To know if you have a good gut microbiome, you can characterize it by three key factors: diversity, balance, and stability. 


First, a healthy person has a highly diverse gut microbiota. As an illustration, imagine a healthy forest ecosystem with different plants and animal species. This variation is essential for the forest to quickly recover from acute stressors like pests and forest fires. Our gut microbiome is similar to that. It needs diversity to be more resilient to disturbances and protect itself from pathogens and diseases. 

For adults, nutrition, medication, and lifestyle significantly affect the variation in gut microbiota. Recent studies have found that a physically inactive lifestyle and an unhealthy diet are associated with a decreased microbiome. Other studies have also shown that people with lower gut microbiome diversity have a higher risk of various health problems, including inflammatory bowel disease and obesity, and type 2 diabetes.

A healthy microbiome is like a diverse forest that protects the plants and animals. When the microbiome is less diverse, there is a higher risk of health problems.
Photo by Felix Mittermeier on Pexels.com


Another key marker for a healthy gut microbiome is a balanced ecosystem of bacterial species. Most species residing in our gut are mutualistic (where humans and microbes benefit from each other) or commensal (where only the microbes benefit while not harming us). Examples of beneficial bacterial species are Bifidobacterium and Lactobacillus, which are known to help boost immunity and improve overall health.

Some bacteria in our gut are also considered pathogenic or can promote diseases. But there’s no need to worry as long as there’s a high proportion of beneficial bacterial species. A healthy body has pathogenic and symbiotic microorganisms that coexist without problems.

However, dysbiosis occurs if there’s an overgrowth of harmful bacteria or an imbalance in the gut microbiome—brought on by changes in eating habits, use of antibiotics, and other psychological or physical stresses. Dysbiosis refers to reduced microbial diversity and the loss of beneficial bacteria. This imbalance often leads to various health problems, including digestive disorders and autoimmune diseases.


Lastly, a healthy gut microbiome is resilient and stable. Although there’s a considerable variation in the gut microbiome, all healthy adults display a remarkably stable microbial community. The microbiome is composed of highly adaptable species, and they are more resilient to sudden changes in diet and medications.

But even though the microbiome is relatively stable during adulthood, it’s still susceptible to change. Long-term changes in environment, lifestyle, and eating habits can eventually affect the composition of our gut microbiome. For instance, a high intake of saturated fats, added sugars, or fast food could decrease beneficial microbial species. In contrast, food rich in fiber and proteins stimulates microbial growth and diversity.

Age can also affect microbial diversity and stability. For example, older individuals tend to have a less robust microbiome, which puts them at a higher risk of diseases.

The Metabolic and Immune Function of Gut Microbes

Because most research and news worldwide have focused on microorganisms that cause disease and drug resistance, many people think bacteria or fungi are harmful and must be avoided. But we shouldn’t be afraid of all of them. It’s important to note that the microbiome exists symbiotically within our bodies and is essential in maintaining our health and well-being.

One of the main functions of the gut microbiome is breaking down food and extracting nutrients that are critical for growth and development. The human body can’t digest certain fibers and fats independently, so the gut microbes help break down these indigestible macromolecules. As they ferment complex carbohydrates, short-chain fatty acids (SCFAs) like butyrate, acetate, and propionate are released, which fuels the cells in the gut lining and reinforces the intestinal wall. Moreover, SFCAs contribute to energy balance, nerve activity, and immune response.

Aside from SCFA, the gut microbiome also extracts essential vitamins in metabolism. For example, Bacteroides fragilis and Eubacterium lentum synthesize vitamin K2, which decreases cholesterol levels and lowers the risk of cardiovascular disorders. The gut microbiota is also an important source of vitamins B5 and B12, necessary coenzymes for normal brain functioning.

The gut microbiota also plays a critical role in regulating our immune system. It communicates with the immune cells and produces antimicrobial compounds, which help fortify the gut barrier and prevent harmful pathogens from entering and colonizing the digestive tract.

Besides metabolism and immune function, there is growing evidence that the gut microbiome can affect brain function and mental health. Our central nervous system is in close communication with our gut microbiota, meaning that the brain can influence intestinal activities, and the gut can affect our mood and cognition. Recent studies show that dysbiosis in the gut microbiome correlates with cognitive and mood disorders, including autism, Alzheimer’s disease, anxiety, and depression.

The Role of the Microbiome in Certain Diseases

The previous section taught us that our bodies would be more prone to communicable and non-communicable diseases without a diverse and stable gut microbiome. Here, we discuss four notable illnesses commonly linked to intestinal microbiota.

1. Inflammatory bowel disease 

Inflammatory bowel disease (IBD) is a disorder characterized by inflammation in the gastrointestinal tract. The most studied forms of IBD are Crohn’s disease and ulcerative colitis, which show symptoms like diarrhea, fever, and abdominal pain.

Studies observed a strong link between the development of IBD and dysbiosis, particularly a decrease in abundance and diversity of the phylum Firmicutes. Firmicutes are known to produce SCFAs with potent anti-inflammatory properties, so the decline in these microbes can result in a higher risk of inflammation. Although there’s no cure for IBD, antibiotics are needed to prevent the spread of bacterial pathogens like Escherichia coli strains and Mycobacterium avium. Other medications ease the symptoms and reduce inflammation.

2. Cardiovascular disease

Changes in gut microbiome composition contribute to the development of cardiovascular diseases like myocardial infarction and stroke. This is more commonly observed in Western diets— characterized by a high intake of refined sugars, red meat, saturated fats, and other processed products. The metabolism of such food produces compounds that can elevate blood pressure, increasing the risk of hypertension. 

To reduce the chances of cardiovascular disease, nutritionists are promoting diets high in fiber and healthy fats because of their anti-inflammatory properties and ability to control blood pressure. Moreover, dietary fibers are metabolized by the gut bacteria to extract SCFAs and other health-promoting metabolites.

3. Obesity

Obesity and metabolic syndrome can exhibit dysbiosis because the gut microbiome can influence host metabolism and energy balance. Researchers have discovered that obese patients have imbalanced proportions of Firmicutes and Bacteroidetes, which promotes more energy production.

Since obesity-related disorders are associated with microbiome dysbiosis, probiotics, and prebiotics may help promote weight loss and improve metabolic health. However, more clinical trials are needed to know this approach’s success.

4. Diabetes

Diabetes is a complex disorder affected by genetics and environmental factors. And recently, there has been growing evidence that the gut microbiome also plays a role in developing this disease. 

A study among adults with Type 2 diabetes shows an increase in bacterial pathogens like Clostridium spp and a decrease in SCFAs, all linked to insulin resistance and impaired glucose metabolism. As such, interventions aimed at modifying the gut microbiome, such as probiotics, prebiotics, or fecal microbiota transplantation, are being considered as a treatment to improve glycemic control and insulin sensitivity.

Diabetes has been associated with a less healthy gut microbiome.
Photo by PhotoMIX Company on Pexels.com


These examples highlight the diverse and complex role of the gut microbiome in health and disease. However, it’s just the tip of the iceberg. Further explorations on the gut microbiome are essential to explore its potential in treating various conditions. 

Teach your children the importance of the gut microbiome. Check out Meike and the Microbiome Bunch and order on Amazon (for $3.59):

Meike and the Microbiome Bunch tells us more about the microbiome and is approachable for children.
Meike and the Microbiome Bunch

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