What is Microbiome

What is Microbiome? The Invisible Ecosystem Inside You

Introduction: It's More Than Just Cells

You probably think of organs, muscles, bones, and blood when you consider your body — the parts that you can see and touch. But beneath the surface, there is a world that you can't see. Trillions of tiny germs, such as bacteria, viruses, fungi, and archaea, live on and inside your body. Together, these microbes make up what's called the microbiome.

The word "microbiome" not only refers to the microbes but also to their genes, their interactions, and the ecosystem that they create. They are essential to digestion, regulation of the immune system, mental well-being, skin health, and even your vulnerability to disease. In their tiny size, they have a macro-level impact on virtually every part of your life.

So, what is the microbiome, anyway? Why do we need it? And how can we better care for this unseen world?

1. Defining the Microbiome

What is a Microbiome?

The microbiome is the population of microorganisms (microbes) that live in a specific environment. In people, the term usually means the human microbiome — the combined genomes of the microbes that live inside and on the human body.

These microbes can be located in all sorts of locations, including:

-The gut (particularly the large intestine)

-The skin

-The mouth

-The respiratory tract

-The urogenital tract

Each of these locations has a unique community of microbes adapted to that particular environment.

Microbiota vs. Microbiome

It's useful to make a distinction between microbiota and microbiome:

-Microbiota is the actual bugs — bacteria, fungi, archaea, viruses.

-Microbiome encompasses the microbiota along with their DNA, their habitat, and their combined effect on the host.

2. The Human Microbiome Project

The U.S. National Institutes of Health initiated the Human Microbiome Project (HMP) in 2007, an innovative project that mapped and understood the human-associated microbiota. This study has exponentially broadened our knowledge of how microbes influence our health and unlocked the possibility of novel methods of disease diagnosis and treatment.

One of the key discoveries? There are more microbial cells in the human body than human cells, and the microbes contain 100 times as many genes as we do. 

image credit: FREEPIK

3. Where Do We Get Our Microbiome?

Birth and Early Life

Our microbiome starts developing from birth. Babies born vaginally are introduced to their mother's vaginal and gut microbiota, while those delivered through cesarean section get exposed to a different set of microbes, frequently from the skin and hospital surroundings. These early exposures determine the composition of the child's microbiome and potentially their later health.

Breastfeeding, exposure to the outdoors, diet, antibiotics, and other environmental exposures during infancy and childhood further mold the formation of the microbiome.

Microbiome Diversity Through Time

As we age, our microbiome develops further according to:

-Diet

-Lifestyle

-Geography

-Medications

-Stress levels

-Environmental exposures

A healthy microbiome is typically diverse, with a broad range of microbial species. Lower diversity has been linked to various health problems.

4. The Role of the Gut Microbiome

Digestion and Nutrition

The gut hosts the highest number of microbes found in the human body. They assist in digestion, particularly of fiber and other complex carbohydrates that can't be digested by our bodies independently. As a reward, they generate essential nutrients such as:

-Short-chain fatty acids (SCFAs), which feed gut cells

-Vitamin K

-Some B vitamins

Regulation of the Immune System

The microbiome assists in "training" the immune system to accept dangerous pathogens and ignore harmless or even helpful organisms. This training assists in:

-Preventing autoimmune diseases

-Preventing allergies

-Preventing chronic inflammation

Mental Health: The Gut-Brain Axis

The gut-brain axis is the communication system between the gastrointestinal tract and the central nervous system. The gut microbiome affects this communication through:

-Production of neurotransmitters such as serotonin (as much as 90% is produced in the gut)

-Regulation of inflammation

-Modulation of stress hormones such as cortisol

Emerging evidence connects gut microbial imbalances with disease states like depression, anxiety, and even neurodegenerative disorders like Parkinson's.

5. Microbiome and Disease

A displaced microbiome — so-called dysbiosis — has been associated with a host of diseases:

Digestive Disorders

-Inflammatory bowel disease (IBD)

-Irritable bowel syndrome (IBS)

-Celiac disease

Metabolic Conditions

-Obesity

-Type 2 diabetes

-Insulin resistance

Autoimmune Diseases

-Rheumatoid arthritis

-Multiple sclerosis

Mental Health Disorders

-Depression

-Anxiety

-Autism spectrum disorders (ASD)

Cancer

There is evidence that some microbiota can impact cancer formation — inhibiting or enhancing tumor growth, particularly in colorectal cancer.

6. Influences on the Microbiome

1. Diet

Perhaps the greatest determinant of microbiome structure. High-fiber, fruit, vegetable, fermented food, low-processed-food diets are optimal for microbiota diversity.

2. Antibiotics

Although lifesaving, antibiotics are capable of upsetting the balance of microbes, at times irreversibly. Overuse and misuse can create antibiotic-resistant bacteria and diminished microbial diversity.

3. Lifestyle

Exercise, sleep, alcohol use, smoking, and stress all have an effect on the microbiome.

4. Environment

Urban vs. rural environments, nature exposure, pollution, and climate can change microbial communities.

5. Age and Genetics

Your age and genetics influence what microbes are able to succeed in your body, yet lifestyle tends to trump genetics.

7. How to Support a Healthy Microbiome

Eat More Fiber

Fiber-rich foods such as whole grains, legumes, veggies, and fruits supply good gut bacteria with nutrients, particularly bacteria that produce anti-inflammatory molecules such as SCFAs.

Include Fermented Foods

Dairy foods such as yogurt, kefir, kimchi, sauerkraut, and kombucha have live good bacteria (probiotics) that can help promote microbiome health.

Avoid Overuse of Antibiotics

Take antibiotics only if prescribed, and never use them to treat viral infections such as the common cold.

Stay Active

Exercise has been proven to enhance microbial diversity and maintain gut health.

Manage Stress

Chronic stress can inhibit the gut-brain axis and microbiome. Mindfulness, meditation, and getting plenty of sleep all aid in lowering stress.

Consider Probiotics and Prebiotics

Probiotics: Live microbes that may provide health benefits

Prebiotics: Non-digestible fibers that provide food for beneficial microbes

8. The Future of Microbiome Research

Personalized Medicine

Your microbiome could one day inform doctors about personalized nutrition or medical therapies tailored to your individual microbial makeup.

Fecal Microbiota Transplantation (FMT)

FMT is a new therapy where stool from a healthy donor is transplanted into a patient with microbial dysregulation. It has been effective for treating Clostridioides difficile infections and is being investigated for other conditions.

Microbiome-Based Therapies

Scientists are designing drugs and therapies that specifically target the microbiome, including engineered probiotics, microbial-derived small molecules, and dietary interventions.

9. Dispelling Microbiome Myths

Myth 1: All Bacteria Are Bad

False. Most of the bacteria in your body are not harmful or even beneficial. Only a few dozen are disease-causing.

Myth 2: You Need to Sterilize Everything

Over-sanitizing your surroundings, particularly for kids, could lower microbial exposure and help lead to autoimmune diseases and allergies.

Myth 3: Probiotics Are a Cure-All

Though useful in certain situations, not all probiotics work, and they are strain-specific.

Conclusion: What is Microbiome

The microbiome is a mind-bogglingly complex, diverse, and indispensable aspect of what we are. It's not merely an inert accumulation of microbes; it's an active, dynamic community that keeps us healthy in so many ways — from digestion and immunity to mood and mental health.

Caring for and understanding your microbiome is not only a health trend — it's essential to maintaining a balanced and healthy existence. By nourishing your microbes with the correct foods, keeping unnecessary antibiotics away, and living a lifestyle conducive to diversity, you're not only taking care of yourself — you're tending to the trillions of microscopic partners that keep you alive and well.