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Understanding the Gut Microbiome

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Table of Contents

We hear time and time again about the importance of diet in maintaining a healthy mind and body. Diet alone can help us maintain a healthy weight, have more energy, and avoid diseases. We’re reminded repeatedly with age-old sayings such as “you are what you eat” or “an apple a day keeps the doctor away.” But it’s not just about calories in and calories out. 

The food that goes into your stomach is just one part of an extremely complex system that affects almost every aspect of our physical and mental health. It is a system that includes trillions of microorganisms inside your digestive tract, and it’s called the gut microbiome. 

What is the Gut Microbiome?

The gut microbiome is a collection of bacteria, fungi, and viruses that live in the gastrointestinal tract. These gut microbes play an important role in digestion, metabolism, and immune function. The gut microbiome is constantly changing, and the composition of microbial communities can vary depending on diet, age, and health status.

What does the gut microbiome do? The gut microbiome is a collection of bacteria, both good and bad, that maintains numerous body systems using the nutrients we provide it. This balanced system provides a number of benefits, including:

  • Aiding in digestion
  • Helping to synthesize vitamins and minerals
  • Protecting against pathogens
  • Producing building blocks for neurotransmitters
  • Altering mood and mental health
  • Influencing a number of chronic conditions, including obesity, diabetes, and inflammatory bowel disease.

A Closer Look

We can say “good bacteria” all day long, but what does that mean? Most of the bacteria in the gut can be broken down into two groups: firmicutes and bacteroidetes.

Firmicutes are involved in fermentation and help break down the foods you eat. They also produce butyrate, a substance that promotes colon health. Bacteroidetes make up the majority of the microbiome and perform a number of the tasks listed above.

Age and Your Gut Microbiota

The health of the gut microbiome starts at or before birth and has significant health implications throughout life. Healthy intestinal microbiota may even help prevent declining health in old age.

What is the gut microbiome of an infant? Babies may receive the beginnings of their gut microbiomes before they are born. After birth, a baby’s microbiome is heavily influenced by its mother’s breast milk. The first bacteria to grow inside babies’ intestines are called Bifidobacteria. They help digest the healthy sugars in breast milk, which are essential for growth. 

The gut microbiota gradually diversifies after solid foods are introduced during early life. It appears to remain fairly stable, depending on dietary and environmental factors. As we get older, there is an enrichment of previously non-dominant bacteria (e.g., potentially pro-inflammatory bacterial groups) and a drop in the number of Bifidobacteria strains. Gut microbiota diversity may decrease after a person reaches around 60-65 years of age. 

How Gut Health Impacts Your Whole Body

The health of our gut microbiome impacts our overall health and wellness in a number of ways. Our brain health, weight, and immunity are all connected to our gut microbiota. 

A healthy gut biome produces enzymes that help us digest our foods and produces certain metabolites such as short-chain fatty acids (also called SCFAs) and amino acids. These enzymes impact nuclear receptors in the gut, which help regulate intestinal inflammation. 

What is the gut microbiome’s relationship to the brain? There is a complex communication network between the gastrointestinal tract and the brain. This system, called the gut-brain axis, is responsible for coordinating many of the body’s functions, including digestion, metabolism, immunity, and mood. Recent studies have made it a hot topic in modern gastroenterology.

How does the gut microbiome affect weight? The gut microbiome affects weight by influencing food intake, nutrient absorption, and energy expenditure.

The gut microbiome helps to regulate metabolism and energy balance. It produces hormones that govern appetite and satiety. Imbalances in the gut microbiome have been linked to obesity and other metabolic disorders. 

What is the role of the gut microbiome in the immune system? The gut microbiome’s role in the immune system is to help regulate the body’s inflammatory response. It also produces short-chain fatty acids that have anti-inflammatory properties. Lastly, the gut microbiome helps to keep the gut barrier intact, preventing harmful bacteria from entering the bloodstream.


The human gut microbiota is a complex ecosystem of bacteria, viruses, and fungi that work together to promote gut health. When the microbial balance is disturbed, it can lead to gut dysbiosis. This can be caused by a number of factors, including: 

  • Excess sugar: Sugary foods can contribute to high blood glucose levels and promote the growth of pathogenic bacteria and reduce the populations of beneficial bacteria.
  • Processed foods: Processed foods contain high levels of unhealthy fats. Like sugary foods, these nutrients can alter the composition of the gut microbiota, promote the growth of harmful bacteria, and decrease the number of beneficial bacteria.
  • Antibiotics: Antibiotics can kill off beneficial, commensal bacteria in the gut. This can allow pathogenic bacteria to take over.
  • Oral contraceptives: Oral contraceptives can contribute to dysbiosis by affecting the hormone levels. This can disrupt the normal balance of the gut microbiota.
  • Stress: Stress and depression can impact the gut barrier, contributing to”leaky gut.” When the gut barrier is not functioning properly, bacteria can seep into circulation.
  • Smoking: Smoking contributes to gut dysbiosis by promoting the growth of harmful bacteria and reducing the growth of beneficial bacteria.
  • Alcohol: Alcohol consumption can lead to a decrease in the diversity of the gut microbiota and an increase in pathogenic bacteria. It can also disrupt the gut barrier.

The symptoms of gut dysbiosis vary depending on the underlying cause. Common symptoms include gastrointestinal distress, fatigue, skin problems, and high cholesterol. Dysbiosis can lead to a variety of health problems, including:

  • Crohn’s disease
  • Irritable bowel syndrome (IBS)
  • Inflammatory bowel disease (IBD) 
  • Ulcerative colitis
  • Cardiovascular disease
  • Type 2 Diabetes
  • Cancer

Probiotics & Other Ways to Keep Your Gut Happy

Foods can have a profound impact on the health of your gut.

How do probiotics work? Probiotics are bacterial species that are beneficial to the human body. They help to keep the gut healthy and prevent the growth of harmful gut bacteria. Probiotic bacteria live in the digestive tract and help to break down food, absorb nutrients, and keep the gut free of harmful bacteria such as clostridium difficile — a bacterium that causes infection.

When looking for a probiotic supplement, keep your eye out for one containing lactobacilli and bifidobacteria.

If you’d rather get your probiotics from food sources, include these foods in your diet:

  • Yogurt
  • Kefir
  • Saurkraut
  • Kimchi
  • Tempeh

Prebiotic-rich foods can also have a positive impact on the human gut microbiome. By feeding the good bacteria in the gut, prebiotics help to promote healthy gut microbiota. Prebiotic foods generally contain high amounts of dietary fiber and fermentable carbohydrates.

Examples of prebiotic foods include:

  • Chicory root
  • Dandelion greens
  • Garlic
  • Onions
  • Leeks

New Science in Gut Health

Metagenomics is a subsect of microbiology that studies the ecology of the gut. By taking samples from the large intestine, experts can study microbial genome sequencing in the gut. Microbial genome sequencing is the process of determining the complete DNA sequence of all the genes in a microbial organism. 

This information can be used to better understand the microbial organism’s role in the gut and how it interacts with other microbes in the gut. It can even be used in microbiome therapeutics. 

Microbiome therapeutics is the use of microorganisms to treat disease. It works by manipulating the microbiome to restore health. One example of this may be microbiota transplantation.

Microbiota transplantation is a medical therapy that involves transferring live microorganisms from a donor to a recipient. The microorganisms are usually transferred through a fecal matter transplant. That means a stool sample from the donor is transplanted into the gastrointestinal tract of the recipient. The science is still fairly new on that one, but results are promising.

Getting Started 

At Sano Health Club, we take a whole-person approach to health and wellness. If you’re concerned about your gut health and how it might be affecting other areas of your body, schedule an Intro Call with a member of our care team.

If you’re not ready to book an appointment, feel free to join our mailing list, subscribe to our blog or follow us on Instagram


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