The Human Microbiome

In the “Last Frontier” of Medicine, as my Trekkie friends would say, scientists and physicians are exploring how the Microbiome and probiotics play a much larger and more vital role in our health. This role is larger than we could ever have imagined.

What is the Human Microbiome?


The human gastrointestinal tract (GI Tract) is home to more than 100 trillion bacteria per person. I have taught my medical and nursing students for years that our GI Tract is the seat of 70 to 80% of our immunity. In fact, studies now show that a newborn infant’s GI Tract, which is sterile and has no bacteria in it during the pregnancy, gets seeded with bacteria from the mother during vaginal birth. In fact, vaginal infants appear to be healthier than C-section infants. This jump-starts an infant’s immune system. This giant bacterial population, which outnumbers our human cells by a factor of 10, is called the “gut microbiota” or “gut microbiome.”

For every gene in our genome, there are 100 bacterial ones. This is our “microbiome.” It has a huge impact on our health including our ability to digest food and our immunity and more. We, in turn, affect these bacteria too, from everything we eat and drink or even to the way we’re born. All of this can influence the species of bacteria that take up residence in our bodies!

For every gene in your genome, there are 100 bacterial ones. This is your ‘microbiome’ and it has a huge impact on your health, your ability to digest food and more. We, in turn, affect them. Everything from the food we eat to the way we’re born influences the species of bacteria that take up residence in our bodies.

The dark tunnels of our intestines house more bacteria than any other part of your body, including those found on our skin. In fact, an international scientific team discovered that each of our bowels carries at least 160 different bacterial species. This means that our collective guts have just under 3.3 million bacterial genes, more than 150 times as many as reside in our own cell genomes. They also showed that the gut “microbiome” of a healthy person looks very different to that of someone with a bowel condition like Crohn’s disease or ulcerative colitis.

In spite of the great diversity of bacterial inhabitants in our guts, researchers have shown that the GI bacteria of people from Europe, North American and Japan collapse into three enterotypes, or gut types. These three (3) clusters cut across age, gender, body weight and nationality – each producing energy in a slightly different way, manufacturing different vitamins (we do not make our vitamins) and possibly, affecting our susceptibility to different diseases.

Why is Our Microbiome Important?

I said earlier that this quest to fully understand these microscopic bacterial inhabitants has shown that these gut microbes are very important for public health. In fact, we actually rely on these microscopic inhabitants more than we realize. New research has shown that:

  • Our “gut microbiome” helps harvest energy from our food, providing us with nutrients that would otherwise be denied to us
  • Prevent the growth of harmful bacteria
  • They can also go “rogue” – changing the content and type of bacteria in ways that are linked to obesity or bowel diseases like Crohn’s or ulcerative colitis.

Breastfeeding influences the types of bacteria that inhabit our GI Tracts from birth to adult.
Breastfeeding influences the types of bacteria that inhabit our GI Tracts from birth to adults.
Our “microbiome” is like a hidden organ – it helps us break down foods that our own cells cannot. And in turn, our food and drink affects our “microbiome.” Our first set of bacteria genes genes for digesting milk proteins, allowing us to make full use of our only source of nourishment as babies. Breast milk might even have evolved to nourish the most beneficial bacteria with special sugars no longer found in our diets in sufficient quantities to protect our health. Just before we move onto solid foods, our “microbiome” appears to start activating genes that help break down the complex sugars and starches in plants. This prepares us for the menu to come. As our diet diversifies, so do our bacteria. They activate genes that use carbohydrates effectively, produce vitamins, and break down unusual and diverse chemicals. As adults, our “microbiome” becomes relatively stable, but the types of bacteria found still depend on the food and water we eat and drink (remember most municipal water supplies have added chlorine to kill bacteria). The gut “microbiome” of people who eat high-fiber diets are different from those who eat high-fat diets.

What is the Rest of the Story?

In the next few weeks, I will write about the expanding evidence that our “gut microbiomes” affect our health and lifestyle. Stay tuned!