The Human Microbiome

Ancient Egyptians preserved the heart, liver and intestines but discarded the brain as they thought it was not important. We now know that the brain is our most important organ. Disregarding microbes is as foolish as throwing away the brain.

  • The total number of microbes in the body weigh about 3 pound, about as much as the brain
  • They outnumber us by 10:1 – we are 10% human
  • Humans have 10 trillion human cells and 100 trillion microbial cells
  • We have 20,000 human genes and 2-20 million microbial genes so genetically we are 0.1-1% human
  • So, the 3 pounds of microbes has ten times as many cells and 100-1000 times as many genes as our own body.
  • We are 99.9% the same as another human genetically but 90% different in terms of our microbiome

The functions of microbes are numerous, for instance determining if medications are toxic to the liver, helping us to digest food, and even stealing genes from the food to aid the digestive process (for instance seaweed eating bacteria transferred genes to the Japanese people). Microbes may determine if your diet works.


Why care about microbes?

  • Microbes train your immune system
  • Microbes influence your behaviour
  • Microbes affect your health


The Human Microbiota (organism level): a particular community of microbes at a particular location on the human body including bacteria archaea, viruses, micro eukaryotes. The particular focus is on bacteria – these form the vast majority of microbes.

The Human Microbiome (genetic level): the genes that are carried by human microbiota.


Microbial communities on the body

Do the same microbes exist everywhere? No! The body contains different habitats like an ecosystem. Just as different areas of the world have landscapes with different animals, so different areas of the body have very different microbes. A map of the body is like a map of the world.

Armpits and forehead have a high bacterial content and low diversity.

The palm has a low bacterial content and high diversity.

Children who have a higher diversity of microbes in the respiratory tract grow up to have less asthma and allergies

Lungs contain living population of microbes which may contribute to diseases

Most of the bacteria in the mouth are beneficial and can lay down biofilms that prevent pathogens from getting a foothold.

The gut is the centre of microbial activity in the human body and most of the cells are here. It is studied more than any other location because:

  1. It has the largest and most important community of microbes
  2. It is easier to study as it is non-invasive and easy to obtain samples.

Microbes in the small intestine and the large intestine are very different.

There are two main microbes in the gut: Bacteroides and Firmicutes. E-coli are not that important.


Where do we get our microbes?

A baby has similar microbes across all body areas and all of these come from the mother’s vaginal microbiome. With babies born by C-section, their microbes look like those found on human skin. There is an association with C-section births and a higher range of diseases such as asthma and food allergies.

Puerto Rico has the highest C-section rate in the US. In Latin American culture half or more babies are born by C-section. To deal with this a gauze may be inserted into the vagina for one hour and then extracted and exposed to the baby. The baby is then monitored for one year.

Breast feeding is important. It provides food for the bacteria living in the baby and induces the flow of microbes from mother to child. Although the baby’s microbes can take a hit from antibiotics it is quite resilient and will soon recover.



The Human Microbiome Course

What is a Microbe?

The Human Microbiome

How we study the Microbiome Part 1

How we study the Microbiome Part 2

Impacts on the Microbiome

Microbiome and Obesity

The gut microbiota, autoimmune diseases and allergies

Human Microbiota and Gut Disease

Interactions between the Gut Microbiota and Immune System

The Gut-Brain Axis

Useful website articles and links

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