This is the second part of three articles on the Microbiome.

After reading part 1 you should be convinced that having a healthy microbiome is key not just to digestive health, but also to health in many other ways as well . Clearly we if we could master our micobiome we could possibly reduce the risk and occurrence of many of our modern ills. But what does a healthy microbiome actually look like?


We don’t really know. The modern diet is so removed from what our ancestors ate that it’s impossible to define. We can learn something from tribes such as the Hadza in North Central Tanzania or the Yanomami of North West Brazil. This modern-day hunter gathers life perhaps something like our ancestors did in the pre-farming era. Their diets contain far more fibre than ours do and as a result, their microbiomes are far more diverse! (1)(2)

There is a lot of genetic material in the bacteria of the microbiome. Millions of different genes in fact while we have a mere 20,000 genes in our chromosomes (3).  This means that our gut microbes produce chemicals, proteins, vitamins and other substances that can interact with our bodies that we do not produce ourselves. Microbes speak to our bodies and get it to do things they want. Often this is to our benefit and sometimes these substances make all the difference to our health. But what happens when we’re missing certain species that hold key roles in our microbiome?

It’s been found that the Yanomani have twice as many species of microbes in their gut than the average American (4). That’s a lot more strains of bacteria carrying out different functions. Could the rise in certain diseases such as autoimmune be traced to strains of microbes no longer living in the western gut?

We know we no longer have the same microbial diversity that our ancestors once had. We’ve lost some of our ancient friends along the way. We can never be sure what impact they had or in what way they protected our bodies from disease. One thing is for sure though, modern chronic illnesses are on the rise while populations of microbes are being decimated. Let’s look at some of the ways we lose our colonies and put our health at risk.


Super Clean Lifestyle

Ok, clearly hygiene is really important. It helps to prevent outbreaks of infectious disease, but we may be going a bit too far in our war against germs.  We often live disconnected from the outside world in our sterile environments. We use hand sanitisers, disinfectants and bleaches. We shower or bathe every day with soaps and chemicals that are unfriendly to the bacterial species that live on our skin.

The result is that we have less opportunities to meet with our bacterial friends while our immune systems have less opportunities to fight our bacterial foes. Take acne for example. Loss of beneficial species of bacteria such as staphylococcal lipoteichoic acid can increase inflammation on the skin promoting acne (5). Also when these beneficial bacteria have been wiped out or washed away there is an opportunity for other strains of bacteria like Propionibacterium acnes to take over which as the name suggests, promotes acne.

Our immune systems are primed by contact with various types of bacteriaand children living in highly sanitised environments don’t get the micro-exposures to friendly and unfriendly bacteria they need to develop a healthy immune system. One that is ready to fight invaders but won’t end up fighting them. It’s theorised that this is a major factor in the development of auto-immune disease and immune regulation.

“Rewinding” means purposefully getting these micro-exposures to bacteria so they can take up residence as part of our microbiome.  Getting outside in nature or letting the kids gets mucky are good ways to come into contact with the worlds mircoflora. Another way is to have a household pet. Animals are teaming with bacteria as they sniff and explore the outside world. They carry these bugs back in with them.  These are easily transferred to humans through hugs, pets and licks, thus providing a wider range of bacterial interaction.

Cesarean section

The vagina is a lot like the gut in terms of bacterial diversity. During childbirth the child is inoculated with its mothers bacteria on the way out of the womb. Recent research shows that the child does inherit some bacteria while in the womb that is transferred from the mother during pregnancy (6). But the first major dose comes at birth. The baby is born covered in bacteria and these will be responsible for colonising the child’s gut.

If a child is born with a cesarean section, as one in three children are these days, it misses out on this opportunity to get colonised with human friendly bacterial species. These bacteria reflect the mothers lifestyle and so are close to what the child will need for the world its born into, providing the mother is of good health.  C-section babies have a higher risk of developing obesity, asthma and autoimmune conditions as a result (7).

One novel way to improve the health of the newborn is to swab the baby down in a cloth coated in its mothers vaginal secretions. This means the baby is coated in bacteria in much the same way as it would had it of been delivered naturally.

A study done earlier this year (2016) documents the procedure for the first time on four infants who received the swab