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 (8). They where found to have the same microbial concentrations as if they had of been born vaginally. It may be some time before hospitals start doing this routinely however. Let’s hope it catches on.

It’s also worth noting the importance of breast feeding children. Mothers milk has been show to have its own colonies of healthy bacteria which benefit the infant. This strains are unique to the mother and represent healthy colonies that are beneficial to her environment (10). Formula doesn’t contain these so a child reared mostly on formula will have to rely on other means of colonisation.


Everyone is aware that antibiotics have saved countless lives. They brought medicine to a new era revolutionising emergency medicine and trauma management. Nobody questions their use in infectious diseases but it comes at a cost. The same antibiotics that are used to kill off infectious bacteria also kill off the friendly residents of out gut microbiotica.

Using antibiotics even for a short while can dramatically reduce the size and diversity of the microbiome (11). Repeated use of antibiotics can devastate our delicate colonies, paving the way for immune dysregulation and disease. Unfortunately the kinds of bacteria we don’t want tend to be more antibiotic resistant and so grow back first. Like scorched earth, there is space for the most opportunistic species to colonize and dominate.

A one potentially deadly pathogen that has become antibiotic resistant is Clostridium Difficile. C. Diff is notorious for causing diarrhea, fever and weight loss. Broadspectrum antibiotics, such as fluoroquinolones, cephalosporins, clindamycin, and penicillins wipe out large portions of the microbiome except for resistant bugs like C. Diff. Given that friendly strains of microbes such as Saccharomyces Boulardii are no longer present to keep C. Diff in check, there is little resistance against infection.

Given the damage done by antibiotics, they should be used only when absolutely necessary. You would be better off enduring a cold and improving your microbiome and immune system than taking an antibiotic which will leave you more prone to infection in the long run. Doctors have a tendency to over-prescribe antibiotics so it’s always worth asking if they are really necessary or are they just being precautious.

It would be wiser still to us natural antimicrobials which are far less damaging to the microbiome such as oregano oil (11) and garlic extract (12). These not only destroy unwanted microbes but enhance the immune function as well, leaving you stronger to deal with the infection in the future. The same is true for livestock. Organic livestock is not only far better for your health but reduces the rapid growth of antibiotic-resistant bacteria. See here for a story on a chicken farm in the states that are now using oregano oil instead of antibiotics.


Whether we have good bugs or bad growing inside us will largely depend on what we eat. A diet rich in sugar and refined grains is the perfect breathing ground for troublesome bacteria and yeasts which like to metabolize simple sugars and starches.

Some diets aimed at healing the gut such as the ‘Selected Carbohydrate Diet’ and ‘GAPS’ eliminate carbs so that unfriendly bacteria have nothing to feed on and go into remission. They won’t die off completely as some may go into spore form. In this form, microbes aren’t affected by antibiotics or antimicrobials but they don’t grow either. This leaves an opportunity to recolonize the gut with friendly microbes while healing the gut. This way you’ll soon crowd out any unwanted guests.

Two strains of Lactobacillus that are very good at neutralizing pathogenic bacteria are L. acidophilus  and L. bifidus. This is why you’ll see them in most probiotic formulas.  E. Coli, Staphylococcus Aureus and Candida Albicans are all inhibited by these strains (13). Many people eat commercial yogurts for their digestion but the strains generally used are Lactobacillus bulgaricus and Streptococcus thermophilus. While these are friendly they do not colonize the gut readily, but rather pass through, limiting their therapeutic value.

What’re more many commercial yogurts contain sugar which feeds unfriendly bacteria and yeasts. So instead of healing the gut, these products may, in fact, be making it worse. Far better instead to make your own Kefir which can have approximately 50 strains of healthy bacteria and yeasts that will colonize the gut and have a therapeutic effect.


Fiber is the food of a healthy microbiome. It’s often the overlooked nutrient. A lot of diets focus on the ratio of carbs to fat to protein but often fiber doesn’t get counted. Fiber is the part of food from plants that we cannot digest. We lack the enzymes to do so. But friendly strains of bacteria such as Lactobacillus do and will gladly make a meal of what we leave behind.

It’s estimated from paleolithic stool samples that our stone-age ancestors ate about 10 times the amount of fiber that we do (14). Jeff Leach a co-founder of the Human Food Project which studies and catalogues the microbiome of anyone who wishes to participate. Curious about fiber intakes he analyzed the stool samples of regular omnivores, those on a paleo diet, vegetarians and vegans.

Jeff found that omnivores ate around 19 grams of fiber a day while those seriously following the paleo diet averaged around 25 grams per day. However, those on a vegetarian diet averaged 33 grams per day and those on the vegan averaged 43g per day. The vegans were nearly twice that of the paleo! There is something to be said for focusing the diet on plants! (15)

Compare that though with the Hadza tribe which hovers between 100-300 grams of fiber per day (16). They will often snack on raw fibrous tubers during the day.  It takes a lot of chewing to swallow but does wonder for the fiber levels. This probably more like what our ancestors used to do and how our digestive systems have been set up.

Fibre gets fermented by healthy bacteria which makes the gut more acidic. This favors our friendly bacteria species which produce short chain fatty acids. These heal the lining of the gut and provide a source of energy for the cells of the gut, the enterocytes. If we focus too much on fats to the exclusion of fiber we may end up creating a dysbiosis as the pH becomes too alkaline, promoting the growth of unfriendly organisms.

Even if we can’t (or choose not to) chew tough fibers during the day like the Hadza, there’s still a lot we can do to increase our fiber levels. Most certainly we should make plants the center of our diet. Unprocessed meats are fine, but better as a side serving and not as the main event. We want to make sure we are getting plenty of fresh fruits and vegetables. Ideally, they would be the bulk of what we are eating.

Feeding the microbiome is the recipe for good health. Choosing an unprocessed plant-based diet is the secret to a long life. When we look at cultures famous for the long life spans around the world such as the Sardinians or Okinawans we find they that even though their cuisine is quite different, it’s all plant-based.

Healthy eating can be summed up in the seven immortal words of Micheal Pollan

“Eat food, not too much, mostly plants’.