Tending your microbiome Part 1

HARNESSING THE POWER OF 100 TRILLION FRIENDLY BUGS


This is the story of how you came to be home to an astonishing number and range of microbes. It’s one of the two hottest topics in health science now – the Human Microbiome and Epigenetics.

The Human Microbiome

is the sum of all the genes from all microbes that live inside and on us.

Microbiome Word Cloud

The term microbiota refers to the microbes themselves. They used to be called microflora, but that term is inaccurate as it implies that the microbes are plants, whereas they are of all types.

According to the American Academy of Microbiology, there are an estimated 100 trillion microbes living inside us. So we host at least three times the number of microbes as we have cells, and some estimates put it at 100 times!

Taken as a whole, these microbes could almost be classed as an additional organ of your body.

The highest number of microbes are bacteria and they occur mostly in the gut – although they also live on the skin, in nasal passages, the mouth and in the urogenital tracts.

Essential microbes

  • For the immune system

We acquire these essential microbes originally at the moment of birth through the birth canal, then via mother’s milk, and subsequently from the food we eat and the environment we live in.

Babies born by Caesarean section are not exposed to the initial contact with the mother’s vaginal microbes and there is some evidence that their immune systems may be slightly compromised, leading to higher allergy rates. So these microbes have a definite role to play in immunity.

  • For digestion

The total number of genes in your biome could be as high as 8 million – contrasting to about 23,000 human genes. And these microbes are absolutely vital.

For example, the human genome has less than 20 enzymes that can digest carbohydrate, so by ourselves we could not break down or digest most of the carbohydrates that we eat. In contrast the genome of just one gut bacterium has over 260 such enzymes.

  • To make vitamins, neurotransmitters and enzymes

We also need microbes to make some vitamins that we could not make on our own – including B and K vitamins. Additionally our gut bacteria play a role in the manufacture of neurotransmitters (including serotonin), enzymes and a range of other signalling molecules that influence the immune and the metabolic systems.

Some of these compounds may play a role in regulating our stress levels and even temperament: researchers found that when gut microbes from adventurous mice are transplanted into the guts of timid mice, they become more adventurous. So maybe the phrase ‘gut reaction’ is literally true.

How did we outsource all these important functions to a horde of microbes?

Fast reproduction and evolution

Bacteria reproduce far faster than we do – some create a new generation every 25 minutes– so their genomes can change far more quickly. They can therefore adapt to both threats and opportunities faster than us – and in addition they can exchange genetic material relatively easily between themselves.

Because they can evolve so quickly, they help our bodies respond faster to changes in our environment. In the past this fast response mechanism enabled us (‘us’ being the combination of ourselves and our 100 trillion guests) to create beneficial abilities we didn’t have before.

Antibiotic crisis

This fast response, however, is also why we have arrived at a crisis for antibiotics. If one bacterium develops resistance to an antibiotic, the gene responsible for that resistance can be transferred to a related gene – and soon general resistance can develop.

It is the gut microbiome that has the biggest impact on health. It helps us extract energy and nutrients from the food we eat.

It also plays a protective role against other potential invasive pathogens by occupying niches they could otherwise occupy, or by making the environment inhospitable to unwelcome ‘foreigners’. This is called “invasion resistance”.

The better resilience of one person’s gut community explains why some people may succumb to food poisoning or ‘Delhi Belly’, while others eat the same meal with no ill-effects.

If the make-up of the gut microbiome is disturbed the result can be injurious to health. For example, antibiotics can reduce the number and range of microbes in the gut, cause gastrointestinal inflammation and vulnerability to pathogens like C difficile. Salmonella can cause infection at a dose 1,000 times lower if the patient is on antibiotics!

This is why you should only take an antibiotic when really necessary and complete the dose. If you do not complete the course it is quite possible that some of the original pathogens will be left and they can develop resistance. That’s one reason we have an antibiotic crisis.

Microbe diversity is important

Gut Bacteria Magnifying Glass

The digestive system with gut microbiota magnified

In an echo of the Blue Zone project, the splendidly named American Gut Project is planning to sequence the microbial genes of thousands of Americans all over the US to see the correlation between their microbe profile and health.

What we already know, however, is that more diversity in the gut is generally better. In the West we have considerably less microbial diversity than in other parts of the world and the likely cause is over use of antibiotics, antibacterial sprays and the prevalence of processed food which is largely produced in a sterile environment.

Significantly, most less developed countries may have higher rates of infectious diseases, but they generally have much lower levels of allergies and asthma.

Inflammation and the microbiota

Health scientists have called inflammation “The Grand Unified Theory of Disease” – because chronic low level inflammation is a driver of almost all so-called ‘age-related diseases’ like heart disease, stroke, diabetes and Alzheimer’s, and it provides an environment that allows cancers to spread.

Professor Patrice Cani at the Université Catholique de Louvain in Brussels may have found the link between this tissue-damaging inflammation and the microbiota.

The lining of our digestive tract is called the epithelium and it occupies a very large surface area – if it was stretched out it would cover a tennis court! The gut epithelium obtains much of its nourishment and protection from the fatty acids that gut microbes produce as they cause plant fibres to be fermented in the large intestine.

Protective pro- and pre-biotics

Some probiotic bacteria, like bifidobacterium and Lactobacillus plantarum, which are common in fermented vegetables, appear to directly enhance the function of the gut epithelium.

If the epithelial barrier isn’t properly nourished it can become more permeable, allowing endotoxins —the toxic byproducts of certain harmful bacteria — to enter the bloodstream. This in turn triggers the body’s immune system to mount a response – and this leads to persistent low-grade inflammation, affecting the entire body.

In the final link of this damaging chain reaction, persistent low-level inflammation leads eventually to ‘metabolic syndrome’ – the insulin resistance that contributes to chronic disease and obesity.

When Professor Cani fed a high-fat, “junk food” diet to mice, he found the junk-food diet did indeed make the animals’ gut barriers notably more permeable, allowing toxins to leak into the bloodstream. Dr Cani concludes that:

“Gut bacteria can initiate the inflammatory processes associated with obesity and insulin resistance” by increasing gut permeability

Conversely he found that an increased intake of prebiotics reduced the level of ghrelin, a hormone that initiates hunger, and simultaneously reduced appetite and increased satiety. Prebiotics can clearly play a role in weight reduction (Klok, Jakobsdottir & Drent, 2007).

pre-and-pro-biotic-foods

Foods high in pre- or pro-biotics

The microbiome influences good and bad health

We have seen that gut bacteria have complex effects on metabolism and changes in their composition have been linked to inflammatory diseases, changes in the immune system and obesity. Intriguingly, if the intestinal microbiota from lean mice is transplanted to obese mice they lose weight – and vice versa.

Diseases as widely different as asthma, diabetes, obesity, cancer and heart disease have been shown to be influenced by the microbiome. Many researchers believe that the increase in auto-immune diseases and allergies is at least partly due to adverse changes in microbiomes.

Whatever the facts – and there is still a lot of work to do – it is now clear that the human body is essentially a community of cells and microbes in a symbiotic relationship. And that there are actions we can take to encourage a healthy microbiome.


Next week – Part 2 – Fermentation is the key to a healthy microbiome


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