Why we need bacteria and viruses to stay healthy

When looking at the statistics, there's no doubt that the health of the population is declining globally with chronic diseases rapidly rising and reaching epidemic levels. What's the reason? Is it our sedentary lifestyle, our diet, increased stress, constant information overflow in a digital world or accumulating levels of toxins in our bodies and the environment? It's most likely a combination of all, but there is one factor above all, a key issue that is mostly overlooked and urgently needs our attention. I'm talking about the microbiome:  the bacteria and viruses that live in and on us in symbiosis and are needed to avoid chronic diseases.

The microbiome includes all microorganisms—bacteria, viruses, fungi and parasites—found throughout the body: in the gut, on the skin or in our nasal and oral cavities, as well as in our blood, organs and cells. We host a lot of them. Actually, estimates suggest that these microbes outnumber our human cells by 10 to 1. And with the number of viruses in our bodies estimated at more than a quadrillion, that adds up to 1'000 trillion. There are so many of these little bugs dispersed throughout our bodies that the microbiome in total weighs around twice as much as our brain.

This fact may sound disturbing or disgusting, but before you reach out for this hand sanitiser or the antibacterial mouthwash, please read on.

When the human genome project project was initiated in 1990, researchers were confident they would find around 120'000 human genes, based on the number of different enzymes and signalling molecules needed to explain human biochemistry.  In reality, scientists identified approximately 23'000.  Recent research has revealed two primary causes for this gap. First, epigenetic (environmental) factors cause us produce more proteins than we have genes for.  The other factor is the microbiome.  Scientists who are currently sequencing the microbiome estimate that it has between 100 to 150 times more genes than our human cells have.

It is also becoming increasingly evident that we rely on microbes for a number of essential processes in our body and need their genes to fully function. We live in symbiosis with our little friends:  we feed them and they support us. Well, not all of them are favourable, there are bad bugs too, but in a well-balanced microbiome most of them are good ones. More on that later.

Let's first have a look at how microbes are supporting us. They are not only a very important part of our digestion and immune system, but also produce signalling molecules that communicate with our human cells on several levels. Did you know that the gut has more neurons than the entire spinal cord and that more signals are being sent from the gut to the brain than the other way round? A whopping 90% of our "feel good" hormone serotonin is produced by our little bacterial friends in the gut. Well, with this knowledge at hand, it shouldn't come as a surprise that a dysbiosis in the gut microbiome can directly affect your mood and raise the risk of sliding into depression. If those serotonin-producing friends are decimated by antibiotics or an unhealthy diet, we simply don't have high enough levels of this crucial neurotransmitter to make us feel happy. Doctors trained in functional medicine therefore will have a closer look at your gut when you present with depression or with any other chronic illness. As Hippocrates put it," all disease begins in the gut." Science is now figuring out he was spot on with this one.

Microbes in our gut also play an essential role in our immune defence. They mark pathogenic invaders with special protein molecules. Once these invaders cross into the bloodstream, our own immune defence will very specifically attack those marked invaders.

These are only two of many examples of the symbiotic co-existence of our human cells with our microbial friends. Cutting edge research now finds that nearly all chronic diseases, from obesity, diabetes, cardiovascular diseases, autoimmune diseases to cancer and even autism can be triggered by a dysfunctional microbiome.

In his 2016 book "The Autoimmune Fix," Dr. Tom O'Bryan, looking at the sheer number of bacteria in our body and their large DNA base, contemplates whether we are humans hosting a lot of bacteria, or if we are actually bacteria having a human experience. In any case, we should appreciate that we are living with a parallel civilization inside of us, each assisting the other.

So what about the bad bacteria and viruses, those chaps that our immune system has a hard time dealing with?

We now know that bacteria are well organised communities and societies that use advanced signalling pathways to communicate not only within their own species, but also with others.

In dysbiosis, the microbial society within us faces the same problem we humans do.  (As above, so below!) In a well-organised society, be it human or microbial, communities can cope with a few bad guys. But if it's getting too many of them and communication infrastructure weakens and breaks down, chaos will arise and it's ever more difficult for the good guys to stay on top. A well-balanced and diverse microbiome can keep the bad guys in bay, while in dysbiosis the bad guys like candida & co. will overgrow and get pathogenic. 


Let's have a look at the main factors that are driving the gut microbiome into dysbiosis and our health into a chronic disease crisis. The most important are:

1.    Toxins
Microorganisms are especially vulnerable to toxins. Heavy metals, antibiotics, herbicides, pesticides and an ever-increasing number of other toxic chemicals are being released into our environment and are decimating the microbiome. An average of 287 known toxins and many more man-made chemicals can be identified in a newborn's umbilical cord. While there is some knowledge available for toxic levels of single substances, there is virtually no scientific research about the effect of a toxin cocktail. Even if the exposure to each individual toxin stays below its “healthy” threshold level, a combination of these toxins might not.

2.    Not enough fiber; too much sugar
The good and synergistic bacteria in us thrive on fiber, but our diet is deprived of it. While it is estimated that our paleo ancestors had more than 100g of fiber in their daily intake of food, we often do not get more than 15g. The daily recommended intake (RDA) sits around 30g, depending on age, gender and weight.  Meanwhile sugar (and refined flour), readily feeds the pathogenic guys. And we all know that we on average consume way too much sugar.

3.    Preservatives in processed foods
Industrially processed foods contain lots of preservatives, which are designed to hinder the growth of microorganisms. Guess what happens when we digest food that contains preservatives?  The preservatives do to your gut what they do to guarantee a long shelf-life:  they act antimicrobial.

4.    Antibiotics
Taking antibiotics at the first sign of uncomfortable but otherwise harmless infections is like throwing bombs on a city filled with civilians and some bad guys. The collateral damage for the microbiome is massive. Frequent use of antibiotics will shift the microbiome towards bacteria that are more resistant, potentially creating antibiotic-resistant superbugs. This is true for humans, as well as in conventional farming where antibiotics are widely used.

5.    Our environment and food contain fewer microbes
Maybe the most alarming factor is the serious decline of microbes in the soil and thus our food. Like humans and all animals, plants live in symbiosis with their microbiome. Roots and bulbs deliver sugars the microbes feed on and the microbes in return create lots of nutrients plants need to thrive. When pesticides and herbicides are sprayed on the plant and soil, they not only kill insects or defoliate plants, they also kill microbes. Glyphosate, the main ingredient in Roundup, is registered as an antibiotic agent.

But there is more trouble for the microbiome. For example, a USDA report states that only about 20% of the chemicals used on conventionally grown California strawberries were pesticides that can leave residues on harvested fruit. The other 80% – more than 9.3 million pounds in 2015 – were fumigants, which are poisonous gases injected directly into the ground to sterilize the soil before planting. Poor microbiome!

Intensive agriculture, with its frequent tilling and liberal use of fertilisers, leads to leaching of the topsoil, drying up of earth and a massive decline in the diversity and number of soil microbes and nutrient density. Levels of magnesium and other micronutrients found in the soil and in the produce grown in it have decreased by up to 90% within the last 100 years.  

The truth is, we are an integral part of nature. If we harm nature, we ultimately harm ourselves. All our food comes from nature.  When farm animals are pumped with growth hormones and antibiotics, fed on soy and corn concentrate they wouldn’t touch in the wild and live a stressful sequestered life, the meat and products that result have low nutrient density and a high toxic load--and compromise our microbiome.

Besides farming, how is the wildlife doing? According to the WWF Living Planet Report 2016, the population of fish, birds, mammals, reptiles and amphibians declined by 58% between 1970 and 2012. There are now 36% less birds and we face a staggering 76% reduction in freshwater animals compared to just 50 years ago. Would you like to be a fish in a river? I would certainly opt out on this one.


Depressing?  Yes.  But here is what we can do to support the microbiome in, on and around us to stay healthy in an increasingly toxic environment:


1.     Reduce exposure to environmental toxins where possible
Preventing exposure to environmental toxins is neither completely possible nor necessary. Our body's detox systems normally are pretty efficient. Problems occur when there is an overload and a chronic build-up of toxins. We all have individual thresholds for individual toxins that our system is able to tolerate. The levels depend on each individual's genetic makeup, health history and current health status. People with chemical sensitivities, allergies or food intolerances or with overall compromised health will exhibit symptoms at much lower toxin levels than others.

2.     Eliminate toxins in your household

Check your cosmetics, household cleaners and gardening products for harmful ingredients using websites like www.ewg.org or www.codecheck.info).  Use glass and stainless steel containers for food and beverages and check your cookware (especially anti-stick coating). Be aware of potentially toxic dye in your clothing and flame-retardant chemicals in furniture, mattresses and sleepwear. Be aware of new products that off-gas.  For example, new or renovated homes and new cars usually gas-off high levels of toxins. And make sure you are not exposed to mold, be it through food or through a moldy environment.  Note that toxic levels are usually higher indoors than outside, with the highest toxic levels usually found in the kitchen. Would you believe that the #1 household toxin source is heating oil when browning and frying? 

3.     Eat clean
Most toxins enter our body through our food and drinks. To limit your exposure to toxins in food, eat organic whenever possible, especially those vegetables and fruits that are especially high in toxins when conventionally grown (see https://www.ewg.org/foodnews/dirty-dozen.php ). On the other hand there are some vegetables that only contain lower amounts of toxins and might be safe to eat conventionally (see https://www.ewg.org/foodnews/clean-fifteen.php).  Be sure to eat foods that support detoxification like broccoli, leafy greens, etc. and cook at low temperatures (for example steaming vegetables, meat and fish.)

4.     Expose yourself to friendly microbes

Eat fermented foods like sauerkraut and kimchi, do some gardening to get in touch with soil microbes and use disinfectants only when necessary. 

5.     Support elimination

Drink enough water (filter your water if necessary) and consume more fiber, both to feed your friendly microbes and to eliminate more often. We should eliminate 2-3 times a day. If it's less often, consider taking magnesium, adding a bit of (himalayan) salt to your drinking water and up your consumption of unsoluble fiber. Sweat to eliminate toxins (using an IR-sauna is very beneficial).

6.     Keep things moving

Exercise regularly to support blood circulation and support the lymph flow through movement, rebounder, sauna, massage, relaxation, alternating hot/cold shower, etc.

7.     Buy sustainable products wherever possible
We as consumers drive the market. Let's be educated and honest consumers. Healthy, organic produce costs more than industrially and conventionally produced food.  The lowest price probably won’t give us the best product, and compromising on the quality of our food can cost us lots of money down the road. Today, more than 50% of healthcare spending globally is for treating chronic conditions. And most of these ailments originate from poor nutritional and lifestyle choices. 


So now you see why you may want to think twice before grabbing that antibacterial soap or agreeing to unnecessary antibiotics.  I’m not trying to scare you with all this talk of bugs and toxins. Rather, I'd like to encourage you to take a pragmatic approach.  Educate yourself, take appropriate measures and steps in your own life and sphere of influence and spread the word. It's not too late to turn the looming health crisis around, but we don't have much time left either. Let's aim to live in harmony and sustainability with nature and our little friends, the microbes. They will thank you and support you.


Wishing you good health,



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