Microbiome
The Microbiome, or the micro-organisms which live in our gut and on other surfaces and organs of our body, has become a hot topic in recent years - with good reason. There are more micro-organisms, mostly bacteria, in our gut than there are cells in our human body (around 10x more) and there is more of their DNA in our body than human DNA. Our functioning is incredibly intertwined and dependent on these micro-organisms which are found throughout our bodies. We have evolved together and many of the functions of the human body aren't carried out by human cells at all. In our war on bacteria and micro-organisms, we have harmed ourselves and the ability of our bodies to function in a healthy way and the way they have evolved to function. In this article we are mainly going to focus on the micro-organisms of the gut, and particularly the small and large intestine.
Along with the skin that you have on the outside of your body, you also have skin that covers the internal surfaces of your body, and its surface area is about the size of two tennis courts. These internal skins start at the sinuses and run all the way to the rectum, and they all contain these micro-organisms which help form the vast majority of the total skin of our body. They are what protects us from what we need to be protected from in the outside world and make available to us things that we need from the outside world to sustain us. Our gut lining or “skin” has three layers, except in this case the first two are made up of mucosa which is maintained, protected, and lived in by lots of amazing microorganisms and only the deepest layer is actually human cells. This layer of human cells is only one cell thick and has tight junctions between these single cells to try maintain integrity and only allow certain molecules into the body (see Leaky Gut).
It is really important that we have the right micro-organisms and in the right proportions, with diversity being important, in the microbiome, in order for it to work well and protect and sustain us. By disrupting this balance and by killing off certain organisms or strains as we are doing with antibiotics, herbicides, pesticides, and other means, we have lessened the diversity and allowed certain strains of “bad” bacteria, yeasts, fungi and other parasites to dominate which are causing further harm. The Mayo Clinic, studying a 5000 year-old frozen human corpse, found it had 20,000 species of micro-organisms, now the average American has 500. People who are overweight have been shown to have a less diverse microbiome than those who are thin. Faecal transplant (a procedure where they transplant faeces from the bowel of one individual into another to introduce different micro-organisms into their system) is the only treatment that has been found to be effective for clostridium difficile infection in humans, because you need to have to right bacteria in your gut to fight it.
The beneficial microorganisms in our gut:
Work as part of our immune system. Their presence will dampen over-activity of the immune system, which is what is occurring in inflammation and auto-immune disease. It is estimated that 2/3 of the immune system is located in the gut and it sends messages to rest of the body.
Fight infections
Have certain strains that can affect cancer
Work together with human cells produce 90-95% of serotonin in the body - the happy hormone
Form: B-group vitamins, vitamin C, vitamin K, potassium, phenylalanine, and tyrosine, and cofactors which help to move phenylalanine and tyrosine into dopamine
Make nutrients available to us and enhance their absorption, including polyphenols, flavonoids, glucosinolates
Balance pH
Keep bowels moving well
Help digest lactose and proteins
Have certain strains that enable immuno-therapies to actually work. The presence of Subtilis Acromancia is necessary for certain immunotherapies to work. You can only get this from consuming juice pressed out fresh pomegranate seeds or cranberries.
Help us break down oxalates like those in spinach, beets, nut butters, rhubarb
Signal Ghrelin levels to drop after eating (the hormone that makes you feel hungry)
Make things that our bodies utilise e.g. cellulase enzyme, antioxidants like lycopene and lutein
Bind to and detox heavy metals from our system including arsenic, cadmium, mercury and lead
Bifidobacteria produces short-chain fatty acids that form buterate, which provides energy to the large intestine.
Communicate with the thymus gland which matures immune cells
Tell belly fat cells not to grow
Boosts anti-tumor immunity
Decreases the ability for breast and colon cancer cells to grow
Keep gonads and testosterone levels in men healthy
Communicate with our brain and ask it to produce oxytocin
Help detox xenoestrogens from our system
The micro-organisms in our gut are completely influential upon and form part of our epigenetics or gene expression. We have been led to think of our genes as being these static things that decide for us whether we are going to develop certain diseases. However, the presence of a gene does not mean we are going to actually have that gene expressed in our bodies and it is estimated that only 1% of our genes are unaffected by environmental factors and how we live our lives. For instance, around 30% of the population carry the genes for Coeliac Disease, but only about 1% of the population develops it. The 1% of genes which are unaffected by environment include the genes for genetic disorders such as Muscular Dystrophy which will always develop if the gene is present for it, and will not if the gene is not present. Micro-RNA produced by bacteria in our gut play a big role in controlling our epigenetics and can suppress or activate the expression of genes and viruses within our DNA. The beneficial bacteria have beneficial effects (which could be the activation or suppression of certain genes), and when we kill off the beneficial bacteria they are no longer there to, for instance, create the RNA necessary to suppress things like endogenous retro viruses which have been incorporated in human DNA for millennia, but been silenced for a long time by bacteria. Theories exist that diseases such as type-I diabetes are the result of beneficial silencing-RNA producing bacteria no longer being present in our guts.
What damages the microbiome?
Antibiotics - it now seems obvious to state this but yes, antibiotics will kill bacteria in your gut. Particularly the broad-spectrum antibiotics that so many of us take when we are sick because they are designed to wipe out a whole heap of different types of bacteria. There are also antibiotics in factory farmed animals and dairy products too.
Herbicides and Pesticides in our food and in the environment that we also end up drinking in our water, inhaling in the air, and putting on our bodies in toxic self-care products. Glyphosate, the most widely used herbicide globally, is also a patented antibiotic, which means it doesn't only kill so called weeds, it also kills bacteria including some of the good bacteria in our gut. One of the stated beneficial effects of Glyphosate is that it kills organisms which use the Shikimate pathway and because humans don’t have this metabolic pathway it is safe for use. However, there are beneficial bacteria in our gut which use the Shikimate pathway to produce things like the essential amino acid tyrosine which is a precursor to Dopamine, phenylalanine, and tryptophan. More on glyphosate here.
Caesarean deliveries, because the microbiome isn't populated properly in the first place
Not breast feeding, there are prebiotics in breast milk that human cells don't digest but do feed bacteria
NSAIDs e.g. ibuprofen
Proton-pump inhibitors e.g. antacids
Poor diet
Excessive sugar consumption – it promotes yeast overgrowth in the gut because they feed on sugar
How many of the things which negatively affect the microbiome have you used or experienced?
What state do you think your microbiome is in and why?
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Much Love,
Sophia Englezos