TL;DR: The microbiome is a collection of single celled organisms in all areas of our body, especially the gut, and is integral to our immune and nervous system. Eat nutritious, natural food and avoid antibiotics unless absolutely necessary to keep it in good condition.
Introduction
All energy for life on Earth comes from the Sun through lower life forms eventually making its way to us, as apex predators. All of the lower layers are needed for us to survive.
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At the very base of the pyramid of life we have bacteria, fungi, and other single celled organisms that break other living things down when they die. We need them to do this to unlock nutrients for plants to use, which then feed herbivores, and then carnivores at the top of the food chain.
Just like the health of an ecosystem rests on decomposers, so too does our health as human beings rest on the ones inside us to break things down for us – which we call our microbiome.
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It has been a hot topic in recent years due to the uncovered importance it has for our health, especially in regards to immunity and neurological function. Some scientists even consider it a separate organ as we learn more about how many functions it has, which shows how far it has come seeing as we didn’t generally recognize it’s existence until the 90s.
What Is the Microbiome?
The microbiome is all of the microscopic organisms that live in and on our body. The word microbiome comes from micro, as in too small to see with the naked eye, bio, meaning life, and -ome, from chromosome.
What Is it Made of?
It is estimated that the average microbiome is composed of roughly 30-100 trillion microorganisms (microbes) including viruses, bacteria, archaea, fungi, and protists – but typically it does not include multicellular organisms. It is made up of microbes that are good for us, bad for us, and ones that are neutral towards us. They are found in many areas throughout the body, mostly in the gut.
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Overall, the microbiome forms a symbiotic relationship with us by making compounds and nutrients we can use. Interestingly, there is a similar amount of microbes in us as there are human cells, though our cells are much bigger [1]. In total, the microbiome weighs a few pounds for the average person, similar to a large organ.
Genes
The microbiome has been explored and understood primarily through knowing its genetic make up from samples, such as from stool, and sequencing it as we do with the human genome.
At a genetic level, our microbiome contains millions of protein-encoding genes (important ones), whereas the human genome contains about 23,000. So, the number of genes working for us through microbes outnumbers our own cells by a factor of roughly 100 times. This is because there is a vast variety of microbes, with at least 1000 species found in the average healthy gut [2].
The two main phyla (categories) of bacteria we know of are Bacteroidetes and Firmicutes – names you’ll see on probiotic supplements [3]. Scientists are still in the beginning stages of understanding the species that make up our microbiome but there are thousands that have been identified to date.
The microbiome not only has its own library of genes that work for us, but also affects the expression of our human genes. This can be bad or good depending on the microbe.
Where Is it Found?
Microbiota are found in the following [1]:
- Skin
- Women’s breasts
- Placenta
- Seminal fluid
- Uterus
- Ovarian follicles
- Lungs
- Saliva
- Oral mucus
- The inside of the eyelids
- Liver, gallbladder, and bile ducts
- Gastrointestinal tract
Each area has its own microbiota – communities that make up our total microbiome. The gut microbiota comprises the vast majority of the total amount, and almost all of it is found in the large intestine.
What Does it Do?
The microbiome does a lot for us. It is deeply involved in our immunity and defense against infection, production of nutrients we absorb in our colon, formation of new blood vessels, helping with fat storage, and helping the gut act as a “second brain” to help manage our nervous system [3].
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A lot of our nutrients get absorbed in our small intestine. Usually, these are foods that are easily broken down into small parts. Food that isn’t, like fiber, is broken down by the microbiome when they release their digestive enzymes. This releases nutrients like short chain fatty acids, B vitamins, vitamin K, and other beneficial compounds we can absorb in the large intestine.
Arguably the most important nerve in our body, the vagus nerve, connects our brain to our other organs, especially our gut – which is why some call the gut the “second brain”. In part, this is related to our microbiome, which creates nutrients, chemicals for signalling, and even neurotransmitters that affect the brain through the vagus nerve. One example of this importance is that gut bacteria manufacture about 95% of the body’s supply of serotonin [6], an integral neurotransmitter. These influences help explain the strong link between gut health and mental health.
Dysbiosis – A Damaged Microbiome
A healthy microbiome has a balance of species, and the ones that help us should predominate. However, when certain parasitic species take over, like E. Coli for example, we can experience very negative effects. The term used for this imbalance is dysbiosis.
Dysbiosis is connected to autism, asthma, cystic fibrosis, cardiovascular disease, type 1 and 2 diabetes, fatty liver disease, metabolic syndrome, obesity, inflammatory bowel syndrome, gut infections, acne, eczema, and allergies [3]. The breadth of bodily systems affected by the microbiome demonstrates its far reaches into our health.
One of the most studied conditions associated with dysbiosis is inflammatory bowel syndrome (IBS), which affects about 1 in 5 people. IBS is really an umbrella term doctors use to refer to the condition we don’t understand referring to inflammation of the digestive tract. When it gets more serious it can turn into inflammatory bowel disease (IBD), which is a similar umbrella term that can include ulcerative colitis, or crohn’s disease. In those with IBS and IBD, a reduced amount of Firmicutes and Bacteroidetes is found, and an increase of Proteobacteria is found compared to microbiomes of healthy people.
Diseases and conditions related to dysbiosis are on the rise, likely due to excessive antibiotic use, chemicals, and other negative environmental impacts.
How Can You Improve Your Microbiome?
The microbiome changes when we change. It most drastically changes during childhood. It also changes in response to other lifestyle factors like diet, antibiotic use, and especially disease.
Your microbiome is like a plant. You need to take care of the conditions like soil, water, sunlight and protect it from harm if you want it to be healthy.
At the centre is your gut microbiome, and to make it healthy you need to eat natural and nutritious foods while avoiding excessive stress and harmful chemicals like antibiotics. Everyone is unique in regards to what diet is optimal for them and their microbiome. See our articles on Nutrition for recommendations on improving your nutrition and finding a diet that works for you.
Avoid Antibiotics
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Antibiotics cause dysbiosis – see the previous section. In many cases, antibiotics are necessary, but they have been massively overprescribed for mild cases of infection as well as for viruses that they have no effect on. This has had a large negative impact on our microbiome, and is a large concern especially as they become more prevalent.
According to some research, it can take at least 6 months for the microbiome to recover from a course of antibiotics, and even then some species may never come back [5].
Birth Choices
Particularly strong impacts on the microbiome begin at birth and depend on antibiotic use, breastfeeding vs. formula, and vaginal vs. c-section delivery.
The microbiome of the mother in the vagina and breasts has a big role in the microbiome of the child in the case of natural birth and breastfeeding. There appears to be significant advantages to these cases because babies need this inoculation to form a strong microbiome later in life. One example of this is that women born by c-section in one study were 11% more likely to be obese and had a 46% higher chance of developing type 2 diabetes compared to women born vaginally [7].
Once the microbiome is formed, it is much harder to change, and seeing as it is still largely a mystery to us, we don’t have many tools to correct it.
Diet
Diet is a very strong factor in determining which species thrive in our microbiome. Different food attracts different types of microbes. A healthy diet of natural foods results in a healthy microbiome over time. See our article on our basic pillars of what a healthy diet looks like here.
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In particular, fiber has a strong impact on our microbiome because we can’t digest it and rely on bacteria to do so. This doesn’t necessarily mean that more fiber is better for our microbiome. Bad species of bacteria can thrive on fiber as well and you can have excessive gas and bloating produced by the microbiome as a by-product of them digesting fiber. Moreover, prebiotics are a particular type of fiber that are especially good for our microbiome.
Read more in our fiber article here.
Our gut itself, including the integrity of the mucus membrane, the level of inflammation, and other factors affecting it all have an effect in turn on our microbiome. In the end, if you intuitively feel your gut is comfortable, that is a good sign your microbiome is doing well.
Stress
Stress affects everything, and the microbiome is quite sensitive to it. We often notice stressful events give us a knot in our stomach, nerves in our gut, and take away our appetite. Like any part of the body, too much stress grinds away at the health of our gut and microbiome.
Give our articles on meditation and gratitude a try if you’re looking to cut down on stress.
Probiotics
The effectiveness of probiotics is debated, as many often don’t leave a lasting impact on the gut, they only have temporary effects. Even still, the probiotic industry is worth $50 billion worldwide and is growing at 8% per year [4]. Many people do find they are helpful even if only for temporary usage.
Foods that contain large amounts of beneficial bacteria include kefir, fermented vegetables like sauerkraut, kimchi, and tempe – these foods often contain much higher quantities of probiotics than capsules or supplements. The microbes in kefir are one of the few species known to be able to colonize the gut and leave a long term impact on the microbiome. One study where subjects took the species L. kefiri LKF01 DSM32079 for one month shows this below:
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Even a month after taking this kefir probiotic, the microbiome composition had changed significantly from before. The study found that many proinflammatory microbes that cause gastrointestinal diseases had reduced due to this probiotic. Perhaps other fermented foods and probiotics are capable of the same. It is often recommended to take some form of probiotic after a course of antibiotics.
A more extreme measure practiced in some clinics is a fecal transplant, which is exactly what it sounds like. It comes with risks, and is not widely used yet.
Conclusion
Microbes form the base of life on Earth, and do the “groundwork” to both break down dead organisms and build nutrients for other living things. Inside and on us, we have microbes everywhere, though there is a large concentration of them specifically in our large intestine where they break down food we can’t and provide us with nutrients. In addition, the microbiome serves integral functions in our immune and neurological health. Disruption of the microbiome through antibiotics and poor diet is linked to several prominent diseases and proper care of the microbiome is essential for good health.
References:
[1] https://en.wikipedia.org/wiki/Human_microbiome
[2] https://ep.bmj.com/content/102/5/257
[3] https://ep.bmj.com/content/102/5/257
[4] https://www.statista.com/statistics/821259/global-probioticsl-market-value/
[7] https://www.ajmc.com/view/csection-birth-associated-with-adulthood-obesity-diabetes
[8] https://www.sciencedirect.com/science/article/pii/S1590865816308155#fig0020
Images
[a] https://upload.wikimedia.org/wikipedia/commons/d/d4/Ecological_Pyramid.png
