What is a microbiome and why it is important

Bars of Snowbunny Soap

by Catherine Haug, December 11, 2016 (Photo of handmade soap, right, by Kathy Mansfield from her ESP presentation, Making Soap at Home)

Often when I mention the microbiome in conversation, people ask me what it is. So I figure our readers might like to know more about it. It is an ecological community of microbes – microscopic species – that share climatic or environmental conditions in which they live; a sort-of mini-ecosystem. These species include bacteria, fungi and viruses. (1)

A  hot topic in health news these days is the human microbiome, which usually refers to the microbes in the gut, but all parts of our bodies each have their own microbiome, including our skin and our eyes. These communities include both ‘good’ and ‘bad’ microbes; even the ‘bad’ or pathogenic microbes have beneficial effects for our health, when kept in balance. (1)

The important take-away is that we, as humans, would not survive without our microbiome. They provide our initial immune response, make vital enzymes, play a role in our psychological health and so much more yet to be understood.

See also my 2014 post: The importance of the microbiome (essential microbes in and on our bodies)

A closer look at ‘microbiome’

In Biology classes I learned that some species, like sea sponges that live in the ocean (6,7)*, are actually a distinct community of interdependent single-cells that coexist in a unit for their mutual benefit. This is how I picture our human bodies – not just our own human cells but also roughly the same amount of microbial cells that make up the whole of what we call ‘us.’ According to the Microbiome Institute (2), a ‘reference’ human body contains on average about 30 trillion human cells and 39 trillion bacteria.  (Note, this count does not include viruses and fungi also present in our microbiome).

*Check out the 2 minute YouTube video, reference 7, to learn more about sea sponges.

An integral and essential part of our human cells – a type of organelle called ‘mitochondria’ – was originally a bacteria, part of our human microbiome, that eventually was taken up by our cells as an organelle to produce the energy currency of the cell, ATP, through respiration, and regulate cellular metabolism. (3)

But the human microbiome is not the only microbiome. Plants that grow in soil would not survive without the soil microbiome that is intimately associated with the plant’s roots, helping them to take up nutrients from the soil (it is this microbiome that is threatened by ag-chemicals like Roundup). And like humans, the plants themselves have more than one internal and external microbiome. The same is true also for all animal species.

A perfect example of an external microbiome is that of the seeds of wheat and other grains; it is their external microbiome that form the sourdough cultures we use to make healthful breads, for example. Similarly, vegetables have an external microbiome that we utilize for fermentation (as for sauerkraut), or for making compost. Another example is the microbiome on our skin; actually that is more than one microbiome, as different areas of skin have their own unique microbiome; for example, that on your right hand is different from that on your left hand.

Maintaining health of our gut microbiome

Our gut is the first line of defense against illness; our immune system, in conjunction with the good bugs in our gut, recognize substances or other life-forms as ‘alien,’ or ‘invasive’ and then mount attack to eliminate the invader. What do the good bugs have to do with all this?

Every single-cell species has the ability to recognize ‘good’ and ‘bad’ neighbors through the release of specialized chemicals that survey the immediate surroundings. When a ‘bad’ neighbor is discovered by a good bug in our gut, it then signals the immune system via different chemicals, that danger is present.

But if our microbiome is out of balance (ill), bad bugs can get out of hand. Even some normally good bugs – like candida – can get out of hand and cause illness (candidiasis in this example).  This, in turn, can lead to a condition commonly called ‘leaky gut.’

Leaky gut means that molecules of partially-digested proteins in the intestines move through cracks in the single-cell-thick intestinal wall, and cause trouble. The primary trouble is attack of the leaked substance by the immune system when it does not recognize that substance as part of ‘self’. Secondary and far worse trouble happens when the immune system then goes on to attack parts of the internal body that have a partial amino acid sequence identical with that of the leaked protein, thus initiating auto-immune reaction that can become a disease if it happens frequently.

Auto-immune diseases include lupus, rheumatoid arthritis, MS, Type-1 diabetes, Celiac, Hashimoto’s, Graves, and others. Note that leaky gut is not the only mechanism that can lead to such disease, but it is a major one.

Most conventional doctors treat this by treating the symptoms with pharmaceuticals that the patient will likely have to take for the rest of his/her life. But there is a better way: balance the microbiome and heal the leaky gut. This is not necessarily a cure, but it is remission that, if maintained, will not allow the problem to re-occur,

How do you heal a leaky gut? By making important changes in your diet. This includes supporting the good bugs in the gut (the microbiome) with prebiotic foods (such as lacto-fermented foods like sauerkraut, and cultured foods like yogurt and kefir) that feed our good bugs, and soil-based probiotic supplements that support a healthy microbiome.

Exposure to toxic chemicals like heavy metals, synthetic pesticides and herbicides, and even some pharmaceuticals, can also cause leaky gut. In this case the solution is the same as for problem proteins, with the added action of avoiding further exposure to these toxins.

Protecting our soil microbiome

As mentioned above, ag chemicals such as Roundup, damage the soil microbiome essential to the immune system of the crops and their ability to take-up vital nutrients from the soil. From a 2010 article in Institute of Science in Society, “Scientists Reveal Glyphosate Poisons Crops and Soil” (5):

“Scientists go public on devastating ecological impacts of Roundup Ready cropping systems while USDA keeps mum. … There has been a general increase in the number of plant diseases in the past 15 to 18 years. Four primary soil fungi,  Fusarium, Phythium, Rhizoccccctonia, and Phytophthora, have become more active with the use of glyphosate [Roundup]; and concomitantly, diseases caused by these fungi have increased, such as head scab in corn, or root rot in soybeans, crown rot in sugar beets.” 

This is because the poisoned soil lacks the beneficial microbiome needed to support health of the plants’ roots and the soil itself.

Another damaging effect of modern agriculture on the soil microbiome is tilling the soil. Tilling breaks up and aerates the soil, devastating the essential microbiome in the soil, the very thing that ties it to the earth. The Great Dust Bowl of the 1930s was a visible negative effect of tilling. Once farmers stopped tilling, the soils settled down and could support crops once again. Unfortunately, once the land again became productive, farmers returned to tilling, as they do today.

Home gardeners, take note: minimize tilling of your garden’s soil. When you add compost, manure and mulch, layer them on the soil rather than tilling them in; moisture such as rain or watering will carry those layers deeper into the soil without damaging its microbiome.

Protecting our skin microbiome

The skin microbiome provides a first line of defense against invasive pathogenic microbes looking to make a home in our warm bodies. But the use of commercial antibacterial ‘soaps’ has had an adverse effect on human health:

  • in the short term by killing not only the bad bugs but also the good bugs in our skin microbiome, and
  • in the long term, by allowing the bad bacteria to mutate into antibiotic-resistant forms.

A far more healthful and protective means of cleansing our skin and hair to minimize the bad bugs is to use real, homemade soap (or their commercial counterparts such as Castile, Dr. Bronner’s or J.R. Liggett’s soaps and shampoos). Such soaps act against the bad bugs without destroying or harming our skin microbiome. See Wellness Mamma (4) for lots more on this. prescript-assist.com/intestinal-health/gut-microbiome


  1. updated link: enviromedica.com/human-microbiome (old link text: prescript-assist .com/intestinal-health/gut-microbiome; note this link has been inactivated). Background for why the link has changed: “Late last year, the manufacturer of Prescript-Assist made substantial changes to the formula of the product which did not align with Enviromedica’s quality standards. Enviromedica was the original distributor of Prescript-Assist. Considering these changes, Enviromedica stopped distributing Prescript-Assist. In light of this discontinuation, Enviromedica is currently in development of an advanced soil-based probiotic that we are excited to launch in the coming months.
  2. microbiomeinstitute.org/blog/2016/1/20/how-many-bacterial-vs-human-cells-are-in-the-body
  3. biology.tutorvista.com/animal-and-plant-cells/mitochondria.html
  4. wellnessmama.com/130266/skin-microbiome
  5. i-sis.org.uk/glyphosatePoisonsCrops.php
  6. seaspongecompany.com/pages/what-is-a-sea-sponge
  7. youtube.com/watch?v=7YFX0lUXFaE

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