The depletion of the human microbiome and how it can be restored

Tobias Rees and Nils Gilman write:

It is a crisis some scientists believe has similar proportions to climate change, but it gets much less coverage: Microbes are disappearing from our bodies.

You may have heard that trillions of microbes — bacteria, fungi, viruses, protists — live on every surface of your body as well as inside your mouth, other orifices and your gut. You may have also heard that these microbes make up the majority of your body’s cells.

But few are aware of how directly these microbes and their genes affect the functioning of our bodies. The human genome found in the nuclei of our cells contains roughly 20,000 genes, but the microbiome — the sum total of genetic material in the microorganisms that live in and on us — contains as many as 20 million genes, all of which are directly or indirectly interacting with and at times even controlling our genes.

Our microbial genes are critical to the regulation of our metabolism, to the ability of our immune system to fight off infection and to the production of the neurotransmitters that power our brain and nervous system. The microbiome, just like our nuclear genome, is heritable. The majority of microbes are transferred from mother to child during childbirth, in a chain of transmission that reaches back to the earliest animals that evolved — which happen to have been microbes.

So why the crisis?

What we eat

The first major issue is the modern diet. Our hunter-gatherer ancestors mostly ate a plant-based and fiber-rich diet, which sustained a diverse microbial population in our guts that could produce all the metabolites our bodies and brains needed to grow and flourish. By contrast, most modern humans rely on a narrow, nutritionally impoverished and fiber-poor diet. This starves large parts of our microbiome and disrupts our health through typical “diseases of modernity,” such as obesity and diabetes.

The microbial diversity found in the guts of contemporary hunter and gatherer societies, such as the Hadza people in Tanzania or the Yanomami of South America, is roughly twice as high as the one found in the average European and American gut (independent of ethnicity). The good news is that in most cases, if we return to a diverse, fiber-rich diet before essential microbes are lost, some of the diversity of our gut’s microbial population can be restored. [Continue reading…]

For the individual, one of the most effective ways of restoring microbial diversity is by drinking kefir — but not the kind you can buy in a supermarket. Real kefir is made at home.

The consumer mindset is one in which we’ve been encouraged to believe that the easiest way of obtaining what we want is to pull it off a shelf, ready-made, attractively packaged, and ready for consumption.

Manufactured kefir not only involves complex, expensive, industrial processes — as shown here — but the end product is a pale imitation of the real thing.

If you make it yourself, once you’ve bought your first batch of kefir grains, you can continue recycling them indefinitely — my home brew is still going strong after a decade! And since I’m not a kefir purist, I don’t rely on raw goats milk or any other hard-to-find product — just organic whole milk, which seems to work fine.


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