Did you know that an autoimmune disease now affects one in five Americans? Of these, 80% are women; autoimmune disease is the fifth leading cause of death in women under 65. Most autoimmune diseases are being diagnosed in increasing numbers, but it is still unclear if all this variance is due to higher awareness, medical literacy, or better diagnosis techniques.

The effects of autoimmune diseases can be devastating. As a person’s immune system attacks their body instead of microbes or cancerous cells, they can experience chronic fatigue, chronic pain, drug dependency, depression, and social isolation. These symptoms annihilate mental health, wreck promising careers, destroy lives, and, often, financially ruin families. For too many, these illnesses result in early death.

The Missing Friends

The Old Friends Hypothesis suggests that early and regular exposure to harmless microorganisms—"old friends" present throughout human evolution and recognized by the human immune system—train the immune system to react appropriately to threats.

Here's the problem: some very specific microbes that we've coevolved with—for potentially millions of years (considering monkeys emerged 35 million years ago)—are no longer in our gut. Those are literally gone; they cannot be replaced by eating fiber, kefir, or any probiotics on the market. And this might be the reason the immune system of many people is dysfunctional—it's missing organisms it's been interacting with for a very long time.

We know this precisely because we've been able to compare the microbiome of industrialized populations with modern hunter-gatherers, who possibly have the microbiome closest to early humans. The Hadza, a protected hunter-gatherer Tanzanian indigenous ethnic group, are known for having the highest gut diversity of every population. The Hadza had an average of 730 species of gut microbes per person. The average Californian gut microbiome contained just 277 species, and the Nepali microbiome fell in between. Ultra-deep sequencing of the Hadza microbiome reveals 91,662 genomes of bacteria, archaea, bacteriophages, and eukaryotes, 44% of which are absent from existing unified datasets. The researchers identified 124 gut-resident species absent or vanishing in industrialized populations.

As seen in the above picture, there is, at the same time, reduced diversity and an entirely different type of microbial eco...

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