Paleolithic Microbiome in the Modern World

A lot of westerners go through life in a state of low-level inflammation, and chronic disease is considered a normal part of life in the modern world. While the apparent “cleanliness” of the western lifestyle removes rare pathogens, modern hygiene also has some hidden costs.

Hunter-gatherer populations and “non-westernized” societies have been mostly free from chronic non-communicable disease, and an “ancestral” lifestyle is associated with a healthy and diverse microbiome. While most of us aren’t going to move into the wild to mimic the paleolithic way of life, we can still get most of the benefits by making some changes to our modern lifestyle.

Our ancestors routinely came in contact with microorganisms through food with clinging soil/dirt, untreated water, fermented foods, hands, birth/breastfeeding, other humans, animals etc.  Most paleolithic and non-westernized populations also had a diverse intake of vegetables and fruits that provided the needed prebiotic fiber for the gut microbiota.

The clean western lifestyle

The modern food system is characterized by monocultures, harsh chemicals and a general belief that “bacteria are bad”. Also, the water supply is closely monitored and filtrated.

While fermented foods are still eaten regularly in a lot of westernized countries, there’s only a minority left who still eat traditionally fermented food. Rather than using foods with naturally clinging microbes needed in the fermentation process, the modern approach is to take commercially produced cow’s milk, reduce the fat content, pasteurize it to remove bacteria, and then add some isolated bacterial cultures to aid fermentation.

Regularly cleaning everything around us (including ourselves) with various chemicals also reduces our exposure to new strains of bacteria from hands, uncleaned surfaces etc.

Contact with other humans and animals is also a source of microorganisms, and it seems that health is contagious. Poor health goes hand in hand with a “poor” microbiome, which is shared through human contact. E.g., when a child picks up bacteria from a mother with type 2 diabetes during birth, breastfeeding and infancy, it predisposes the child to that conditions. If health is contagious, which it seems to be, it’s likely that individuals with conditions closely linked to alterations in the human microbiome (e.g., obesity, overweight, diabetes, IBS) are able to spread their microbiota to other humans. It remains to be seen to which extent microbes from other humans and animals are able to alter the adult microbiome.

Are some “old friends” gone forever?

Some scientists believe that species of microbes that used to be a part of the human microbiome are now gone as a reult of modenr hygiene and widespread use of antibiotics. The “old friends” hypothesis suggests that our immune systems can neither develop nor function properly without these microbes that we have co-evolved with for millions of years. These “old friends” include some ambient species that exist in the same environments as humans, microbial species that inhabit the humans and animals, and some viruses and helminths.

While it could be that we are missing some organisms that used to inhabit the human body, the following measures should help increase the diversity and resillience of the human superorganism, and make the microbiome look more like that of our paleolithic ancestors.

Basic guidelines

  • Get high quality drinking water
  • Food
    • Choose organic, grass-fed and unprocessed whole foods
    • Eat a variety of vegetables and fruits to supply gut flora with soluble fiber
    • Buy produce at the farmers market or from other quality sites.
    • Don’t be afraid of dirt/soil clinging to vegetables, berries, mushrooms, spices/herbs etc. you get from a trusted source
    • Eat some plants raw
    • Eat a variety of high quality fermented foods
  • Hygiene and cleaning
    • Avoid harsh chemicals
    • Avoid excessive hand washing and the use of hand sanitizers
    • Children should be allowed to play, get dirty and pick up microorganisms, both inside and outside
    • Gardening is great
  • Birth, breastfeeding and infancy
    • Avoid cesarean section if possible
    • A newborn child should be breastfed
    • Kissing, chewing the child’s food etc. will provide the newborn with new microbial strains
  • Contact with humans and animals
    • Contact with healthy humans and animals is a possible source of beneficial bacteria
    • Health is contagious – be healthy not just for yourself, but for your partner, children, future children etc.
  • Supplements and pharmaceuticals
    • Avoid pharmaceuticals, especially antibiotics, if possible
    • Probiotic- and prebiotic supplements can be usedif necessary


  1. […] of a new type of probiotic supplement. Maybe Probiotic 2.0 will make it possible to get a “paleolithic gut flora” in the modern world… Although a healthy diet seems to be the most important factor in regards to maintaining a […]


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