It’s not just elephants and tigers we’re driving extinct – we’ve been drastically wiping out far tinier organisms too. This extinction of microbes brought about by the human era – known as the Anthropocene – could be behind some of our physical and mental health problems, as well as the current antimicrobial resistance crisis.

Cultural practices including agriculture, diet, sanitation and the widespread use of antibiotics are responsible for the low diversity of microorganisms in the guts of people living in rich nations.

This loss of diversity began 350,000 years ago, when we learned to use fire. Through cooking, we were able to unlock more calories from our food, allowing us to evolve larger brains but smaller digestive tracts. Bacterial diversity likely declined further around 10,000 years ago, when humans invented agriculture. As we switched to farming, we began to eat much narrower diets, which would have affected our internal fauna.
But farming affected the microbes associated with other animals too. As we started to raise animals for food, we began a trend which eventually meant that, today, the bulk of animals living on Earth are sheep, pigs, cattle and poultry.

This has narrowed the range of animal environments in which microbes could live. Around 12,000 years ago, the majority of the world’s digestive microbiota would have been living inside wild animals – an estimated 200 million tonnes of microbes globally. By the year 2000, the microbes living inside wild animals became tiny, compared with the 600 million tonnes living in farm animals, and the 200 million tonnes that live inside us.

The fact we only use four species of livestock – and as we all eat the same food – we completely lose the diversity needed to always replace genes when they’re needed. However, for humans, the biggest changes likely occurred sometime after the beginning of the industrial revolution.

The arrival of disinfectants, sanitation, processed food, caesarean births, bottle feeding, widespread international travel, and – most of all – antibiotic drugs, has prompted a major loss of diversity and homogenisation of the bacteria and other species that live inside humans across the planet.

The sudden loss of so many species that co-evolved with us is suspected to play a role in a wide range of health problems and as diversity has declined, valuable and protective genes have likely been lost forever.