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.

That’s the bleak message from an in-depth analysis of the effect our history as a species has had on the Earth’s microbes, especially those that live inside us. “Diversity of gut bacteria is declining with civilisation,” Michael Gillings of Macquarie University in Sydney, Australia, told the annual meeting of the American Society for Microbiology in Boston on Sunday.

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, said Gillings. He suggests 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. “If you have a smaller gut, that means you have less room for microbiota,” said Gillings.

Agricultural apocalypse

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,” says Antje Boetius of the Max Planck Institute of Marine Microbiology in Bremen, Germany. As diversity has declined, valuable and protective genes have likely been lost forever.

Health problems

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, including obesity, asthma, inflammatory bowel disease, psoriasis and even psychological conditions. “It’s beginning to look like the microbiome has effects on brain activity, and anxiety and depression have been linked with irritable bowel syndrome,” said Gillings.

But we could stop the trend, says Boetius. “By increasing crop diversity and [changing] how we live, we can decide how to manage this,” she says. “It’s about behaviour, and we can change that.”