People can brush their teeth as much as they like, but our mouths will never be as healthy as those of our ancient ancestors.
Modern food, particularly processed sugar and flour, has decreased the amount of good bacteria in the human mouth, allowing bad bacteria to take over, which results in tooth decay and gum disease.
A team led by Prof Cooper's centre has published research in the journal Nature Genetics. They studied teeth from prehistoric northern European human skeletons and found oral bacteria in modern man are much less diverse than historic populations.
"We tend not think of ourselves from a bacterial perspective, but 90 per cent of our cells are bacteria," Prof Cooper told AAP on Tuesday.
The loss of diversity of bacteria "is nearly always associated with disease" and has been linked to obesity, autism and diabetes.
The best things humans can do is reduce processed sugars and carbohydrates in their diet.
"It is best to eat a wide variety of organic locally produced fresh foods," says Prof Cooper.
Children should be allowed to play outside and "get dirty and be exposed to microbes".
The rampant use of antibiotics is something else that is quite concerning, particularly in children, he says.
Mouthwash probably also does more harm than good, by removing the diversity that can suppress disease-causing bacteria, he says.
According to the research, the composition of oral bacteria initially changed markedly with the introduction of farming around 7500 years ago, and deteriorated further with the introduction of processed foods in the industrial revolution.
Prehistoric people had no cavities and their breath was "probably not bad", says Prof Cooper, who started the project 17 years ago with archaeologist and co-leader Professor Keith Dobney.
The research, conducted with the Department of Archaeology at the University of Aberdeen and the Wellcome Trust Sanger Institute in England, is described as the first record of how evolution over the past 7500 has affected human bacteria.
This is the first fossil record of human bacteria, and has important health consequences," says Prof Cooper.
The researchers extracted DNA from tartar (calcified dental plaque) from 34 prehistoric northern European human skeletons and traced changes in the nature of oral bacteria from the last hunter-gatherers, through the first farmers to the Bronze Age and medieval times.
Dental plaque represents the only easily accessible source of preserved human bacteria, says lead author Dr Christina Adler.
The research team is expanding its studies through time and around the world, including other species such as Neandertals.