"In subjects consuming the non-nutritive sweeteners, we could identify very distinct changes in the composition and function of gut microbes, and the molecules they secrete into peripheral blood," said senior author Professor Eran Elinav, an immunologist and microbiome researcher at the Weizmann Institute of Science, Israel, and the German National Cancer Centre.
"This seemed to suggest that gut microbes in the human body are rather responsive to each of these sweeteners."
The team were also able to prove that the effect was causal by implanting samples of the sweetener gut microbiome from human subjects into mice, who also became glucose intolerant.
Elinav said that the effects of the sweeteners will vary person to person because of the unique composition of each person's microbiome.
"We need to raise awareness of the fact that non-nutritive sweeteners are not inert to the human body as we originally believed," he added.
"We need to continue searching for solutions to our sweet tooth craving, while avoiding sugar, which is clearly most harmful to our metabolic health."
Latest figures suggest around 2.2 million people in Britain use artificial sweeteners four times a day or more. As well as being used as an alternative for sugar, they are also found in drinks, desserts, ready meals, cakes, chewing gum and toothpaste.
Previous research has suggested that artificial sweeteners may have a stimulating effect on appetite and, therefore, may play a role in weight gain and obesity, but there have been conflicting reports.
'Avoid consuming sweeteners in excess'
Commenting on the research, Dr Sarah Berry, senior lecturer, at King's College London, said many people are unaware that artificial sweeteners are used in processed foods.
"Many people aren't even aware that they are consuming sweeteners as they are in such a wide range of foods.
"Therefore, these results are relevant to a large proportion of the population, especially for those who select low-sugar drinks and foods as a healthy alternative.
"The evidence from this new research and other studies show that sweeteners are not inert and whilst they are a better option than full sugar alternatives, my recommendation would be to try and avoid consuming them in excess."
The British Nutrition Foundation said that more research was needed to back up the findings and said that sweetener was still useful for people trying to cut calories and lose weight.
Dr Duane Mellor, registered dietitian and senior teaching fellow, at Aston Medical School, Aston University, said that people could use sweeteners as a "stepping stone" to reduce sugar.
That way they can "still enjoy what they eat and drink, on the way to reducing both added sugar and sweeteners in their diet," he said.
The NHS website currently states that sweeteners are "perfectly safe to eat or drink on a daily basis as part of a healthy diet".
The research was published in the journal Cell Press.
