As well as aspartame, the scientists also assessed sucralose, saccharine, neotame, advantame and acesulfame potassium-k.
Ten sports supplements that contain these sweeteners were also analysed for the study, published in the journal Molecules.
The study was led by a team at Ben-Gurion University of the Negev and Nanyang Technological University in Singapore.
In their laboratory trial, all six of the sweeteners were exposed to bacteria that are commonly found in the human gut.
These bacteria were genetically modified to contain fluorescent compounds that glow when they detect toxins.
The researchers discovered toxins are released when gut bacteria are exposed to artificial sweeteners in the lab.
It only took one mg/ml of the artificial sweeteners to turn the bacteria toxic.
And the higher the amount of artificial sweetener, the more toxins that are released, according to the team led by Professor Ariel Kushmaro.
He said: "This is further evidence consumption of artificial sweeteners adversely affects gut microbial activity which can cause a wide range of health issues.
"The results of this study might help in understanding the relative toxicity of artificial sweeteners and the potential of negative effects on the gut microbial community."
Diet drinks account for a quarter of the sweetened beverages market but there is growing evidence they are not as healthy as previously thought.
Although marketed as a diet-friendly alternative to sugary drinks, scientists say they should no longer be regarded as the healthier alternative.
Artificial sweeteners have repeatedly been linked to obesity, cancer, type 2 diabetes, migraines and even liver toxicity.
The sweeteners are also emerging as environmental pollutants due to them being resistant to wastewater treatment processes.
Professor Kushmaro added the findings could also help to detect the damage that artificial sweeteners have on the environment.
Aspartame has established itself as an important component in many low-calorie, sugar-free foods and beverages.
It is consumed by more than 200 million people around the world and is found in more than 6,000 products, it was reported in 2015.
These include carbonated soft drinks, powdered soft drinks, chewing gum, dessert mixes, puddings and fillings and some vitamins and sugar-free cough drops.
Aspartame is a nutritive sweetener made by joining two amino acids L-phenylalanine and L-aspartic acid, with a third component called a methyl ester group.
Very little is needed for a sweet taste, making aspartame virtually non-caloric. It is thought to be up to 200 times sweeter than sucrose.
More people may be opting for artificially-sweetened drinks after a sugar tax on soft drinks was introduced in the UK on April 6.
Drinks with more than 8g of sugar per 100ml are taxed 24p per litre. Those containing 5-to-8g of sugar per 100ml are hit with a lower rate of tax of 18p per litre.
Many drink manufacturers have slashed the amount of sugar in their drinks in order to escape the tax.
