The infection process of bacterial gastroenteritis often relies on the initial binding of toxins to carbohydrate receptors on host cells. We screened the human gut microbiota for microorganisms naturally expressing toxin-binding carbohydrate structures. Out of stool samples from four healthy adult donors, we isolated bacterial strains specifically binding the cholera toxin and the heat labile toxin. These results suggest a new mechanism by which the microbiome may shape peoples individual sensitivity to gastrointestinal infections. This study may also pave the way for the development of non-antibiotic microbiome based strategies to treat and prevent gastrointestinal infections.