The present disclosure provides methods and compositions for treating skin diseases, comprising an engineered microorganism expressing therapeutically relevant recombinant fusion polypeptides. In one embodiment, the disclosure provides a method for treating skin disease, such as atopic dermatitis, comprising administering a to a subject in need thereof a composition comprising live biotherapeutic product (LBP) comprising human filaggrin-secreting Staphylococcus epidermidis. In a further aspect, the present invention provides a pharmaceutical composition comprising a filaggrin polypeptide described herein. Further still, the present invention provides a kit comprising a composition disclosed herein and instructions for use.