In this paper we use the Lyndon-Shirshov basis to study the shuffle type polynomials. We give a free noncommutative binomial (or multinomial) theorem in terms of the Lyndon-Shirshov basis. Another noncommutative binomial theorem given by the shuffle type polynomials with respect to an adjoint derivation is established. As a result, the Bell differential polynomials and the $q$-Bell differential polynomials can be derived from the second binomial theorem. The relation between the shuffle type polynomials and the Bell differential polynomials is established. Finally, we give some applications of the free noncommutative binomial theorem including application of the shuffle type polynomials to bialgebras and Hopf algebras.