We conclude that there is a complex microbiota associated with WSL that can include S. wiggsiae and possibly G. elegans, Veillonellaceae, and Bifidobacteriaceae, in addition to S. mutans. Of clinical significance, procedures to prevent the development of WSL should include testing more bacterial taxa than mutans streptococci and Lactobacillus species, and consider the impact of treatment regimens on the diverse microbiota.