BioTransformer 3.0 is a software tool that predicts small molecule metabolism in mammals, their gut microbiota, as well as the soil/aquatic microbiota. Moreover, it can also assist scientists in the identification of metabolites, which is based on the metabolism prediction. BioTransformer uses both a knowledge-based approach and a machine learning based approach to predict small molecules metabolism. In particular, BioTransformer consists of five independent modules: EC-based, CYP450, Phase II, Human Gut Microbial and Environmental Microbial. The BioTransformer library is available at this Bitbucket page.