 The CIMA algorithm was developed to identify the responsible species and enzymes for chemical transformations in their human gut. This algorithm uses chemical and protein similarity algorithms to accurately predict the responsible species and enzymes for a querid reaction, unlike previous methods. The algorithm was validated using external datasets and provided an in vitro validation of its predictions for metabolism of methotrexate, an anti-ethritic drug. CIMA is now available as a command line and web tool, providing flexible input and output options for determining chemical transformations within the human gut. By making this algorithm available, it enables researchers to make informed hypotheses before embarking on the lengthy laboratory experiments required to characterize novel bacterial enzymes that can alter human ingested compounds. This article was authored by Annamarie E. Bustion, Renuka A. Noyok, or Yushi Agrawal, and others.