More causative clues emerged when researchers began manipulating microbiomes to change phenotypes (observable traits, such as disease symptoms). Scientists would find a mouse model of fatty liver disease, for example, and then treat the mouse with antibiotics to erase its microbiome. If erasing the microbiome changed the liver disease or cured it, that suggested the microbiome was somehow involved.
— Read on magazine.hms.harvard.edu/articles/decoding-chemistry-microbiome