Muth received his Ph.D. in cell biology from the Yale University School of Medicine in 1998, where he studied protein targeting in epithelial and neuronal cells in the lab of Dr. Michael Caplan. Muth went on to complete postdoctoral training at The Hebrew University in Jerusalem studying bacterial multidrug resistance transporters with Dr. Shimon Schuldiner, and a second postdoc at the University of California, Berkeley, studying DNA transfer by the plant pathogen, A. tumefaciens with Dr. Patricia Zambryski. In 2000, Muth began his independent research career at Brooklyn College. His lab studies the unique ability of A. tumefaciens bacteria to transfer DNA into host plant cells, and more recently, his lab has begun to investigate the diversity and dynamics of urban microbial communities using a metagenomic approach coupled with next generation sequencing.