Over the last 20 years, Ausubel's lab has worked on the development of so-called multi-host pathogenesis systems[4] that involve the infection of hosts, including the well-studied nematode Caenorhabditis elegans and the reference plant Arabidopsis thaliana, with a variety of bacterial and fungal pathogens.

[5] His laboratory currently uses the C. elegans pathogenesis model to study intestinal epithelial immunity and how hosts distinguish pathogens from beneficial commensal microorganisms.

Related work in his laboratory concerns the identification and characterization of low molecular weight compounds that specifically activate C. elegans immune signaling pathways.

In addition to serving on a variety of editorial boards, Ausubel is founding editor of Current Protocols in Molecular Biology.

Ausubel received the 2014, Thomas Hunt Morgan Medal, for lifetime achievement in the field of genetics.