CBCB scientists Matthew Oberhardt and Eytan Ruppin publish a paper in Nature Communications on predicting new organism-media pairings

Tue Oct 13, 2015

Lead author and CBCB postdoctoral associate Matthew Oberhardt and CBCB faculty Eytan Ruppin, along with collaborators, have published a paper titled “Harnessing the landscape of microbial culture media to predict new organism-media pairings” on October 13, 2015 in the journal Nature Communications.

Culturing microorganisms is a critical step in understanding and utilizing microbial life. In this paper, Dr. Oberhardt, Dr. Ruppin, and collaborators map the landscape of existing culture media by extracting natural-language media recipes into a Known Media Database (KOMODO).

They leverage KOMODO to predict new organism–media pairings using a transitivity property (74% growth in new in vitro experiments) and a phylogeny-based collaborative filtering tool (83% growth in new in vitro experiments and stronger growth on predicted well-scored versus poorly scored media). These resources are integrated into a web-based platform that predicts media given an organism’s 16S rDNA sequence, facilitating future cultivation efforts.

“Harnessing the landscape of microbial culture media to predict new organism–media pairings” article: http://www.nature.com/ncomms/2015/151013/ncomms9493/full/ncomms9493.html