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Michael Fischbach: Mining Bacterial Genomes

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Recommended by: Joe DeRisi, University of California, San Francisco

The Fischbach lab at the University of California, San Francisco, is about one-third computational and two-thirds experimental. The computational arm is developing algorithms to mine bacterial genome sequences and metagenomic samples for gene clusters that encode small molecules, while the experimental group isolates and characterizes small molecules produced by the human microbiota.

One of the biggest challenges in his research is prioritization. "Our computational results suggest a huge trove of molecules waiting to be discovered and characterized," says Michael Fischbach. "We are still constantly refining the criteria by which we choose which of these gene clusters and molecules are interesting enough to pursue as projects."

Publication of note

In October, Fischbach and his colleagues published a paper in Nature Chemical Biology that introduced "natural product peptidogenomics," a new mass spectrometry-guided genome-mining method that connects the chemotypes of peptide natural products to their biosynthetic gene clusters.

Looking ahead

In the future, Fischbach hopes that increased effort is focused on experimental efforts to characterize the diffusible and cell-surface-associated small molecules and proteins from the human microbiota that exert a direct effect on host physiology.

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