Final Report Summary - FUME (Functional Metagenomics – Harnessing the Biotechnological Potential of Completely Novel Protein Families)
Today the vast amount of genomic data released by the scientific community to public databases is not derived from individual organisms, but from microbiomes, i.e. complex communities of microorganisms. Recent advances in sequencing technology allow for unraveling of the totality of the genetic information contained in an environmental sample. These so-called metagenomes provide us with an overabundance of literally millions of genes from organisms that have never been studied in the lab. Some of these genes encode useful biocatalysts that might help us in a transition from a petroleum-based to a bio-based economy, but identifying these biocatalysts among the millions of proteins encoded by a metagenome amounts to finding the proverbial needle in the haystack. In our FuMe (functional metagenomics) project we have developed methods to streamline the identification of biocatalysts from environmental samples. We combined bioinformatic methods with biochemistry and bacterial genetics to single out proteins to test for biocatalytic activity in Escherichia coli. In this way, we could identify several heretofore unknown lipases and cellulases (biocatalysts that can used to synthesize biofuels) as well as 27 novel oxidoreductases (biocatalysts that can help in the production of biopharmaceuticals). We furthermore devised a strategy to move beyond the DNA-only approach in current microbiome research and are now able to detect biocatalytic activity in a microbial community directly on the protein level.