Our collaborators in New Zealand, led by Dr. Milica Ciric and Dr. Dragana Gagic have just published a really lovely proof of principle study of the combined use of phage display and high-throughput sequencing to target the surface, secreted and transmembrane proteins from environmental microbial communities (the metasecretome). This is a very interesting approach as the portion of the metagenome that is actively secreted is very small, but they also happen to be some of the most interesting genes and proteins from a biotechnological perspective.
Phage display is a laboratory technique that can be used to identify the genes that encode certain proteins. A gene is incorporated into a phage coat protein gene, causing the phage to externally "display" the protein. This allows the protein produced by the gene to be identified.
Dr. Ciric and colleagues applied this approach to a whole metagenomic library from the rumen of a Friesian dairy cow and used the presence of membrane-targeting sequence motifs displayed by the phages to select those that contained genes which were trans-membrane or secreted (Figure 1). The resulting enriched library was then sequenced both through E. coli transformation and by direct high-throughput sequencing to obtain the secretome-enriched metagenome.
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| Figure 1. |
See the fully open access paper here: Ciric et al. BMC Genomics 2014 15:356