Open Access Methodology article

Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community

Milica Ciric12, Christina D Moon1, Sinead C Leahy1, Christopher J Creevey3, Eric Altermann1, Graeme T Attwood1, Jasna Rakonjac2* and Dragana Gagic1*

Author Affiliations

1 Animal Nutrition and Health, AgResearch Ltd, Palmerston North 4442, New Zealand

2 Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand

3 Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion SY23 3DA, UK

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BMC Genomics 2014, 15:356  doi:10.1186/1471-2164-15-356

Published: 12 May 2014

Abstract

Background

In silico, secretome proteins can be predicted from completely sequenced genomes using various available algorithms that identify membrane-targeting sequences. For metasecretome (collection of surface, secreted and transmembrane proteins from environmental microbial communities) this approach is impractical, considering that the metasecretome open reading frames (ORFs) comprise only 10% to 30% of total metagenome, and are poorly represented in the dataset due to overall low coverage of metagenomic gene pool, even in large-scale projects.

Results

By combining secretome-selective phage display and next-generation sequencing, we focused the sequence analysis of complex rumen microbial community on the metasecretome component of the metagenome. This approach achieved high enrichment (29 fold) of secreted fibrolytic enzymes from the plant-adherent microbial community of the bovine rumen. In particular, we identified hundreds of heretofore rare modules belonging to cellulosomes, cell-surface complexes specialised for recognition and degradation of the plant fibre.

Conclusions

As a method, metasecretome phage display combined with next-generation sequencing has a power to sample the diversity of low-abundance surface and secreted proteins that would otherwise require exceptionally large metagenomic sequencing projects. As a resource, metasecretome display library backed by the dataset obtained by next-generation sequencing is ready for i) affinity selection by standard phage display methodology and ii) easy purification of displayed proteins as part of the virion for individual functional analysis.

Keywords:
Phage display; Nxt generation sequencing; Metagenomics; Rumen; Cellulosome; Surface and secreted proteins