Proteomic tools to decipher microbial community structure and functioning.

Florence Arsène-Ploetze,Philippe N Bertin,Christine Carapito

doi:10.1007/s11356-014-3898-0

Abstract

Recent advances in microbial ecology allow studying microorganisms in their environment, without laboratory cultivation, in order to get access to the large uncultivable microbial community. With this aim, environmental proteomics has emerged as an appropriate complementary approach to metagenomics providing information on key players that carry out main metabolic functions and addressing the adaptation capacities of living organisms in situ. In this review, a wide range of proteomic approaches applied to investigate the structure and functioning of microbial communities as well as recent examples of such studies are presented.

Highlights

Microbial communities are complex biological assemblies, whose study has been difficult for a long time because a large fraction of the species is unknown (Bertin et al 2008)
This study revealed that depending on the protocols used, a taxonomic bias may be observed
Nowadays metaproteomics is usually combined with other high-throughput “omics” methods, such as metatransciptomics, metametabolomics as well as more traditional methods of genetics, molecular biology and/or biochemistry

Summary

Introduction

Microbial communities are complex biological assemblies, whose study has been difficult for a long time because a large fraction of the species is unknown (Bertin et al 2008). Many types and combinations of chromatographies have been explored in the field of proteomics to fractionate complex protein mixtures prior to identification Each of these approaches has advantages and disadvantages and the choice of the best adapted separation method is highly dependent on the sample type to be analyzed. These approaches are at the origin of the proteogenomics field, defined as the use of proteomics results to improve genome annotations (Delalande et al 2005; Gallien et al 2009; Armengaud et al 2014) Such an approach may be combined with labeling methods such as specific labeling of protein N-termini, allowing the identification of peptides corresponding to protein starts.

Objective

Findings

Conclusion