Challenges and perspectives of metaproteomic data analysis

Abstract

In nature microorganisms live in complex microbial communities. Comprehensive taxonomic and functional knowledge about microbial communities supports medical and technical application such as fecal diagnostics as well as operation of biogas plants or waste water treatment plants. Furthermore, microbial communities are crucial for the global carbon and nitrogen cycle in soil and in the ocean. Among the methods available for investigation of microbial communities, metaproteomics can approximate the activity of microorganisms by investigating the protein content of a sample. Although metaproteomics is a very powerful method, issues within the bioinformatic evaluation impede its success. In particular, construction of databases for protein identification, grouping of redundant proteins as well as taxonomic and functional annotation pose big challenges. Furthermore, growing amounts of data within a metaproteomics study require dedicated algorithms and software. This review summarizes recent metaproteomics software and addresses the introduced issues in detail.

Metaproteomics of Microbiota in Naturally Fermented Soybean Paste, Da‐jiang

“…The general process of metaproteomics analysis is that protein extraction and purification, separation, identification and bioinformatics analysis (Robert et al, 2017). At present, the research challenges are mainly protein extraction methods and protein data analysis.…”

A robust, cost‐effective method for DNA, RNA and protein co‐extraction from soil, other complex microbiomes and pure cultures

“…A suite of meta‐omics tools, as reviewed by Abram (), is now available which allows for a systems biology‐based experimental approach to investigating the complex interactions in mixed microbial communities that lead to their displayed functional phenotype. These include metagenomics (Quince, Walker, Simpson, Loman, & Segata, ), which provides insights into microbial potential, metatranscriptomics (Bashiardes, Zilberman‐Schapira, & Elinav, ) and metaproteomics (Heyer et al, ) inferring microbial function, and metabolomics (Trivedi, Delgado‐Baquerizo et al, ) informing on microbial activity, as reviewed in the relevant citations. Recent advances in HTS technology accompanied by increasingly competitive prices have vastly improved accessibility to this suite of omics tools, which can now be used in conjunction.…”

SDS‐PAGE fractionation to increase metaproteomic insight into the taxonomic and functional composition of microbial communities for biogas plant samples

“…Each microbial community may consist of up to 1000 different species expressing numerous proteins and using various metabolic pathways. The comprehensive investigation of microbial proteins (metaproteomics) represents a promising tool for the identification of actually existing metabolic pathways and allows the taxonomic composition of microbial communities to be revealed.…”