Metaproteomics Research Articles

MOSCA 2.0: A bioinformatics framework for metagenomics, metatranscriptomics and metaproteomics data analysis and visualization.

The analysis of meta-omics data requires the utilization of several bioinformatics tools and proficiency in informatics. The integration of multiple meta-omics data is even more challenging, and the outputs of existing bioinformatics solutions are not always easy to interpret. Here, we present a meta-omics bioinformatics pipeline, Meta-Omics Software for Community Analysis (MOSCA), which aims to overcome these limitations. MOSCA was initially developed for analysing metagenomics (MG) and metatranscriptomics (MT) data. Now, it also performs MG and metaproteomics (MP) integrated analysis, and MG/MT analysis was upgraded with an additional iterative binning step, metabolic pathways mapping, and several improvements regarding functional annotation and data visualization. MOSCA handles raw sequencing data and mass spectra and performs pre-processing, assembly, annotation, binning and differential gene/protein expression analysis. MOSCA shows taxonomic and functional analysis in large tables, performs metabolic pathways mapping, generates Krona plots and shows gene/protein expression results in heatmaps, improving omics data visualization. MOSCA is easily run from a single command while also providing a web interface (MOSGUITO). Relevant features include an extensive set of customization options, allowing tailored analyses to suit specific research objectives, and the ability to restart the pipeline from intermediary checkpoints using alternative configurations. Two case studies showcased MOSCA results, giving a complete view of the anaerobic microbial communities from anaerobic digesters and insights on the role of specific microorganisms. MOSCA represents a pivotal advancement in meta-omics research, offering an intuitive, comprehensive, and versatile solution for researchers seeking to unravel the intricate tapestry of microbial communities.

The metaphenome of a calaminiferous soil

The aim of the present research was to determine the metaphenome (the expressed microbial functions) of a calaminiferous soil mostly contaminated with Zn and Pb. For that, three 'omics approaches were combined using soil samples: shotgun metagenomics (MG), metatranscriptomics (MT) and shotgun metaproteomics (MP). Results show that several indexes of bacterial diversity were significantly reduced. The soil was dominated by Acidobacteria, Chloroflexi and Gemmatimonadetes. Although many of the species were not identified, the mean percentages of reads for Candidatus_Solibacter, Bryobacter, Rhodomicrobium and Niastella were significantly more elevated in the contaminated soil when compared to a control soil. For functionality, the identified proteins were classified in 28 functional SEED categories. The MG approach detected many genes that may be used to degrade various types of organic materials, among which chitin, N-acetylglucosamine, cellulose and glycogen. This suggests that the important carbon cycle functions of the heterotrophic communities are maintained in the soil. For metal resistance, the most abundant proteins were P-type ATPases efflux systems.

Embracing complexity and diversity: metaproteomics within the Galaxy framework

Embracing complexity and diversity: metaproteomics within the Galaxy framework