Bart Mesuere

Unipept: tryptic peptide-based biodiversity analysis of metaproteome samples.

The Unipept web application (http://unipept.ugent.be) supports biodiversity analysis of large and complex metaproteome samples using tryptic peptide information obtained from shotgun MS/MS experiments. Its underlying index structure is designed to quickly retrieve all occurrences of a tryptic peptide in UniProtKB records. Taxon-specificity of the tryptic peptide is successively derived from these occurrences using a novel lowest common ancestor approach that is robust against taxonomic misarrangements, misidentifications, and inaccuracies. Not taking into account this identification noise would otherwise result in drastic loss of information. Dynamic treemaps visualize the biodiversity of metaproteome samples, which eases the exploration of samples with highly complex compositions. The potential of Unipept to gain novel insights into the biodiversity of a sample is evaluated by reanalyzing publicly available metaproteome data sets taken from the bacterial phyllosphere and the human gut.

The Unipept metaproteomics analysis pipeline

Unipept (http://unipept.ugent.be) is a web application that offers a user‐friendly way to explore the biodiversity of complex metaproteome samples by providing interactive visualizations. In this article, the updates and changes to Unipept since its initial release are presented. This includes the addition of interactive sunburst and treeview visualizations to the multipeptide analysis, the foundations of an application programming interface (API) and a command line interface, updated data sources, and the open‐sourcing of the entire application under the MIT license.

Faecal proteomics: A tool to investigate dysbiosis and inflammation in patients with cystic fibrosis

BACKGROUND Several microbial studies reported gut microbiota dysbiosis in patients with cystic fibrosis (CF). The functional consequences of this phenomenon are poorly understood. Faecal metaproteomics allows the quantitative analysis of host and microbial proteins to address functional changes resulting from this dysbiosis. METHODS We analysed faecal protein extracts from fifteen patients with CF that have pancreatic insufficiency and from their unaffected siblings by shotgun proteomics. Novel computational and statistical tools were introduced to evaluate changes in taxonomic composition and protein abundance. RESULTS Faecal protein extracts from patients with CF were dominated by host proteins involved in inflammation and mucus formation. Taxonomic analysis of the microbial proteins confirmed the strong reduction of butyrate reducers such as Faecalibacterium prausnitzii and increase of Enterobacteriaceae, Ruminococcus gnavus and Clostridia species. CONCLUSION Faecal metaproteomics provides insights in intestinal dysbiosis, inflammation in patients with CF and can be used to monitor different disease markers in parallel.

Unipept web services for metaproteomics analysis.

UNLABELLED Unipept is an open source web application that is designed for metaproteomics analysis with a focus on interactive datavisualization. It is underpinned by a fast index built from UniProtKB and the NCBI taxonomy that enables quick retrieval of all UniProt entries in which a given tryptic peptide occurs. Unipept version 2.4 introduced web services that provide programmatic access to the metaproteomics analysis features. This enables integration of Unipept functionality in custom applications and data processing pipelines. AVAILABILITY AND IMPLEMENTATION The web services are freely available at http://api.unipept.ugent.be and are open sourced under the MIT license. CONTACT Unipept@ugent.be SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

High-throughput metaproteomics data analysis with Unipept : a tutorial

In recent years, shotgun metaproteomics has established itself as an important tool to study the composition of complex ecosystems and microbial communities. Two key steps in metaproteomics data analysis are the inference of proteins from the identified peptides, and the determination of the taxonomic origin and function of these proteins. This tutorial therefore introduces the Unipept command line interface (http://unipept.ugent.be/clidocs) as a platform-independent tool for such metaproteomics data analyses. First, a detailed overview is given of the available Unipept commands and their functions. Next, the power of the Unipept command line interface is illustrated using two case studies that analyze a single tryptic peptide, and a set of peptides retrieved from a shotgun metaproteomics experiment, respectively. Finally, the analysis results obtained using these command line tools are compared with the interactive taxonomic analysis that is available on the Unipept website.

The unique peptidome: Taxon-specific tryptic peptides as biomarkers for targeted metaproteomics.

The Unique Peptide Finder (http://unipept.ugent.be/peptidefinder) is an interactive web application to quickly hunt for tryptic peptides that are unique to a particular species, genus, or any other taxon. Biodiversity within the target taxon is represented by a set of proteomes selected from a monthly updated list of complete and nonredundant UniProt proteomes, supplemented with proprietary proteomes loaded into persistent local browser storage. The software computes and visualizes pan and core peptidomes as unions and intersections of tryptic peptides occurring in the selected proteomes. In addition, it also computes and displays unique peptidomes as the set of all tryptic peptides that occur in all selected proteomes but not in any UniProt record not assigned to the target taxon. As a result, the unique peptides can serve as robust biomarkers for the target taxon, for example, in targeted metaproteomics studies. Computations are extremely fast since they are underpinned by the Unipept database, the lowest common ancestor algorithm implemented in Unipept and modern web technologies that facilitate in‐browser data storage and parallel processing.

123 A shotgun metaproteomics approach to study the faecal microbiome of patients with cystic fibrosis reveals a reduction of butyrate-producing bacteria

123 A shotgun metaproteomics approach to study the faecal microbiome of patients with cystic fibrosis reveals a reduction of butyrate-producing bacteria G. Debyser1, B. Mesuere2, L. Clement2, G. Duytschaever1, P. Van Hecke1, P. Dawyndt2, K. De Boeck3, P. Vandamme1, B. Devreese1. 1Ghent University, Department of Biochemistry and Microbiology, Ghent, Belgium; 2Ghent University, Department of Applied Mathematics and Computer Science, Ghent, Belgium; 3University Hospital of Leuven, Department of Pediatrics, Leuven, Belgium

Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework

The impact of microbial communities, also known as the microbiome, on human health and the environment is receiving increased attention. Studying translated gene products (proteins) and comparing metaproteomic profiles may elucidate how microbiomes respond to specific environmental stimuli, and interact with host organisms. Characterizing proteins expressed by a complex microbiome and interpreting their functional signature requires sophisticated informatics tools and workflows tailored to metaproteomics. Additionally, there is a need to disseminate these informatics resources to researchers undertaking metaproteomic studies, who could use them to make new and important discoveries in microbiome research. The Galaxy for proteomics platform (Galaxy-P) offers an open source, web-based bioinformatics platform for disseminating metaproteomics software and workflows. Within this platform, we have developed easily-accessible and documented metaproteomic software tools and workflows aimed at training researchers in their operation and disseminating the tools for more widespread use. The modular workflows encompass the core requirements of metaproteomic informatics: (a) database generation; (b) peptide spectral matching; (c) taxonomic analysis and (d) functional analysis. Much of the software available via the Galaxy-P platform was selected, packaged and deployed through an online metaproteomics “Contribution Fest“ undertaken by a unique consortium of expert software developers and users from the metaproteomics research community, who have co-authored this manuscript. These resources are documented on GitHub and freely available through the Galaxy Toolshed, as well as a publicly accessible metaproteomics gateway Galaxy instance. These documented workflows are well suited for the training of novice metaproteomics researchers, through online resources such as the Galaxy Training Network, as well as hands-on training workshops. Here, we describe the metaproteomics tools available within these Galaxy-based resources, as well as the process by which they were selected and implemented in our community-based work. We hope this description will increase access to and utilization of metaproteomics tools, as well as offer a framework for continued community-based development and dissemination of cutting edge metaproteomics software.

WS16.7 A cross-sectional and longitudinal metaproteomics approach reveals intestinal dysbiosis, and the presence of markers of chronic inflammation and mucus-related proteins in faecal samples of patients with cystic fibrosis

Objectives In patients with cystic fibrosis (CF) changes in the faecal microbiota have been detected. These may be due to antibiotic treatments and CF-associated intestinal changes. To gain further insight into the CF gut, a metaproteomic approach was used to investigate the bacterial and host proteins present in faecal samples. Methods A cross-sectional and longitudinal study was performed on faecal samples from respectively 15 and 5 children with CF and their unaffected siblings. Tryptic peptides obtained after whole protein extraction and SDS-PAGE separation were analysed with liquid chromatography in combination with mass spectrometry (LCMS). Taxonomic (Unipept) and protein cluster (Scaffold) information were obtained. Results Our results demonstrate intestinal dysbiosis in the children with CF, i.e. a decrease of butyrate-producing bacteria such as Faecalibacterium prausnitzii and an increase in Ruminococcus gnavus and Enterobacteriaceae. Furthermore, higher amounts of inflammatory proteins in combination with porcine proteins (pancreas enzyme replacement therapy, PERT) and mucus-related proteins were found in the patients. The longitudinal study confirms the data of the cross-sectional study and shows that the faecal microbiota in patients is unstable. Conclusion We can conclude that intestinal dysbiosis is present in patients with CF. In the faecal samples of the patients markers of chronic inflammation were detected in combination with mucus- and PERT-related proteins. Our results may allow to select a panel of biomarkers, which can be used to evaluate the gut health status and how this can be improved by pre- and probiotics via targeted LC-MS.