3rd International Metaproteome Symposium

3rd IMS 2018

Introduction

The Helmholtz-Centre for Environmental Research – UFZ and the German Network for Bioinformatics Infrastructure - de.NBI invites you to participate to the 3rd International Metaproteome Symposium with the topic “Microbiome Research and Integrating Metaproteomics into a Multi-Omics Pipeline”.

The symposium is the leading event in the field of metaproteomics with an average of around 60 attending international scientists.

Research examining microbiomes are currently exploding and results are providing new perspectives. Multi-omics analysis is accepted as the gold standard to assess the microbiome samples but a variety of analytical and bioinformatics approaches are available. Therefore, we think the symposium will be a great opportunity to broaden the discussion on the integration of different datasets in different areas of microbial ecology and maybe learn from other people's experience on different systems. Apart from description of biological samples using Multi-Omics, we are interested in developing ideas how to integrate metaproteome data.

Lennart Martens (Ghent), Sergio Uzzau (Porto Conte Ricerche), Dirk Benndorf (Magdeburg) and Paul Wilmes (Luxembourg) are in the scientific committee.

We hope to welcome you from 03.-05.12.2018 in Leipzig at the UFZ!
Please use the links for more information, our competition, keynote speakers, on how to submit an abstract (oral or poster), important dates, or just send us an e-mail if you want to know more.


General Information

Contest: Multi-Omics study of microbiome samples
The success of protein identification in metaproteomics relies on whole genome sequencing. Therefore, multi-omics analysis is accepted as the gold standard to assess the microbiome samples in-depth. Thus, a variety of analytical and bioinformatics approaches are available.

Therefore, the scientific committee decided to announce a cooperate study of two microbiome samples. The results will be discussed in a workshop during the 3rd Metaproteomics Symposium. A final collaborate publication is anticipated. All labs working in the fields of Meta-Omics are invited to participate unless they are working only in Metagenomics, Metatranscriptomics, Metaproteomics, or Bioinformatics.

The combined study should target the following issues

  • sample preparation (Multi-Omics protocols versus specialized protocols)
  • impact of sequencing methods and sequencing depth on metaproteomics
  • impact of processing methods and processing state of metagenome and metatrancriptome sequences (reads, contigs, gene prediction, binning) on metaproteomics
  • impact of mass spectrometers types and measurement strategies (data-dependent versus data-independent, non-targeted versus targeted) on protein identification
  • bioinformatics workflow for protein identification, inference and annotation
  • suitability of metaproteome data to assist processing and annotation of sequencing data (proteogenomics)
  • bioinformatics tools for visualization and comparison of multi-omics data

Samples

  • Sample 1 (provided by UFZ): defined mixed culture from a lab-scale bioreactors consisting of 8 sequenced microbes (SIHUMI)
  • Sample 2 (provided by OVGU): fecal sample from human gut, a minimal metagenome (reads, contigs) is provided

Conditions

  • participants send a request to Dirk Benndorf (benndorf@mpi-magdeburg.mpg.de) or Nico Jehmlich (nico.jehmlich@ufz.de)
  • after registration the samples and access to a platform for data exchange will be provided
  • raw data has to be submitted to the data exchange platform until September 30th, processed data until Nov 30th (this allows other participants to apply the data in bioinformatics workflows)
  • all participants with submitted data are invited to present the highlights of their results in a workshop (short presentation, 5-10 min)

Publication of results in a Special Issue of Microorganisms

  • only participants with submitted data are accepted
  • all participants are invited to submit a dataset brief
  • for each sample a full paper merging the data will be prepared
  • finally a review discussing major outcomes will be prepared