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

Data collection template

Please use the following Excel  template to fill your details of measurements and data analysis.


Sample 1 (provided by UFZ): defined mixed culture from a lab-scale bioreactors consisting of 8 sequenced microbes (SIHUMI)

Species Strain (collection no) Phylum
Anaerostipes caccae (=Eubacterium entericum) DSMZ 14662, CIP 108612, NCIMB 13811 Firmicutes
Bacteroides thetaiotaomicron DSMZ 2079, ATCC 29148, NCTC 10582 Bacteroidetes
Bifidobacterium longum NCC 2705 Actinobacteria
Blautia producta DSMZ 2950 Firmicutes
Clostridium butyricum DSMZ 10702, ATCC 19398 Firmicutes
Clostridium ramosum (Erysipelatoclostridium ramosum) DSMZ 1402, ATCC 25582, NCIB 10673 Firmicutes
Escherichia coli K-12 MG1655 Proteobacteria
Lactobacillus plantarum DSMZ 20174 Firmicutes

LC-MS data provided by Nico Jehmlich

Protein-coding sequence database provided by Nico Jehmlich

LC-MS data provided by Robert Hettich:

LC-MS data provided by Jean Armengaud:

  • Download: Q23598 (60 min gradient, in-gel, 1 band)
  • Download: Q23599 (120 min gradient, in-gel, 1 band)
  • Download: Q23600-Q23603 (4x 60 min gradient, in-gel, 4 bands)

Sample 2 (provided by OVGU): fecal sample from human gut, a minimal metagenome (reads, contigs) is provided

Metagenome sequencing information:

  • DNA sequencing library preparation using Agilent SureSelect QXT
  • Sequencing / 150 nt / PE / 75 mio reads / 11.25 GB
  • Paired-end sequencing, read length 150 nt, NextSeq 500

LC-MS data provided by Robert Hettich:

LC-MS data prvided by Jean Armengaud:

  • Download: Q23604 (60 min gradient, in-gel, 1 band)
  • Download: Q23605 (120 min gradient, in-gel, 1 band)
  • Download: Q23606-Q23609 (4x 60 min gradient, in-gel, 4 bands)

LC-MS data provided by Catherine Juste:

  • participants send a request to Dirk Benndorf ( or Nico Jehmlich (
  • 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