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.

Samples

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

LC-MS data provided by Nico Jehmlich

• Download: Contest_Sample_1_SIHUMI_raw Shotgun LC-MS raw file (120 min gradient, in-gel, 1 band)

Protein-coding sequence database provided by Nico Jehmlich

• Download: Contest_Sample_1_SIHUMI (12.9 MB) (protein-coding sequence)

LC-MS data provided by Robert Hettich:

• Download: ORNL_Easy_2ug_240min_ac50cm (240 min gradient)
  

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

• Download: Contest_Sample_2_feces.zip (fastq.gz)

LC-MS data provided by Robert Hettich:

• Download: ORNL_Easy_2ug_510min_ac50cm (510 min gradient)
• Download: MudPIT_QE3_01-04 (MudPIT, 4 fractions)
  

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:

• Download: 14_Leipzig_env (20181130_14_env)
• Download: 16_Leipzig_cyto (20181130_16_cyto)
  

• 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