Metaproteomics is a growing field that involves the global analysis of protein expression within microbial communities using mass spectrometry. From the ‘good and bad’ bacteria in the human gut to the production of biofuels to help tackle climate change - metaproteomic tools have great potential to provide important novel insights with implications for human, animal and plant health and disease, as well as environmental sustainability (see image above).
A Global Initiative
There are currently several research groups across the world with a focus on metaproteomics, including NAPI partners at our NMBU node, where Magnus Arntzen has a central role, together with Phil Pope and Vincent Eijsink, leaders of the Microbial Ecology and Meta-Omics and Protein Engineering and Proteomics (PEP) groups, respectively. Now, a number of these research groups have come together to form the Metaproteomics Initiative – an international collaborative effort where members will share knowledge, tools and techniques in a bid to accelerate advances in a range of metaproteomics disciplines. The Metaproteomics Initiative is part of the European Proteomics Association (EuPA).
In addition to Norwegian researchers, the initiative involves partners from Germany, France, USA and Canada. A full list of members and their affiliations is provided at the bottom of this page.
Comparing Metaproteomic Workflows
One of the first goals of the initiative involves comparison and sharing of workflows established within the various partner laboratories. To achieve this, partners have applied their own metaproteomic workflows (broadly divided into sample preparation, MS analysis, and bioinformatic tools to process and interpret the generated MS data) to detect proteins from the same two samples: an artificial human intestine model and a human fecal sample. By comparing the results generated by each workflow, the partners can assess which aspects of the workflow are robust and which lead to variability in the data generated by different research groups.
This comparative approach revealed that, in general, the various workflows appeared to be very robust; the number, nature and amounts of the proteins detected in each test sample were similar across the analyses performed by the partners. However, there were notable differences in the individual peptides detected by each workflow, and these differences could be traced to variation in sample preparation prior to MS analysis. Thus, although the major conclusions related to protein content of the samples would be similar using each workflow, the comparison highlighted key steps of sample preparation techniques that could favour/disfavour the detection of certain peptides/proteins.
Improving future studies
In the long term, these findings will help to work towards a consensus approach (or approaches) to metaproteomic analyses that yields the most accurate and comprehensive overview of protein expression within microbial communities. While microbial communities are central in the initiative, its outcomes will be relevant for other types of proteomic studies of complex systems.
You can learn more about the comparative study by reading the article pre-print on the BioRxiv website.
Update December 2021: The article is now published in Nature Communications.
You can find out more about the metaproteomics initiative and their research aims and activities on the infrastructure's website (under construction).
Full list of Initiative members:
Belgium
CompOmics (Ghent, Belgium), bioinformatics lab led by Prof. Lennart Martens
Germany
Microbial Communities (Magdeburg, Germany), MS and bioinformatics lab led by Dr. Dirk Benndorf Functional Microbiology in Animal Science group (Stuttgart, Germany), led by Prof. Jana Seifert Microbiome Biology (Leipzig, Germany), MS lab led by Dr. Nico Jehmlich and Prof. Martin von Bergen Microbial Proteomics (Greifswald, Germany), MS Lab led by Prof. Katharina Riedel and Prof. Dörte Becher eScience Group (Berlin, Germany), eScience lab led by Dr. Thilo Muth Data Analytics & Computational Statistics Group (HPI Potsdam, Germany), led by Bernhard Renard
MF1 - Bioinformatics Group (RKI Berlin, Germany), led by Stephan Fuchs
France
PAPPSO proteomic facility (Paris, France), MS lab led by Céline Henry, and bioinformatics lab headed by Olivier Langella ProGenoMix platform (Bagnols-sur-Cèze, France), MS lab led by Dr. Jean Armengaud
Italy
Center for Research and Education on the Microbiota (Sassari, Italy), lab led by Prof. Sergio Uzzau
Norway
Microbial Ecology and Meta-Omics Group (Aas, Norway), led by Assoc. Prof. Phil Pope, Protein Engineering and Proteomics (PEP) group, led by Dr. Magnus Arntzen and Prof. Vincent Eijsink
Luxemburg
EcoSystemsBiology Group (Luxembourg, Luxembourg), led by Prof. Paul Wilmes
Austria
Institute of Soil Research (Vienna, Austria), soil lab led by Prof. Sophie Zechmeister-Boltenstern
Switzerland
Bioinformatics and Proteogenomics Group, SIB Swiss Institute of Bioinformatics and Agroscope, led by Dr. Christian Ahrens
USA
Galaxy-P Team (Minneapolis, MN, USA), bioinformatics lab led by Dr. Pratik Jagtap and Prof. Timothy Griffin Microbiome metaproteomics and microbial ecology (Oak Ridge, TN, USA), led by Dr. Robert L. Hettich Microbiome and virome metaproteomics, ecophysiology, and metaproteomics method development with focus on stable isotopes (North Carolina State University, NC, USA), led by Dr. Manuel Kleiner
Canada
Northomics lab (Ottawa, Canada), bioinformatics (MetaLab) and human gut microbiome lab led by Prof. Daniel Figeys Bioinformatics of Proteomics and Network Biology lab (Ottawa, ON, Canada), led by Prof. Mathieu Lavallée-Adam
