Function is what counts: how microbial community complexity affects species, proteome and pathway coverage in metaproteomics

ABSTRACT

Introduction: Metaproteomics is an established method to obtain a comprehensive taxonomic and functional view of microbial communities. After more than a decade, we are now able to describe the promise, reality, and perspectives of metaproteomics and provide useful information about the choice of method, applications, and potential improvement strategies.

Areas covered: In this article, we will discuss current challenges of species and proteome coverage, and also highlight functional aspects of metaproteomics analysis of microbial communities with different levels of complexity. To do this, we re-analyzed data from microbial communities with low to high complexity (8, 72, 200 and >300 species). High species diversity leads to a reduced number of protein group identifications in a complex community, and thus the number of species resolved is underestimated. Ultimately, low abundance species remain undiscovered in complex communities. However, we observed that the main functional categories were better represented within complex microbiomes when compared to species coverage.

Expert opinion: Our findings showed that even with low species coverage, metaproteomics has the potential to reveal habitat-specific functional features. Finally, we exploit this information to highlight future research avenues that are urgently needed to enhance our understanding of taxonomic composition and functions of complex microbiomes.

KEYWORDS:

• Big data
• bioinformatics
• environmental microbiology
• mass spectrometry
• metaproteomics
• microbial communities

Article Highlights

• We integrated four microbial community datasets to determine the effect of increasing community complexity on proteome, species, and pathway coverage

• The taxonomic resolution is reduced in microbial communities with increasing complexity

• The identification of low abundance proteins present in complex microbial communities is challenging

• A unique strength of metaproteomics is the robust identification of habitat-specific pathways, regardless of the underlying microbial community complexity

Declaration of Interest

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

Reviewer Disclosures

Peer reviewers on this manuscript have no relevant financial or other relationships to disclose.

Additional information

Funding

This work was supported by the Collaborative Research Centre 1076 AquaDiva (CRC AquaDiva) which is funded by the Deutsche Forschungsgemeinschaft (DFG). The first author Patrick Lohmann was also supported by the Helmholtz Interdisciplinary Graduate School for Environmental Research (HIGRADE) and the integrated research training group (iRTG).