Operational Taxon-Function Framework in MetaX: Unveiling Taxonomic and Functional Associations in Metaproteomics

Metaproteomics
analyzes the functional dynamics of microbial
communities
by identifying peptides and mapping them to the most likely proteins
and taxa. One challenge in this field lies in seamlessly integrating
taxonomic and functional annotations to accurately represent the contributions
of individual microbial taxa to functional diversity. We introduce
MetaX, a comprehensive tool for analyzing taxon-function relationships
in metaproteomics by mapping peptides to their lowest common ancestors
and assigning functions based on proportional thresholds, ensuring
accurate peptide-level mappings. Importantly, MetaX introduces the
Operational Taxon-Function (OTF), a new conceptual unit for exploring
microbial roles and interactions within ecosystems. Additionally,
MetaX includes extensive statistical and visualization tools, establishing
it as a robust platform for metaproteomics analysis. We validated
MetaX by reanalyzing ex vivo gut microbiome metaproteomic data exposed
to various sweeteners, yielding more detailed results than traditional
protein analysis. Furthermore, using the peptide-centric approach
and OTF, we observed that Parabacteroides distasonis significantly responds to certain sweeteners, highlighting its role
in modifying specific metabolic functions. With its intuitive, user-friendly
interface, MetaX facilitates a detailed study of the complex interactions
between microbial taxa and their functions in metaproteomics. It enhances
our understanding of microbial roles in ecosystems and health.