Topic: Functional Decoding of Microbiome–Host Interactions: From Metaproteomics to Translational Applications

The microbiome plays an fundamental role in host physiology,health and disease, yet microbial composition alone does not fully capture the functional activities of complex microbial communities. Metaproteomics provides a direct approach to characterize proteins expressed by microbial communities and their hosts, enabling functional characterization of microbial communities and their interactions with the host. Recent advances in mass spectrometry, bioinformatics, artificial intelligence, and multi-omics integration are further expanding the application of metaproteomics in microbiome research and the investigation of host–microbiome interactions.

This Special Topic aims to highlight recent advances in decoding microbiome function and microbiome–host interactions, with metaproteomics serving as a central technological and conceptual framework. We welcome methodological, computational, and biological studies that advance the characterization of microbial functions, molecular interactions, and functional responses to environmental, dietary, pharmacological, or clinical perturbations. Particular interest is placed on approaches that integrate metaproteomics with complementary omics, computational modelling, and AI, as well as studies translating functional microbiome insights into biomarkers, intervention strategies, precision nutrition, therapeutics, and other health-related applications.

Topics of interest include, but are not limited to:

● Metaproteomics and emerging proteomic technologies for functional microbiome profiling;

● Computational methods, bioinformatics, AI and data resources for metaproteomics;

● Integration of metaproteomics with metagenomics, metabolomics, transcriptomics and other omics;

● Molecular mechanisms of microbiome–host and microbe–microbe interactions;

● Functional microbiome signatures in health and disease;

● Microbiome functional responses to diet, drugs and other perturbations;

● Microbiome-derived targets, biomarkers and interventions for translational applications;

● Standards, benchmarking, reproducibility and community resources for functional microbiome research.