MicrobioLink

MicrobioLink infers functional effects of microbiome–host protein interactions by integrating predicted microbial (bacterial and viral)–host protein interactions with host molecular networks and applying network diffusion to analyze downstream modulation of host gene and protein expression.

Key Features:

• Integration of predicted interactions: Integrates predicted interactions between microbial proteins (including bacteria and viruses) and host proteins into host molecular networks.
• Network diffusion: Applies a network diffusion concept to propagate effects of microbial proteins through host networks.
• Network-based prioritization: Uses network-based approaches to prioritize and integrate interaction predictions.
• Downstream effect analysis: Infers modulation of host gene and protein expression and downstream cellular processes by microbial proteins.
• Source-agnostic inputs: Operates agnostically with respect to the source of microbial proteins (e.g., bacterial or viral proteins).
• Scalable computational inference: Enables scalable, computational inference of microbiome–host interactions for large-scale analyses.

Scientific Applications:

• Disease mechanism discovery: Elucidates mechanisms by which microbial proteins modulate host genes and processes implicated in disease pathogenesis, as demonstrated with Crohn’s disease.
• Clinical and medical research: Supports investigation of inter-kingdom cross-talks relevant to health, disease pathogenesis, and potential therapeutic target identification.
• Agricultural research: Facilitates study of microbiome–host interactions in agricultural organisms and contexts.
• Ecological research: Enables analysis of inter-kingdom communications in ecological systems.

Methodology:

Predict microbial protein–host protein interactions, integrate these predictions with host molecular networks, apply network diffusion and network-based prioritization, and analyze downstream modulation of host gene/protein expression; demonstrated using gut metaproteomic data from Crohn’s disease patients and healthy controls.