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Pathway Tools Management of Pathway/Genome Data for Microbial Communities
Peter D Karp1, Suzanne Paley1, Markus Krummenacker1
1Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States.
Frontiers in Bioinformatics
|October 28, 2022
Summary
Pathway Tools (PTools) software analyzes microbial communities by creating Pathway/Genome Databases (PGDBs) from metagenome-assembled genomes (MAGs). This enables detailed metabolic reconstruction and comparative analysis for understanding community-level interactions.
Area of Science:
- Microbiology
- Bioinformatics
- Systems Biology
Background:
- Pathway Tools (PTools) is a software suite for managing genomic and metabolic data.
- Organism-specific Pathway/Genome Databases (PGDBs) integrate diverse biological information.
- Metagenome-assembled genomes (MAGs) represent individual organisms within complex microbial communities.
Purpose of the Study:
- To describe the application of Pathway Tools (PTools) for analyzing microbial communities using metagenome-assembled genomes (MAGs).
- To highlight PTools' capabilities in metabolic reconstruction, operon prediction, and comparative analysis of microbial communities.
- To showcase PTools' utility in visualizing community-level metabolic networks and integrating omics data.
Main Methods:
- Generating individual PGDBs for each MAG within a microbial community.
- Utilizing PTools' built-in functions for metabolic reconstruction and operon prediction for each MAG.
- Performing community-wide searches and comparative analyses across multiple PGDBs.
- Generating metabolic network diagrams and overlaying omics data for community visualization.
- Employing PTools' tools for searching metabolic transformation routes across the community.
Main Results:
- PTools successfully creates organism-specific PGDBs from MAGs, enabling detailed analysis of individual microbial members.
- Metabolic reconstructions and operon predictions provide insights into the functional capabilities of each organism.
- Community-level analyses allow for the investigation of interactions and shared metabolic pathways.
- Visualization tools facilitate the understanding of community structure and function, including the integration of omics data.
- The software supports the exploration of metabolic routes and potential cross-feeding interactions within the community.
Conclusions:
- Pathway Tools (PTools) is a powerful and versatile software for the in-depth analysis of microbial communities represented by MAGs.
- The integrated approach of PTools allows for both individual organism investigation and holistic community-level understanding.
- PTools facilitates the exploration of microbial metabolism, interactions, and the potential for novel metabolic pathways within complex ecosystems.
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