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Bioremediation Pathway Tool
Summary
Scientists have released a new free software tool that can scan bacterial genomes and reliably identify which bacteria have the genetic "tools" to break down pollutants, including plastics like PET (common in bottles) and other microplastics. This matters because finding naturally occurring bacteria that can digest plastic waste could help develop cleanup methods for environmental pollution, which is increasingly linked to human health concerns as microplastics accumulate in our water, food, and even our bodies. The tool itself doesn't clean up plastic yet, it's a research aid that helps scientists more accurately pinpoint promising bacteria for future bio
Bioremediation Pathway Tool v0.1.0 First public release of Bioremediation Pathway Tool, a pathway-level bioinformatics tool for conservative evidence-based detection of bioremediation-associated reactions and pathways from annotated bacterial genomes. Highlights Pathway-level analysis of annotated bacterial genomes in GenBank format. Curated core database containing 34 pathway/modules, 81 reactions, and 379 reference proteins. Conservative separation of supported, review, candidate, and not-detected evidence. Cross-reaction adjudication to reduce inflation of evidence from shared loci. Hybrid sequence-based rescue of unresolved annotations. Component-aware handling of multi-component reactions. Table-first HTML reporting with pathway completeness and evidence interpretation. Optional microplastics module covering curated PET, PCL, PBAT, and PU-associated reactions. GenBank input validation and normalization without modification of the original input genome. Release audit and regression tests included for reproducibility. Validation The v0.1.0 release passed the bundled release audit, including core database integrity, PET regression locking, PCL strict-gate testing, synthetic annotation positive controls, and checks for unintended local absolute paths. Citation Citation metadata is provided in CITATION.cff. This release is archived through Zenodo for persistent citation and DOI assignment. Authors Monira Mehzabin Khandoker Md Rezwan License Released under the MIT License.