DiTing

DiTing infers the relative abundance of metabolic and biogeochemical pathways from metagenomic and metatranscriptomic reads to characterize microbial-driven biogeochemical processes, including dimethylsulfoniopropionate (DMSP) metabolism.

Key Features:

• Pathway inference and comparison: Infers and visually compares biogeochemical pathways from metagenomic or metatranscriptomic reads using KEGG and a manually curated DMSP cycling gene database.
• Normalization model: Applies specific formulae developed for over 100 pathways to calculate normalized relative abundances and estimate the environmental importance of pathways.
• Output formats: Generates text and graphical reports detailing the relative abundance of biogeochemical pathways across datasets.
• Validation and benchmarking: Validated with simulated metagenomic data and benchmark genomic data and applied to natural datasets from hydrothermal vents and the Tara Oceans project, with pathway predictions correlating with environmental changes.

Scientific Applications:

• Microbial ecology and biogeochemical cycling: Enables inference and comparison of metabolic pathways to elucidate microbial roles in nutrient and biogeochemical cycles.
• Environmental response analysis: Supports linking changes in pathway abundances to environmental conditions across diverse datasets.
• DMSP cycling and sulfur dynamics: Facilitates investigation of DMSP metabolism and associated sulfur cycling in marine environments.

Methodology:

Analyzes metagenomic and metatranscriptomic reads by integrating KEGG pathways with a manually curated DMSP gene database, inferring and visually comparing pathways in a single step, and applying pathway-specific normalization formulae for over 100 pathways to estimate relative abundances and produce text and graphical outputs.