HTSSIP

HTSSIP implements R-based analyses of high-throughput sequencing stable isotope probing (HTS-SIP) data to identify and quantify isotopic incorporation in microbial taxa.

Key Features:

• R package implementation: Provides an R package implementation for computational analysis of HTS-SIP datasets.
• High-resolution stable isotope probing (HR-SIP): Determines isotopologue distributions in DNA sequences to identify organisms actively incorporating labeled substrates.
• Multi-window high-resolution stable isotope probing (MW-HR-SIP): Analyzes multiple regions within sequences to enhance resolution and reliability of isotopic incorporation mapping.
• Quantitative stable isotope probing (q-SIP): Quantifies the extent of substrate incorporation into microbial DNA across taxa.
• ΔBD: Examines shifts in base distribution patterns to refine associations between isotopic signatures and microbial functions.

Scientific Applications:

• Mapping metabolic processes: Maps in situ metabolic processes across thousands of microbial taxa using HTS-SIP sequencing data.
• Identification of active taxa: Identifies microorganisms incorporating labeled substrates to link taxa to specific biochemical pathways.
• Quantification of activity levels: Compares levels of substrate incorporation to assess relative metabolic activity among taxa.
• Microbial ecology and function studies: Supports investigation of microbial community function in environmental and ecological contexts.

Methodology:

Computational methods explicitly include high-resolution stable isotope probing (HR-SIP), multi-window HR-SIP (MW-HR-SIP), quantitative SIP (q-SIP), and ΔBD analyses applied to high-throughput sequencing DNA data to determine isotopologue distributions, analyze multiple sequence regions, quantify substrate incorporation, and examine shifts in base distribution patterns.