humann

humann (HUMAnN 3) profiles the functional potential and activity of microbial communities by producing pathway presence/absence and abundance estimates from metagenomic or metatranscriptomic sequencing data.

Key Features:

• Input data types: Processes metagenomic and metatranscriptomic sequencing data for community-level functional profiling.
• Pathway quantification: Determines presence/absence and quantifies the abundance of microbial pathways to infer metabolic potential and activity.
• Reference-based profiling: Leverages a comprehensive set of reference sequences, including the latest microbial reference genomes and strain-level diversity, to refine functional assignments.
• Integration with taxonomic and strain tools: Integrates with MetaPhlAn 3 for taxonomic profiling and StrainPhlAn 3 for strain-level analysis as part of the bioBakery 3 suite.
• Multi-omics support: Enables comparative functional analyses across metagenomes and metatranscriptomes for multi-omic studies.

Scientific Applications:

• Functional potential inference: Elucidates the metabolic potential and activities of microbial communities to address what microbes in a community are doing or capable of doing.
• Colorectal cancer studies: Applied to identify functional microbiome links in colorectal cancer (CRC) using 1262 metagenomes.
• Inflammatory bowel disease profiling: Applied to inflammatory bowel disease (IBD) using 1635 metagenomes and 817 metatranscriptomes.
• Species- and strain-level analysis: Resolved phylogenetic and functional structure of Ruminococcus bromii beyond what was known from limited isolate genomes.

Methodology:

Computationally, HUMAnN 3 executes a functional profiling pipeline on metagenomic or metatranscriptomic sequencing data to determine pathway presence/absence and abundance, leveraging comprehensive reference sequences and strain-level reference genomes and integrating taxonomic profiling from MetaPhlAn 3 and strain analysis from StrainPhlAn 3.