Functional Annotation

In this lesson, we will finish our metatranscriptomics analysis by extracting the functional information from the microbial community. Instead of focusing on which organisms are present, we now ask: “What are the microbes doing?” and “Which functions are active in the environment?”.

Using the HUMAnN pipeline, we can map the community’s expressed genes to known gene families and metabolic pathways. This allows us to quantify the contribution of each organism to particular functions and to explore the overall metabolic potential of the community. The analysis focuses on non-ribosomal RNA sequences and incorporates prior knowledge from the taxonomic profile generated with MetaPhlAn.

By the end of this lesson you will be able to:

• explain the purpose of functional profiling in metatranscriptomics
• run HUMAnN to identify expressed gene families and pathways from RNA-seq data
• interpret HUMAnN output tables for gene family and pathway abundances
• stratify gene family abundances by contributing species
• generate pathway abundance profiles to understand the metabolic capabilities of the community