Exploring the functional activity of microbial communities

profiling of community-wide gene expression (RNA-seq)

While Metagenomics tells us which microbes are present and what genomic potential they have, Metatranscriptomics tells us about their activity: the genes that are highest expressed in a specific mircobial environement. Thus, Metatranscriptomics is the study of the function and activity of the complete set of transcripts (RNA-seq) from environmental samples.

  • Gene activity diversity

    • How many different genes are expressed in a microbial community across all species? How is the functional and pathway diversity?

  • Key genes and pathways of highest activity

    • Which are the highest expressed genes in a specific environmental condition? What is the most important functionality (highly activated pathway) needed in an environment?

    • Gene expression is log-like distributed: Top 100 genes of highest expression can cover up to 30% of all transcripts. Even a single gene can cover up to 10%. Thus, a very high sequencing depth is required to see also lower expressed genes.

  • Gene expression comparison

    • Which genes show the highest change in expression levels between different conditions (biomarker detection)?

    • Before comparison, expression levels can be normalized by RPKM to correct for differences in sequencing depth and gene length.

Software tools

    • Kallisto - RNA-seq transcript abundance estimation

    • Kraken - assigns taxonomic labels to short sequencing reads

    • HUMAnN - community-wide gene transcription and pathway analysis

      • requires pairs of DNA and RNA sequencing of the same biological sample (to get corrected RNA transcription levels, normalized by the sample's DNA bacteria abundance)

    • PanPhlAn - strain-specific transcriptomics analysis

      • requires pairs of DNA and RNA sequencing of the same biological sample

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