Bioinformatics ServicesFunctional Metagenomics and Metatranscriptomics


Revealing the functional potential of a microbiome is undoubtedly one of the biggest advantages to generating shotgun metagenomic data, alongside CosmosID’s strain-level resolution capabilities. By combining the CosmosID functional analysis pipeline with taxonomic profiling and other -omics and metadata collected as part of your study, this is where one can truly unlock the microbiome.

To take functional profiling with CosmosID to the next level, have you thought about metatranscriptomics? By running metatranscriptomic data through the CosmosID functional analysis pipeline, find out which genes are actually expressed in the microbiome and discover potential biomarkers that could fuel your discovery efforts.

Functional MetagenomicsHow does it work?

By querying databases like the UniRef90 database which contains non-redundant protein clusters, protein families against which hits were generated are annotated with MetaCyc reactions (metabolic enzymes) to reconstruct and quantify complete MetaCyc metabolic pathways in the microbial community sample. In addition, the UniRef_90 gene families are also mapped to GO terms functional system in order to get an overview of GO functions in the community. Lastly, to facilitate comparisons across multiple samples with different sequencing depths, the abundance values are normalized using Total-sum scaling (TSS) normalization to produce “Copies per million” (analogous to TPMs in RNA-Seq) units.

Functional MetagenomicsHow do I get started?

Simply consult with a member of our business development team and build a study plan to answer your principle study question. From there, the CosmosID bioinformatics services team will execute your downstream analysis where in addition to tabular abundance profiles for GO terms and MetaCyc Metabolic Pathways, you will also have the opportunity to opt into downstream statistics and reporting of functional metagenomes to visualize variations between your study cohorts.

Functional MetagenomicsDownload the Product Sheet - End-to-End Microbiome Analysis via Next Generation Sequencing

Frequently Asked Questions

Is functional metagenomics included within the hub?

We provide AMR and Virulence characterization as well as MetaCyc pathways and GO terms via the CosmosID-HUB!

When would I utilize functional profiling?

Revealing the functional potential of samples has a huge range of applications, including but not limited to:

  • Discovery research in human health and disease
  • Clinical sample analysis in pharmaceutical and nutritional studies
  • Agricultural and environmental research
  • Mechanism of Action studies: pre-clinical and clinical
  • Probiotic/LBP discovery & characterization”
Does functional profiling show what genes or metabolites are expressed?

The CosmosID functional analysis pipeline can either reveal functional potential or measure gene expression depending on the upstream sequencing workflow. This will be determined by whether DNA or RNA is extracted from the sample first.

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