Bioinformatics ServicesFunctional Metagenomics and Metatranscriptomics


Unlock the microbiome by combining the CosmosID functional analysis pipeline with taxonomic profiling and other omics and metadata collected as part of your study.

To take functional profiling with CosmosID to the next level, we offer 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 MetagenomicsWhy Choose CosmosID For Functional Metagenomic Analysis?

When it comes to exploring the functional diversity of microbial communities, CosmosID stands as a leading choice for functional metagenomic analysis. Our unique approach includes the analysis of metagenomic DNA extracted directly from an environmental sample, offering real-time insights into microbial community structure, including bacteria, fungi, and other constituents of the human microbiome.

Our advanced techniques allow for a comprehensive examination of antibiotic resistance genes, providing crucial information that can impact public health decisions. We even delve into the specifics of environmental DNA, aiding in the preservation and understanding of biodiversity in environmental samples.

At CosmosID, we also employ the use of a bacterial artificial chromosome, enabling us to isolate genomic DNA of interest and study the interaction of genes therein. This empowers us with the ability to not only identify, but understand the functional roles these genes play within their respective communities.

Choose CosmosID for an in-depth, accurate, and reliable functional metagenomic analysis, and unlock the wealth of knowledge hidden within your samples today.

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

Functional MetagenomicsGenome Sequencing: Uses, Availability and Benefits

Shotgun sequencing data analysis (whole genome sequencing) is a method that allows the extraction of whole DNA sequences from a sample that would then be exposed to random fragmentation before NGS. When using our metagenomics services, you will gain access to metagenomic sequencing and analysis of functional gene information. We will advise you based on a variety of technical and medical criteria.

The sequencing data analysis is useful for researching microbial communities, microbial species and other genetic materials. Genetic materials, such as microbial cells and various microbial systems, can be reviewed and tested in specialised laboratories. At the same time, the resulting metagenomic sequencing data can be used for genetic analysis, biochemical characterization, complete genome sequencing, and more.

The benefits of our metagenomics sequencing services are abundant, from discovering hidden facts about the microbial communities and genetic diversity of your environmental samples to ways to treat and medicate medical conditions.

Functional MetagenomicsUsing Metagenomics to Understand Microbial Ecology

With our metagenomic sequencing analysis, you will gain access to the world of microbial communities. Microbial ecology focuses on the interactions of microorganisms with their environments and each other. The link between studying microbial ecology and our functional metagenomic analysis is obvious, as it studies the diversity, distribution and abundance of microbial communities across different ecosystems.

By analyzing the genes present in an environmental DNA sample, metagenomics can predict the metabolic pathways and functional roles of microorganisms in an ecosystem. This helps us understand how microbial communities contribute to ecosystem functions such as nutrient cycling, carbon sequestration, and pollution degradation.

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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