Microbiome profiling: Who is there and what are they doing?
After performing quality filtering of the sequencing data, it is time to generate the microbiome profiles. A taxonomic microbiome profile contain information on which taxa are found in the community and their relative abundances.
If shotgun metagenomic sequencing is used, it is also possible to profile the functional capacity of the microbiome community. This will provide information on the individual genes found in the community and an estimate of the functional pathways they contribute to.
What we do
We take quality filtered data and generate microbiome profiles. The specific software and reference data we use depend on the type of data. For example are different software used to profile 16S and shotgun metagenomic data, and different software and/or reference data will be used to profile stool, saliva or soil samples. The decisions we make also in part depend on the goal of the project, such as the selection of marker-based or assembly-based approaches for shotgun data.
What you get
- Taxonomic profiles for amplicon data
- Taxonomic and functional profiles for shotgun data
- Alpha diversity (including observed and extrapolated species/genera richness).
- Beta diversity
- Illustrations that support data evaluation and further analysis decisions. The illustrations include ordination plots and stacked barplots.
Microbiome Profile Report
The report includes:
- Details of the microbiome profiling performed
- Explanations to the provided tables and illustrations
- Summary of our evaluations and considerations (e.g. do we see potential issues, how we suggest samples and taxa should be filtered in further analysis)