Microbiome Analysis


Microbiome analysis involves determining the composition and function of a community of microorganisms in a particular location. Within the medical field, this location is commonly the human gut.


We typically use QIIME 2™ as the preferred method for analyzing next-generation microbiome data. Our typical workflow steps include:

  1. Quality Control:
    • We view the GC content and insert size of each library to determine if any are highly variable or unexpectedly different.
  2. Read Trimming:
    • Removal of sequencing adapters that are unintentionally sequenced due to a reduced insert size is an essential step in accurate variant calling.  We also trim the low-quality bass from the ends of the sequence.
  3. Merge paired ends if needed:
    • Long-read platforms may not need this step, but short paired-end Illumina data are merged to provide a single DNA sequence fragment.
  4. Sequence dereplication:
    • Sequence fragments are collapsed to Amplicon sequence variant (ASV) or operational taxonomic unit (OTU), depending on the analysis.
  5. Taxonomies are assigned:
    • Taxonomy is assignedBayesian classifier based on a pre-trained Silva database curated to the exact 16s amplicon region
  6. Alpha rarefaction:
    • Curves using Shannon, Chao1, Simpson
  7. Beta diversity:
    • Bray-Curtis and Jaccard (Non-Phylogenetic), Weighted and unweighted Unifrac (Phylogenetic)


Click the link to be redirected to our: Example report

Please consult with the staff at the Microbiome Hub prior to starting your experiments.


Free Design Consultation

We offer free consultations as part of the initial experimental design. We want to ensure that you have thought about all the necessary design components before you conduct your experiment. This way BRC has high-quality data when it comes time for us to analyze the data. We offer this service at no charge because it is more cost-effective to catch design errors before we start the analysis.

Data Analysis and General Consultation ($/hr)

We will offer custom analysis or training at our hourly rate.

Grant Support (% effort)

We can provide project-specific analysis beyond our standard pipeline services when we are written into grants. This may be a cheaper option for labs requiring a lot of analysis time as we dedicate a percent of our effort to the project.