Overview of the benchmarking exercise

1. We collected fecal samples from seven healthy human donors.
2. We used shotgun metagenomics and deep-sequencing to identify differences in microbiome composition.
3. Based on these results, we selected samples from three donors with different microbial communities.
4. These three selected samples were spiked with our standard, a known community of 45 phylogenetically diverse, evenly distributed bacteria.
5. Each spiked sample was then divided into 1000 aliquots, and a fourth aliquot of the microbial standard spiked into PBS was also prepared.
   
   Here’s where you come in.
   
   
6. We’re distributing these standards (for free!) to researchers across Canada who will use their own pipelines to isolate DNA, prepare libraries, sequence (16S rRNA gene sequencing), and analyze the microbial communities. We’ll collect information from each lab on their storage conditions, isolation kits/techniques, library prep protocols, analysis methods, as well as their final data. Don’t worry, all data will be anonymized, and only aggregate data will be shared with the microbiome community.
7. Comparing the results from different labs will help us identify key factors influencing data outcomes, and will help us improve data interpretation.
8. Ultimately, this benchmarking exercise will help us develop guidelines to harmonize protocols and pipelines to improve data accuracy, research quality, and reproducibility.

No experiment is perfect, but by sharing our results with a common standard, we can update our knowledge of the ‘dos’, ‘don’ts’ and ‘trade-offs’ in microbiome sequencing. Help us by getting your standards today and incorporating them in your regular workflows.

More details about our benchmarking exercise to come!