At the start of the HMP project, there was no standardized protocol for ensuring high throughput consistency of 16S amplification & sequencing protocols. Therefore the HMP evaluated a number of protocols using a synthetic mock community of 21 known organisms, before adopting the HMP 16S 454 Protocol. These organisms included a variety of genera commonly found on or within the human body. Genomic DNA from each organism was mixed, based on qPCR of 16S rRNA measurements, and two mock mixtures formulated to contain:
- - 100,000 16S copies per organism per aliquot (even mock community), or
- - 1,000 to 1,000,000 16S copies per organism per aliquot (staggered mock community)
Mock communities are available to the community through the BEI Resource as both a cell mixture (BEI:HM-280, HM-281) and a genomic DNA extract (BEI:HM-278D, HM-279D).
Here we provide a mock community composition table, as well as links to data available at NCBI from three 16S studies and a wgs pilot study using the mock communities. This data will be useful to the community in facilitating benchmarking of new molecular and analytical approaches.
Protocols and Tools
- Mock community generation - coming soon
- HMP 16S 454 protocol