The Microbiome Quality Control project

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Welcome to the MicroBiome Quality Control (MBQC) project. The human microbiome has the potential to become one of the most important new tools for personalized health and precision medicine. In order to transition from a basic research environment to the clinic, technologies and computational methods for assessing human-associated microbial communities must be standardized and quality controlled. Inspired by progress in related areas such as the gene expression microarray (MAQC), the MBQC is a collaborative effort to comprehensively evaluate methods for measuring the human microbiome. This includes tools for sampling human-associated microbes at different body sites, techniques and protocols for handling human microbiome samples, and computational pipelines for microbiome data processing. We hope to improve the state-of-the-art in each of these areas and promote open sharing of standard operating procedures and best practices throughout the field. Everyone is welcome to participate in the MBQC.

The MBQC is currently piloting two of the several steps typically used to obtain and analyze the human microbiome.  If you run a research team that would like to participate in assessing either sample handling or bioinformatics protocols, please click on the link above to register for one or both tasks. The pilot project is designed to accommodate a variety of sample and nucleotide handling protocols, and we expect most teams will be able to participate with minimal changes to established lab operating procedures. However, be sure to read the module protocols carefully before registering to ensure compatibility and documentation, and we ask that each team commit to handle samples or data in complete increments of 96.

  • Samples. For the pilot phase of the MBQC, all samples will be provided by a central repository for convenience and efficiency, and we will focus only on the human gut as represented by stool samples. Additional body sites, sample sources, and sample collection methods will be incorporated in future phases of the project. Samples will be provided to participants in sets of 94 tubes, leaving two blanks for controls, and will comprise three formats: frozen stool, freeze-dried stool, and pre-extracted DNA.
  • Handling. For the pilot phase of the MBQC, labs must commit to perform all necessary sample handling steps in serial on the provided samples. Labs registering for the sample handling module will receive samples as specified above and produce raw sequencing files as output for downstream processing by performing three sub-modules:
    • Extraction. DNA extraction is known to have a large impact on the apparent abundance of some members of microbial communities, and many distinct commercial kits are available. The extraction sub-module begins with the provided frozen and freeze-dried stool samples as input and produces quantified isolated DNA as output.
    • 16S amplification. The pilot phase also includes only 16S amplicon based surveys of the human microbiome; other technologies such as metagenomics will be evaluated after the prototype. The choice of 16S rRNA gene amplification primers and protocol can have a profound effect on studies' results. The 16S amplification sub-module begins with isolated DNA (as provided or from extraction) as input and generates pooled barcoded libraries suitable for sequencing as output.
    • Sequencing. A variety of sequencing platforms are now appropriate for human microbiome studies. The pilot will include only assessments based on the Illumina MiSeq and HiSeq platforms, although several kits are appropriate for these platforms and can be accommodated by the prototype. The sequencing sub-module begins with 16S amplicons as input and provides raw sequence reads as output.
  • Bioinformatics. In some cases, differences in computational data handling can have a larger effect than differences in physical sample handling on the final measurement. The MBQC pilot can accommodate any bioinformatic protocol that results in an Operational Taxonomic Unit (OTU) table with standardized annotations. Bioinformatics modules receive raw sequence reads as input and provide annotated OTU tables as output.

Labs are currently participating in the MBQC-pilot phase on a volunteer basis. If you'd like to participate but lack immediate resources, please contact us for more information.