Standardization is the name of the game

The latest press release from the White House describing the National Microbiome Initiative (NMI) demonstrates the commitment of the government, funding agencies and the scientific community to understand the microbiome and its impact on human health.  After some celebration, it is essential for the scientific community to ensure that the outcome of these projects will advance our understanding of the interaction between the microbial community, our genes and the environment.  Achieving this requires standard methods, reference materials and algorithms that enable scientists to establish and test new hypothesis, reproduce each other’s results, and one day, translate their work into innovative therapies, diagnostic assays, personalized treatments and preventive medicine.

Two recent publications provide some clues about what will be needed to properly understand the role of the microbial community.

1. Julia Goodrich and collaborators¹ analyzed stool samples from thousands of participants and established the heritability of some members of the gut microbial community and their association with host gene alleles.
2. David Zeevi and colleagues² developed an algorithm that is able to predict the glycemic response to real-life meals. This algorithm was developed using a framework observed in clinical research, a healthy control group, a validated independent cohort and a blinded randomized controlled dietary intervention.

These studies demonstrate that the translation of microbiome discoveries will rely on reliable, accurate, scalable and compliant procedures.

Many scientific groups already concentrate on establishing viable procedures and demonstrating the impact of improper practices. Recent publications on sample collection (Song et al., 2016³) and pre-analytical methods (i.e. library prep, Jones et al., 2015⁴) provide stringent validations of procedures that should be considered for the advancement of the microbiome field.  In addition to the effort by the scientific community, the National Institute of Standards and Technology will host a workshop to discuss reference materials, reference data and reference methods for human microbiome community measurements (http://www.nist.gov/mml/microbiome-standards.cfm).

The vast and varied research projects supported by the NMI definitely have microbiome researchers excited about what the future of microbiome research has in store.  To ensure that the most value possible is extracted from the $521 M pledged requires that all the stakeholders involved discuss, test, agree and adopt standard protocols before the projects start. Standardization is now the name of the game from sample collection through to analysis!

References

 ¹ Goodrich et al., 2016, Genetic Determinants of the Gut Microbiome in UK Twins, Cell Host & Microbe 19, 731–743

² Zeevi et al., 2016, Personalized Nutrition by Prediction of Glycemic Responses, Cell 163, 1079-1094

³Song et al., 2016 Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies, mSystems 1(3):e00021-16.

⁴Jones et al., Library preparation methodology can influence genomic and functional predictions in human microbiome research, PNAS, 112, 140247-14029