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Microbiome Biobanks Need Urgent Upgrade

Scientists are struggling to properly preserve tiny microbial communities, significantly hindering vital research efforts.

A new study reveals that current infrastructure for microbiome biobanking is fragmented and unprepared for the unique challenges of storing complex microbial communities.

The Crucial Bottleneck: Preserving Microbiomes

Researchers with the EU project MicrobiomeSupport assessed the infrastructure needed for microbiome research to explore this critical bottleneck. Their goal was to understand what to preserve, why it needs preservation, and how best to support this rapidly growing scientific field.

The team reviewed existing knowledge on current microbiome storage methods, including techniques like freezing solid (cryopreservation) or freeze-drying. Instead of focusing on human samples, the study considered a diverse range of samples such as soil, stool, and seeds.

The Preservation Challenge

The study identified a major hurdle: optimally preserving these microscopic communities is incredibly difficult. While freezing has been the "gold standard" for storing single microbes since the 1960s, keeping entire, functioning communities intact is far more intricate.

One notable instance involved Kerckhof and colleagues, who successfully preserved both the structure and functionality of microbiomes using cryopreservation. However, even this process is likened to "trying to perfectly reassemble a car from its parts while making sure it still drives exactly the same."

The authors highlight this complexity with a poignant question:

"How would you distinguish a 'whisker' from a 'heart' and assess what a component does in the microbiome and its relationship with the total functionality of the whole system?"

This vividly illustrates the deep complexity involved in saving these mini-ecosystems.

Why This Struggle Matters

This struggle is significant because microbiomes influence nearly everything, from human health to soil fertility and even the overall health of our planet. Without improved storage methods, scientists cannot reliably study these communities over time or share them widely. This limitation significantly slows down discoveries that could lead to new medicines or agricultural breakthroughs.

Key Takeaways from the Study

The study acknowledges that it did not offer new data on specific preservation methods or their results. Instead, it powerfully highlights that the biggest challenge lies in:

  1. Developing optimal methodologies for microbiome preservation.
  2. Rigorously testing if preserved microbiomes still maintain their original composition and functionality after storage.

According to the authors:

"The biggest technological bottleneck is the development of optimized methodologies for the preservation of microbiomes and for the assessment of preservation's success in terms of maintaining the composition and functionality of microbiomes."

Moving Forward: Recommendations

To advance the field, the scientists recommend:

  • Agreeing on a prioritized list of microbiomes that need preservation, considering their benefits for science, the economy, society, and the environment.
  • Emphasizing the urgent need for a united effort, bringing together various culture collections and biobanks to tackle this shared challenge collaboratively.

Unlocking the secrets of the microbiome fundamentally depends on our collective ability to properly preserve them for future research and understanding.

Citation

Ryan, M.J., Schloter, M., Berg, G., Kostic, T., Kinkel, L.L., Eversole, K., Macklin, J.A., Schelkle, B., Kazou, M., Sarand, I., Singh, B.K., Fischer, D., Maguin, E., Ferrocino, I., Lima, N., McClure, R.S., Charles, T.C., de Souza, R.S.C., Kiran, G.S., Krug, H.L., Taffner, J., Roume, H., Selvin, J., Smith, D., Rybakova, D., & Sessitsch, A. (2020). Development of Microbiome Biobanks – Challenges and Opportunities. Trends in Microbiology, doi: https://doi.org/10.1016/j.tim.2020.06.009.