Biodiversity farming

Unearthing, taming and preserving the hidden species

Critical in the search for new natural compounds is the ability to unearth novel microbial species. The biodiversity farming unit identifies and explores environmental niches where it collects samples in search of bacterial diversity. For example, 1cm3 of earth can contain over 10 million bacterial cells that belong to an estimated 10’000 species, mostly unculturable or slow-growing bacteria, which predominate in soil environments. The challenges are many once a sample has been collected: from identifying and classifying the diverse species, to isolating them, growing them, establish their metabolic profile and storing them safely for future use.

Core activities

Environmental sampling

Collection of samples of different nature (soil, water, sand, decomposing organic matter, etc.) at diverse geographical locations and geological formations, as well as diverse man-made environments. Environmental sites for collection are selected in collaboration with DEINOVE’S data scientists and academic partners.

Bacterial identification

In collaboration with the synthetic biology unit, metagenomic analysis of the samples collected is performed to identify the different bacterial species that are present. The sequencing data is analyzed in collaboration with the data science team allowing its classification in the prokaryote phylogenetic tree.

Advanced fermentation

Isolation of previously unculturable bacteria is achieved, in collaboration with the fermentation engineering unit, using a panel of growing techniques on solid and liquid media: performing cocultures with other environmental bacteria, recreating the original environmental conditions, incubating the samples in a mini-bioreactor before attempting other growing conditions and testing a variety of conditions and growing media of natural or synthetic origin. Recent microfluidics-based cultivation technique also allows high-throughput microcultivation of single bacterial cells to assess a wide arrays of growing conditions in parallel. Finally, biosafety of the strains is analyzed to uncover potentially pathological species that might have been isolated.

Next generation biobanking

The biodiversity team constantly adds new strains and bacterial extracts to the biobanking library that it manages, to ensure its growth, as well as the quality and preservation of the bacterial strains and extracts collected over time. In collaboration with the Data Science unit, it also continuously develops and improves an automated, computer-assisted library management system in order to minimize human intervention and error. Strains, samples and extracts are cryopreserved in 2D barcoded tubes for rigorous identification, handling and traceability.

Support activities

  • Provide strains as requested by the synthetic biology et fermentation engineering units.
  • Produce crude extracts from growing bacteria under a panel of extraction conditions. The supernatants produced are handed over to the activity testing unit in search of an antimicrobial or other biological activity.
  • Cryopreserve strains, constructs, extracts, molecules, etc., generated by other technology units.

 

References

Stewart, E. J. Growing Unculturable Bacteria. J. Bacteriol. 194, 4151–4160 (2012).

Chaudhary, D. K., Khulan, A. & Kim, J. Development of a novel cultivation technique for uncultured soil bacteria. Sci. Rep. 9, 1–11 (2019).

Lombard, N., Prestat, E., van Elsas, J. D. & Simonet, P. Soil-specific limitations for access and analysis of soil microbial communities by metagenomics: Limitations in soil metagenomics. FEMS Microbiol. Ecol. 78, 31–49 (2011).

Dance, A. The search for microbial dark matter. Nature 582, 301–303 (2020).