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Scientists repurpose gene editing tool to help uncover hidden microbial diversity

Pioneering research led by the University of Bristol has repurposed a gene-editing tool to help shed light on the true biodiversity present in natural environments. The study, in the journal Royal Society Open Science, could help pave the way for more productive soils and improved health.
Microscopic organisms play a key role in the function of all ecosystems, from the cycling of nutrients in soils to the protection of the human gut. But characterizing the wide array of species present within these environments is hugely challenging, with most methods only capturing a small fragment of what is actually there.
First author Lucia Nikolaeva-Reynolds, a Biology graduate from the University of Bristol, said, "Microbes rule the world. Although they are invisible to us, they are found virtually everywhere and play crucial roles throughout nature. Unfortunately, current technologies for monitoring microbes are limited to observing only a small fraction of those present. This leads to gaps in our knowledge about how this hidden microbial world supports the health of ecosystems."

The team of biologists overcame this issue by repurposing CRISPR—a revolutionary gene-editing tool—to gain a fuller picture, using it to extract long DNA "barcodes" that could more accurately identify the microbes present within a sample.
Nikolaeva-Reynolds explained, "By capturing long DNA signatures that are unique to each type of microbe and reading these using DNA sequencing, we can provide a clearer picture of the communities present, giving biologists a more complete picture of these intricate microbial worlds."
This advance is even more remarkable given that it arose from Nikolaeva-Reynolds's final year undergraduate project, which involved initial testing of the approach. Nikolaeva-Reynolds then completed a summer internship to push the research toward a fully fledged methodology.
More information: Lucia Nikolaeva-Reynolds et al, Cas9-based enrichment for targeted long-read metabarcoding, Royal Society Open Science (2025).
Journal information: Royal Society Open Science
Provided by University of Bristol