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Genome editing in complex microbial communities

Researchers have characterised and validated a strategy for editing the genomes of specific organisms in microbial communities using tools called ET-seq and DART.

Exploring microbial gene functions is done through the application of experimental genetics in cultured microorganisms. This requires the manipulation of isolated species, which can limit findings in several ways. For example, microorganisms grown and studied in isolation can quickly adapt to the lab environment and subsequently obscure their ‘wild-type’ physiology. Additionally, the vast majority of bacteria and archaea remain uncultured and are largely untouched by molecular genetics. The majority of genes involved in interactions between microorganisms also remain unexplored.

Studying microbial communities

As most microorganisms relevant to the environment, industry and health live in communities, approaches for precision genome editing in community contexts is highly significant. Now, the researchers who invented the CRISPR-Cas9 genome editing technology nearly 10 years ago, at University of California, Berkeley, have found a way to add or modify genes within a community of many different species simultaneously. They characterised and validated a strategy for editing the genomes of specific organisms in microbial communities and published their findings in Nature Microbiology.

The group applied environmental transformation sequencing (ET-seq) to map non-targeted transposon insertions after they were delivered to a microbial community. Additionally, DNA-editing all-in-one RNA-guided CRISPR-Cas transposase (DART) systems were used to enable organism- and locus-specific genetic manipulation in a community context. Essentially, the researchers used a combination of ET-seq and DART in soil and infant gut microbiota to conduct both species- and site-specific edits in several bacteria.

Genetically editing microbial communities

This study demonstrated that individual organisms within microbial communities can be targeted for site-specific genome editing and that the manipulation of species can be carried out without requiring previous isolation or engineering. Additionally, the researchers showed that ET-seq and DART are tools that could be applied for species- and locus-specific genome editing within microbial communities.

Traditionally, the several steps required to culture an environmental microbe, determine the ideal means to transform it, and implement targeted editing take years to carry out. Moreover, these lengthy processes may fail in the end, and hence can be a waste of researchers’ time. ET-seq and DART could act as alternatives for microbial community genome editing. These tools could accelerate the time taken to conduct culturing, transformation and targeted editing to a matter of weeks, and enhance the processes to enable a more information-rich context. Furthermore, ET-seq and DART decrease the need for isolation as a prerequisite for genetics and provide technologies that are essential for in situ genetics.

Image credit: Future Learn

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Bacteria / Genome Editing / Microbiology