New CRISPR methods with potential for microbiome genome editing

Researchers have developed several new approaches using CRISPR to modify the genomes of bacterial populations on a large scale.

Two landmark studies have reported successfully using CRISPR to alter bacterial genomes within their natural populations. The advances could pave the way for so-called 'community editing', where diverse populations of bacteria are modified simultaneously, and in-situ.

Currently, CRISPR can only perform targeted edits in one cell-type at a time. Community editing, however, would allow the study of bacterial populations on an unprecedented scale, in a less artificial model. 'Breaking and changing DNA within isolated microorganisms has been essential to understanding what that DNA does,' explained Dr Benjamin Rubin at the University of California (UC) Berkeley, lead author of one study.

'This work helps bring that fundamental approach to microbial communities, which are much more representative of how these microbes live and function in nature,' he added.

The study from UC Berkeley, published in Nature Microbiology, described two methods of genome editing that could work together to target particular bacterial species within a mixed population. First, the researchers developed a screening technique called ET-Seq (Environmental Transformation Sequencing) to identify bacteria which were most susceptible to genome editing within a population. They then used a modified CRISPR system called DART (DNA-editing all-in-one RNA-guided CRISPR-Cas Transposase) to target specific loci within these bacteria, and insert a barcoded DNA sequence that allowed the researchers to track the bacteria's activity.

The researchers cultured a community of microbes both from human infant stool and soil, and were able to enrich for strains of E.coli carrying a gene of interest – in this case, antibiotic resistance genes inserted by DART. Led by Professor Jennifer Doudna, who was awarded the 2020 Nobel Prize in Chemistry for the invention of CRISPR/Cas9 genome editing (see BioNews 1070), the team are hopeful ET-Seq and DART could be used to accelerate research of bacterial communities.

Elsewhere, at the University of California San Francisco (UCSF), researchers successfully manipulated the composition of the gut microbiome in mice – the first study to alter microbial genomes in living mammals.

Published in Cell Reports, the researchers used a bacteria-infecting virus called M13 to deliver a destructive CRISPR/Cas9 system to a strain of E.coli they wanted to eliminate from the gut. Following analysis of the mice's faeces, they found that the E.coli strain, which was prominent before M13 targeting, diminished to only one percent of the bacterial population.

Professor Peter Turnbaugh, senior author of the study at UCSF, described the work as 'the starting point for trying to engineer bacteria within the gut.'

The new techniques developed by UC Berkeley and UCSF have significant implications for microbial research, which relies on being able to isolate and grow bacteria and is not possible for many species. Similarly, it is difficult to study processes where multiple species cooperate, such as in nutrient breakdown.

The methods could also aid medical research into conditions such as autoimmune disorders, cardiovascular disease and even depression, which are linked to imbalances in the gut microbiome.

'Eventually, we may be able to eliminate genes that cause sickness in your gut bacteria or make plants more efficient by engineering their microbial partners,' summarised Dr Brady Cress, co-author of the UC Berkeley study.

He added: 'But likely, before we do that, this approach will give us a better understanding of how microbes function within a community.'