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New Genome Editing Tool Developed for Human Gut Microbiome

Jan 13, 2022

Bacteroides is the most abundant genus in the human gut microbiome. Bacteroides species are associated with various diseases, such as obesity, inflammatory bowel disease, and colorectal cancer.  

Genome editing tools are essential for studying the function of gut commensal microbes within host health. However, existing genetic tools for human gut Bacteroides are inconvenient and not efficient.  

A research group led by Prof. DAI Lei at the Shenzhen Institute of Advanced Technology (SIAT) of the Chinese Academy of Sciences proposed a versatile and efficient CRISPR/Cas-based editing tool for human gut Bacteroides. This genome editing tool is streamlined, markerless, and easily followed. 

The study was published in ACS Synthetic Biology on Jan. 6.

The researchers constructed multiple CRISPR/Cas systems in all-in-one Bacteroides-E. coli shuttle plasmids and systematically evaluated the genome editing efficiency in Bacteroides thetaiotaomicron, including the mode of Cas protein expression (constitutive, inducible), different Cas proteins (FnCas12a, SpRY, SpCas9) and sgRNAs.

They found that when Cas expression was controlled by the inducible promoter, FnCas12a displayed the highest efficiency of genome editing in B. thetaiotaomicron. This CRISPR/Cas-based tool could delete large genomic fragments (up to 50 kb) of metabolic gene clusters in B. thetaiotaomicron and also could achieve targeted and markerless insertions.  

The new CRISPR/Cas-based genome editing tool was applied to edit the genomes of multiple Bacteroides species, including B.fragilis, B.ovatus, B.uniform and B.vulgatus. In addition, it is possible to obtain a markerless mutant by passaging in antibiotics-free medium for plasmid curing.

This genome editing tool may facilitate basic and applied research on gut microbiota and human health. 

Contact

ZHANG Xiaomin

Shenzhen Institute of Advanced Technology

E-mail:

CRISPR/Cas-Based Genome Editing for Human Gut Commensal Bacteroides Species

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