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. 2022 Sep 16;3(3):101525.
doi: 10.1016/j.xpro.2022.101525. Epub 2022 Jul 2.

Extraction of CRISPR-targeted sequences from the metagenome

Ryota Sugimoto  1 , Luca Nishimura  2 , Phuong Thanh Nguyen  2 , Ituro Inoue  3
Affiliations

Extraction of CRISPR-targeted sequences from the metagenome

Ryota Sugimoto et al. STAR Protoc. .

Abstract

Homology-based search is commonly used to uncover mobile genetic elements (MGEs) from metagenomes, but it heavily relies on reference genomes in the database. Here we introduce a protocol to extract CRISPR-targeted sequences from the assembled human gut metagenomic sequences without using a reference database. We describe the assembling of metagenome contigs, the extraction of CRISPR direct repeats and spacers, the discovery of protospacers, and the extraction of protospacer-enriched regions using the graph-based approach. This protocol could extract numerous characterized/uncharacterized MGEs. For complete details on the use and execution of this protocol, please refer to Sugimoto et al. (2021).

Keywords: Bioinformatics; CRISPR; Genomics; Sequence analysis; Systems biology.

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Conflict of interest statement

Declaration of interests The authors declare no competing interests.

Figures

None
Graphical abstract
Figure 1
Figure 1
Classification results of CRISPR-targeted terminally redundant sequences from the human gut metagenome The most popular elements among the large (>20 kb) CRISPR-targeted sequences in the human gut metagenome were tailed phages. Conversely, ssDNA viruses, plasmid-like elements, and many unclassified sequences were common among the small (<20 kb) sequences. This result was obtained from our previous study (Sugimoto et al., 2021).
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