CRISPR detection in metagenome-assembled genomes (MAGs) of coal mine

Bacterial and archaeal CRISPR-Cas systems provide adaptive immune protection against foreign mobile genetic elements. When viruses infect bacteria, a small portion of the viral DNA is inserted into the bacterial DNA in a specific pattern to produce segments known as CRISPR arrays. Metagenome assembled genomes (MAGs) were used in our study to identify the CRISPR sequence for determining the interacted phage. Metagenomic data from a coal mine was used to perform a computational study. From raw reads, 206151 contigs were assembled. Then contigs were clustered into 150 Metagenome assembled genomes from which 78 non-redundant MAGs were selected. Using the CHECKM standard, seven MAGs were found to have >80 completeness and <20 contaminations. Those MAGs were analyzed for the presence of CRISPR elements. Out of seven MAGs, four MAGs have the CRISPR elements and are searched against the VIROblast database. CRISPR arrays have 4, 1, 3, and 7 spacer sequences in the MAGs of Burkholderia, Acinetobacter, Oxalobacteraceae, and Burkholderia multivorans respectively. The uncultured Caudovirales phage genomic regions were present in the genomes of Burkholderia, Oxalobacteriaceae, and Burkholderia multivorans. This study follows the unconventional metagenomics workflow to provide a better understanding of bacteria and phage interactions.

Automated summary

Bacterial and archaeal CRISPR-Cas systems provide adaptive immune protection against foreign mobile genetic elements. Metagenome assembled genomes (MAGs) were used to identify the CRISPR sequence and study the interactions between bacteria and phages. Through computational analysis of metagenomic data from a coal mine, the study identified 78 non-redundant MAGs containing CRISPR elements. By searching against the VIROblast database, the study found that these MAGs have interactions with uncultured Caudovirales phages. This unconventional metagenomics workflow provides insights into bacteria and phage interactions.