Abstract
BackgroundBacteria and archaea develop immunity against invading genomes by incorporating pieces of the invaders' sequences, called spacers, into a clustered regularly interspaced short palindromic repeats (CRISPR) locus between repeats, forming arrays of repeat-spacer units. When spacers are expressed, they direct CRISPR-associated (Cas) proteins to silence complementary invading DNA. In order to characterize the invaders of human microbiomes, we use spacers from CRISPR arrays that we had previously assembled from shotgun metagenomic datasets, and identify contigs that contain these spacers' targets.ResultsWe discover 95,000 contigs that are putative invasive mobile genetic elements, some targeted by hundreds of CRISPR spacers. We find that oral sites in healthy human populations have a much greater variety of mobile genetic elements than stool samples. Mobile genetic elements carry genes encoding diverse functions: only 7% of the mobile genetic elements are similar to known phages or plasmids, although a much greater proportion contain phage- or plasmid-related genes. A small number of contigs share similarity with known integrative and conjugative elements, providing the first examples of CRISPR defenses against this class of element. We provide detailed analyses of a few large mobile genetic elements of various types, and a relative abundance analysis of mobile genetic elements and putative hosts, exploring the dynamic activities of mobile genetic elements in human microbiomes. A joint analysis of mobile genetic elements and CRISPRs shows that protospacer-adjacent motifs drive their interaction network; however, some CRISPR-Cas systems target mobile genetic elements lacking motifs.ConclusionsWe identify a large collection of invasive mobile genetic elements in human microbiomes, an important resource for further study of the interaction between the CRISPR-Cas immune system and invaders.
Highlights
Bacteria and archaea develop immunity against invading genomes by incorporating pieces of the invaders’ sequences, called spacers, into a clustered regularly interspaced short palindromic repeats (CRISPR) locus between repeats, forming arrays of repeat-spacer units
We applied CD-HIT-EST [38] to remove contig redundancy, resulting in 20,504 non-redundant mobile genetic elements (MGEs) contigs. We note that these numbers are conservative estimates, as we applied stringent criteria in defining putative MGEs, and generous criteria in eliminating redundancy
The actual MGEs may in some cases be shorter, as contigs can contain parts of the flanking bacterial genomes, but there are still four MGE segments with dense protospacers covering more than 100 kbp, including: SRS050669_LANL_scaffold_47865 containing 250 protospacers between 855 and 159,934 bp; SRS022530_LANL_scaffold_21325 with 194 protospacers between 2,493 and 123,573 bp; SRS062761_LANL_scaffold_30103 with 256 protospacers between 216 and 118,723 bp; and SRS051791_LANL_scaffold_3222 with 61 protospacers between 3,062 and 116,815 bp (Figure S1 in Additional file 1 shows the histogram of the segment sizes)
Summary
Bacteria and archaea develop immunity against invading genomes by incorporating pieces of the invaders’ sequences, called spacers, into a clustered regularly interspaced short palindromic repeats (CRISPR) locus between repeats, forming arrays of repeat-spacer units. Many human pathogens acquire strain-specific properties and functions through foreign DNAs delivered by bacteriophages and plasmids - important factors in the spread of antibiotic resistance [1,2,3,4] Another class of MGEs is Bacteria have developed various defense systems to limit the exchange of MGEs. Bacterial innate immunity is achieved by adsorption-blocking, methylation-restriction systems, and production of extracellular matrix, among other mechanisms [8], whereas adaptive immunity systems acquire invasive DNAs and use them for interference against further invasion of matching foreign DNA molecules. The clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) proteins systems are an RNA-guided adaptive immunity system that provides sequence-directed defense against MGEs [8,9,10,11,12,13,14]. A bacterial type II CRISPR-Cas system (which uses cas9) has been engineered to achieve guided genome engineering in human cells [17,18], Saccharomyces cerevisiae [19] and Zebrafish embryos [20], and to achieve selective repression of gene expression in Escherichia coli (by using a catalytically dead Cas lacking endonuclease activity) [21]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
