CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog

Cell Host Microbe. 2019 Sep 11;26(3):325-335.e5. doi: 10.1016/j.chom.2019.08.008. Epub 2019 Sep 3.

Abstract

Bacteriophages are abundant within the human gastrointestinal tract, yet their interactions with gut bacteria remain poorly understood, particularly with respect to CRISPR-Cas immunity. Here, we show that the type I-C CRISPR-Cas system in the prevalent gut Actinobacterium Eggerthella lenta is transcribed and sufficient for specific targeting of foreign and chromosomal DNA. Comparative analyses of E. lenta CRISPR-Cas systems across (meta)genomes revealed 2 distinct clades according to cas sequence similarity and spacer content. We assembled a human virome database (HuVirDB), encompassing 1,831 samples enriched for viral DNA, to identify protospacers. This revealed matches for a majority of spacers, a marked increase over other databases, and uncovered "hyper-targeted" phage sequences containing multiple protospacers targeted by several E. lenta strains. Finally, we determined the positional mismatch tolerance of observed spacer-protospacer pairs. This work emphasizes the utility of merging computational and experimental approaches for determining the function and targets of CRISPR-Cas systems.

Keywords: CRISPR spacer; CRISPR-Cas systems; bacteriophage; heterologous expression; human microbiome; hyper-targeting; virome.

MeSH terms

  • Actinobacteria / virology
  • Bacteria / genetics
  • Bacteria / virology*
  • Bacteriophages / genetics*
  • Base Sequence
  • CRISPR-Cas Systems*
  • DNA, Bacterial / analysis
  • DNA, Viral / analysis
  • Databases, Genetic
  • Gastrointestinal Tract / microbiology*
  • Genome, Bacterial
  • Genome, Viral
  • Humans
  • Metagenomics
  • Microbiota / genetics
  • Sequence Analysis, DNA

Substances

  • DNA, Bacterial
  • DNA, Viral