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

• Published in: Cell host & microbe Vol. 26; no. 3; pp. 325 - 335.e5
• Main Authors: Soto-Perez, Paola, Bisanz, Jordan E., Berry, Joel D., Lam, Kathy N., Bondy-Denomy, Joseph, Turnbaugh, Peter J.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 11.09.2019
• Subjects: Actinobacteria - virology; Bacteria - genetics; Bacteria - virology; bacteriophage; Bacteriophages - genetics; Base Sequence; CRISPR spacer; CRISPR-Cas Systems; Databases, Genetic; DNA, Bacterial - analysis; DNA, Viral - analysis; Gastrointestinal Tract - microbiology; Genome, Bacterial; Genome, Viral; heterologous expression; human microbiome; Humans; hyper-targeting; Metagenomics; Microbiota - genetics; Sequence Analysis, DNA; virome; virome; human microbiome; hyper-targeting; CRISPR spacer; heterologous expression; bacteriophage; CRISPR-Cas systems
• ISSN: 1931-3128; 1934-6069
• DOI: 10.1016/j.chom.2019.08.008

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. [Display omitted] •Eggerthella lenta, a human gut Actinobacterium, encodes a functional CRISPR-Cas system•Strain-level variations exist in system presence, cas gene sequence, and spacer content•HuVirDB is a generalizable human virome database to search for CRISPR targets•Hyper-targeted phages that harbor multiple protospacers were discovered Soto-Perez, Bisanz, et al. focus on a type I-C CRISPR-Cas system encoded by Eggerthella lenta, a prevalent human gut Actinobacterium implicated in metabolism and pathogenesis. Through computational and experimental approaches, they determine the system’s activity and strain-level variation while also generating a human virome database to identify common phage predators.