TY - JOUR

T1 - Escherichia coli CRISPR arrays from early life fecal samples preferentially target prophages

AU - Dion, Moïra B.

AU - Shah, Shiraz A.

AU - Deng, Ling

AU - Thorsen, Jonathan

AU - Stokholm, Jakob

AU - Krogfelt, Karen A.

AU - Schjørring, Susanne

AU - Horvath, Philippe

AU - Allard, Antoine

AU - Nielsen, Dennis S.

AU - Petit, Marie Agnès

AU - Moineau, Sylvain

N1 - Publisher Copyright: © The Author(s) [2024]. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.

PY - 2024

Y1 - 2024

N2 - CRISPR-Cas systems are defense mechanisms against phages and other nucleic acids that invade bacteria and archaea. In Escherichia coli, it is generally accepted that CRISPR-Cas systems are inactive in laboratory conditions due to a transcriptional repressor. In natural isolates, it has been shown that CRISPR arrays remain stable over the years and that most spacer targets (protospacers) remain unknown. Here, we re-examine CRISPR arrays in natural E. coli isolates and investigate viral and bacterial genomes for spacer targets using a bioinformatics approach coupled to a unique biological dataset. We first sequenced the CRISPR1 array of 1769 E. coli isolates from the fecal samples of 639 children obtained during their first year of life. We built a network with edges between isolates that reflect the number of shared spacers. The isolates grouped into 34 modules. A search for matching spacers in bacterial genomes showed that E. coli spacers almost exclusively target prophages. While we found instances of self-targeting spacers, those involving a prophage and a spacer within the same bacterial genome were rare. The extensive search for matching spacers also expanded the library of known E. coli protospacers to 60%. Altogether, these results favor the concept that E. coli's CRISPR-Cas is an antiprophage system and highlight the importance of reconsidering the criteria use to deem CRISPR-Cas systems active.

AB - CRISPR-Cas systems are defense mechanisms against phages and other nucleic acids that invade bacteria and archaea. In Escherichia coli, it is generally accepted that CRISPR-Cas systems are inactive in laboratory conditions due to a transcriptional repressor. In natural isolates, it has been shown that CRISPR arrays remain stable over the years and that most spacer targets (protospacers) remain unknown. Here, we re-examine CRISPR arrays in natural E. coli isolates and investigate viral and bacterial genomes for spacer targets using a bioinformatics approach coupled to a unique biological dataset. We first sequenced the CRISPR1 array of 1769 E. coli isolates from the fecal samples of 639 children obtained during their first year of life. We built a network with edges between isolates that reflect the number of shared spacers. The isolates grouped into 34 modules. A search for matching spacers in bacterial genomes showed that E. coli spacers almost exclusively target prophages. While we found instances of self-targeting spacers, those involving a prophage and a spacer within the same bacterial genome were rare. The extensive search for matching spacers also expanded the library of known E. coli protospacers to 60%. Altogether, these results favor the concept that E. coli's CRISPR-Cas is an antiprophage system and highlight the importance of reconsidering the criteria use to deem CRISPR-Cas systems active.

KW - bacteriophage

KW - CRISPR

KW - E. coli

KW - gut

KW - microbiome

KW - phage

KW - phage resistance

KW - virome

U2 - 10.1093/ismejo/wrae005

DO - 10.1093/ismejo/wrae005

M3 - Journal article

C2 - 38366192

AN - SCOPUS:85186319565

VL - 18

JO - I S M E Journal

JF - I S M E Journal

SN - 1751-7362

IS - 1

M1 - wrae005

ER -