Phages infecting the common gut commensal Escherichia coli HS reveal tropism for its Klebsiella-like capsule

Shenfeld, A.; Kotovskaya, O.; Petrikov, K.; Golomidova, A.; Demkina, A.; Zavialova, M.; Dorozh, O.; Komarova, O.; Iarema, P.; Krasilnikova, V.; Volozhantsev, N.; Severinov, K.; Letarov, A.; Isaev, A.

doi:10.64898/2026.05.19.726188

bioRxiv · 10.64898/2026.05.19.726188

Phages infecting the common gut commensal Escherichia coli HS reveal tropism for its Klebsiella-like capsule

Shenfeld, A.·Kotovskaya, O.·Petrikov, K.·Golomidova, A.·Demkina, A.·Zavialova, M.·Dorozh, O.·Komarova, O.·Iarema, P.·Krasilnikova, V.·Volozhantsev, N.·Severinov, K.·Letarov, A.·Isaev, A.

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Abstract

Tailed dsDNA phages are ubiquitous and thought to infect almost any bacterial species. Escherichia coli HS - a commensal strain used as a model in gut colonization studies - has not been reported as a host for dsDNA phages and is resistant to more than 100 coliphages from the BASEL collection. Here, we report the first phages infecting E. coli HS, characterize their interaction with an endogenous BREX system, and provide a detailed genomic and phylogenetic description. Phages {phi}HS1 (Queuovirinae) and {phi}HS2 (Ackermannviridae) possess dPreQ and 5-NeOmdU modifications that confer resistance to restriction digestion. {phi}HS3 is a temperate phage, related to the native HS prophage {phi}HS4, and represents a founding member of a novel genus (Hueyvirus) of P22-like phages capable of lateral transduction. We reveal exchange of tailspike genes between {phi}HS2, {phi}HS3, and Klebsiella-specific phages. Furthermore, we demonstrate that E. coli HS encodes a Klebsiella-like K47 capsule required for phage infection. These results suggest that the broad phage resistance of E. coli HS may be linked to its capsular type.

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Shenfeld, A., Kotovskaya, O., Petrikov, K., Golomidova, A., Demkina, A., Zavialova, M., Dorozh, O., Komarova, O., Iarema, P., Krasilnikova, V., Volozhantsev, N., Severinov, K., Letarov, A., Isaev, A.. 2026-05-19. Phages infecting the common gut commensal Escherichia coli HS reveal tropism for its Klebsiella-like capsule. https://doi.org/10.64898/2026.05.19.726188

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