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.

View original source ↗Export metadata ↓

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.

Explore related subjects

microbiology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

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

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

A population-scale landscape of the subgingival microbiome reveals divergent routes to periodontal dysbiosis

Periodontitis is an archetypical mucosal inflammatory disease in which microbiome dysbiosis at the tooth-epithelial interface interacts with host genetic and behavioral risk factors to drive immune-mediated tissue destruction. Although subgingival microbiome compositional shifts are thought to parallel disease severity, microbiome variation at the population-level and its relationship to periodontal clinical phenotypes and disease-modifying factors remain poorly defined. Here, we use unsupervised manifold learning to map the compositional landscape of the subgingival microbiome in 1,355 adults spanning periodontal health to severe periodontitis. We identified eight latent microbiome states organized along a branching continuum from eubiosis to dysbiosis. An intermediate microbial configuration marked ecological destabilization and bifurcation into two distinct periodontitis-associated dysbiotic trajectories, distinguished by links to gingival inflammation and smoking. Although the microbiome trajectories broadly tracked periodontal destruction, a minority of individuals showed discordant microbiome-clinical phenotypes, with some individuals with periodontitis retaining otherwise eubiotic microbiomes enriched for low-abundance pathobionts, while some cases of health or mild disease had highly dysbiotic communities, suggesting distinct host susceptibility. Together, these findings define a population-scale ecological landscape of the subgingival microbiome, reveal divergent trajectories to periodontal dysbiosis, and highlight heterogeneity in the relationship between microbial community structure and clinical disease expression.

microbiology↗

bioRxiv2026

The iron-binding siderophore enterobactin is required for the response of multi-drug resistant Klebsiella pneumoniae to zinc limitation

To persist during infection Klebsiella pneumoniae must overcome nutrient iron and zinc limitation imposed by the host immune system through a process called nutritional immunity. Secreted small molecule siderophores are a major virulence determinant of Klebsiella pneumoniae pathogenesis and are presumed to overcome nutritional immunity by binding iron for bacterial acquisition. In this work, we set out to identify how a multi-drug resistant K. pneumoniae grows in zinc limited environments. Using unbiased transcriptomics, proteomics, and an arrayed transposon screen, we identified that synthesis and uptake of the siderophore enterobactin is required to allow for growth in low zinc conditions. Iron-specific chelators did not replicate this phenotype and addition of supplemental iron through heme in growth media could not complement severe growth defects of enterobactin mutant K. pneumoniae experiencing zinc limitation. Finally, zinc starvation induced enterobactin production independent of the canonical zinc uptake regulator (Zur) transcription factor suggesting an unidentified regulatory mechanism by which Gram-negative pathogens may respond to zinc stress. Together, these studies expand the role of enterobactin beyond iron regulation and highlight a previously unreported link between iron and zinc homeostasis in Klebsiella pneumoniae.

microbiology↗

bioRxiv2026

A microbiota-derived protease links phage susceptibility to host epithelial responses

Bacteriophages are major ecological drivers of gut microbial ecology, yet whether bacterial mechanisms that determine phage susceptibility have consequences for the mammalian host remains poorly understood. Here, we identify dipeptidyl peptidase 11 (Dpp11a), the predominant active serine protease of the prevalent gut commensal Phocaeicola vulgatus, as an unexpected bacterial defence factor. Dpp11a protects against environmental proteases and confers resistance to bacteriophage infection. Metatranscriptomic analyses further reveal increased expression of both dpp11a and P. vulgatus-associated phage transcripts in ulcerative colitis stool samples, indicating that both components of this interaction are transcriptionally active in disease-associated human microbiomes. Using the microfluidic gut-on-a-chip co-culture model HuMiX, we show that the absence of Dpp11 is accompanied by altered epithelial tight-junction remodelling during phage-bacterial infection. Together, our findings reveal that the consequences of bacterial phage defence can extend beyond phage-bacterium interactions to the mammalian epithelium.

microbiology↗