Genomic sequencing and biological characteristics of a novel Escherichia coli bacteriophage 9g, a putative representative of a new Siphoviridae genus.

Eugene Kulikov,Alla Golomidova,Andrey Letarov,Nikolai Prokhorov,Alexandr Zelenin,Maria Letarova,Elena Kostryukova

doi:10.3390/v6125077

Eugene Kulikov, Alla Golomidova + Show 5 more

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https://doi.org/10.3390/v6125077

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Abstract

Bacteriophage 9g was isolated from horse feces using Escherichia coli C600 as a host strain. Phage 9g has a slightly elongated capsid 62 × 76 nm in diameter and a non-contractile tail about 185 nm long. The complete genome sequence of this bacteriophage consists of 56,703 bp encoding 70 predicted open reading frames. The closest relative of phage 9g is phage PhiJL001 infecting marine alpha-proteobacterium associated with Ircinia strobilina sponge, sharing with phage 9g 51% of amino acid identity in the main capsid protein sequence. The DNA of 9g is resistant to most restriction endonucleases tested, indicating the presence of hypermodified bases. The gene cluster encoding a biosynthesis pathway similar to biosynthesis of the unusual nucleoside queuosine was detected in the phage 9g genome. The genomic map organization is somewhat similar to the typical temperate phage gene layout but no integrase gene was detected. Phage 9g efficiently forms stable associations with its host that continues to produce the phage over multiple passages, but the phage can be easily eliminated via viricide treatment indicating that no true lysogens are formed. Since the sequence, genomic organization and biological properties of bacteriophage 9g are clearly distinct from other known Enterobacteriaceae phages, we propose to consider it as the representative of a novel genus of the Siphoviridae family.

Highlights

The horse gut ecosystem was found to be the habitat of a large spectrum of different virulent bacteriophages, though [1,2,3] while the prevalence of temperate phages appears to be low in the free phage pool of horse feces
Bacteriophage 9g was isolated from a horse feces sample using the Escherichia coli K12 derivative
We were able to propagate it on the derivatives of the E. coli 4s strain selected for the resistance to bacteriophage G7C [4]

Summary

Introduction

The horse gut ecosystem was found to be the habitat of a large spectrum of different virulent bacteriophages, though [1,2,3] while the prevalence of temperate phages appears to be low in the free phage pool of horse feces. Our preliminary data [1,4] suggests that the ecosystem of the horse gut may be more open for acquisition of the new bacteriophage types than the intestinal microbiomes of humans and some other mammal species where the associated viromes instead are remarkably stable [5,6,7]. The unusually high strain-level diversity of coliform bacteria in the individual gut microbiomes in horses [8] is suggestive of an active lateral flow of bacterial strains between adult animals. The horse gut may act as a natural enrichment cultivator that facilitates the detection and identification of the novel types of bacterial viruses, especially the phages of family Enterobacteriaceae. There is a tendency to split larger genera that include very distantly related phages and to introduce subfamily levels into phage taxonomy

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