A Novel High-resolving Method for Genomic PCR-fingerprinting of Enterobacteria

Prokhorov

et al. 2016

Viruses

The T5-like siphoviruses DT57C and DT571/2, isolated from horse feces, are very closely related to each other, and most of their structural proteins are also nearly identical to T5 phage. Their LTFs (L-shaped tail fibers), however, are composed of two proteins, LtfA and LtfB, instead of the single Ltf of bacteriophage T5. In silico and mutant analysis suggests a possible branched structure of DT57C and DT571/2 LTFs, where the LtfB protein is connected to the phage tail via the LtfA protein and with both proteins carrying receptor recognition domains. Such adhesin arrangement has not been previously recognized in siphoviruses. The LtfA proteins of our phages are found to recognize different host O-antigen types: E. coli O22-like for DT57C phage and E. coli O87 for DT571/2. LtfB proteins are identical in both phages and recognize another host receptor, most probably lipopolysaccharide (LPS) of E. coli O81 type. In these two bacteriophages, LTF function is essential to penetrate the shield of the host’s O-antigens. We also demonstrate that LTF-mediated adsorption becomes superfluous when the non-specific cell protection by O-antigen is missing, allowing the phages to bind directly to their common secondary receptor, the outer membrane protein BtuB. The LTF independent adsorption was also demonstrated on an O22-like host mutant missing O-antigen O-acetylation, thus showing the biological value of this O-antigen modification for cell protection against phages.

Section: Discussionmentioning

confidence: 99%

Branched Lateral Tail Fiber Organization in T5-Like Bacteriophages DT57C and DT571/2 is Revealed by Genetic and Functional Analysis

Golomidova

Prokhorov

et al. 2016

Viruses

“…This mode of stable growth of the host and phage in the form of colonies or microcolonies without extinction of the host population or replacement of the total host population by a phage resistant mutants may explain the stable maintenance of some virulent phages in the horse gut ecosystem (see refs [ 1 , 4 ]) despite the occurring drop of the overall concentration of the phage and suitable host below the expected phage replication threshold. It has to be noted that due to very high intraspecies diversity of the individual E. coli populations in horses, only a small fraction of E. coli cells can be infected by any given coliphage strain present in this system [ 1 , 8 ].…”

Section: Discussionmentioning

confidence: 99%

“…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 also suggestive of an active lateral flow of bacterial strains between adult animals. Thus, 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.…”

Section: Introductionmentioning

confidence: 99%

Genomic Sequencing and Biological Characteristics of a Novel Escherichia Coli Bacteriophage 9g, a Putative Representative of a New Siphoviridae Genus

Golomidova

Letarova

et al. 2014

Viruses

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.

“…Our metagenomic data does not provide any direct estimates of the bacterial diversity and/or phage-host relationships at the strain level. However high intraspecies diversity of E. coli within horse feces associated with high diversity of co-occurring coliphages, having relatively narrow host ranges, was previous demonstrated using the culture-based approaches(41,42). Additional culture-based evaluation of the strain-level diversity of a more prevalent species than E. coli combined with characterization of its co-occurring phages, may help to shed more light over the pattern of the phage-host relationships in the horse gut ecosystem.Despite the observed high virome diversity, our data suggest that a healthy horse (in the feral population the animals without visible abnormalities, wounds and marked anomalies were considered as heathy) intestinal virome includes a certain number of conserved components.…”

mentioning

confidence: 93%

“…The E. coli host population was found to be highly divergent, and represented by hundreds of strains simultaneously present in the same sample. The overlap of the sensitivity of these strains to co-occuring bacteriophages was limited (41,42) with ~1-5 % of the total E. coli counts being suitable hosts for any particular phage isolate. The data of Golomidova et al (41,43) and the results of the longitudinal study of G7C-related bacteriophages persistence and evolution within the ecosystem of a horse stable (44) indicated the flow of the coliphage genotypes between the animals.…”

Section: Introductionmentioning

confidence: 99%

The ecogenomics of dsDNA bacteriophages in feces of stabled and feral horses

Babenko

Millard

et al. 2020

Preprint

The viromes of the mammalian lower gut were shown to be heavily dominated by bacteriophages; however, only for humans were the composition and intervariability of the bacteriophage communities studied in depth. Here we present an ecogenomics survey of dsDNA bacteriophage diversity in the feces of horses (Equus caballus), comparing two groups of stabled horses, and a further group of feral horses that were isolated on an island. Our results indicate that the dsDNA viromes of the horse feces feature higher richness than in human viromes, with more even distribution of genotypes. No over-represented phage genotypes, such as CrAssphage-related viruses found in humans, were identified. Additionally, many bacteriophage genus-level clusters were found to be present in all three geographically isolated populations. The diversity of the horse intestinal bacteriophages is severely undersampled, and so consequently only a minor fraction of the phage contigs could be linked with the bacteriophage genomes. Our study indicates that bacteriophage ecological parameters in the intestinal ecosystems in horses and humans differ significantly, leading them to shape their corresponding viromes in different ways. Therefore, the diversity and structure of the intestinal virome in different animal species needs to be experimentally studied.Short abstract (needed in some journals as eLife)The viromes of the mammalian gut were shown to be heavily dominated by bacteriophages; however, only for humans were the composition and intervariability of the bacteriophage communities studied in depth. Here we present an ecogenomics survey of dsDNA bacteriophage diversity in the feces of horses (Equus caballus), comparing stabled horses, and feral horses that were isolated on an island. The viromes equine fecal viromes feature higher richness than in human viromes, with more even distribution of genotypes. No over-represented phage genotypes were identified. Additionally, many bacteriophage genus-level clusters were found to be present in geographically isolated populations. Only a minor fraction of the phage contigs could be linked with the bacteriophage genomes. Our study indicates that bacteriophage ecological parameters in the intestinal ecosystems in horses and humans differ significantly, leading them to shape their corresponding viromes in different ways.Importance. (needed for mBio)The study presents the first in depth analysis of the composition and variability of the gut dsDNA bacteriophage community in the mammalian species, other than humans. The study demonstrates that the bacteriophage ecology in the gut is substantially different in different animal species. The results also indicate that the genetic diversity of the equine intestinal bacteriophages is immense and almost totally unexplored by the moment.