Bacteriophages are viruses that infect bacteria. In this perspective, we discuss several aspects of a characteristic feature of bacteriophages, their host range. Each phage has its own particular host range, the range of bacteria that it can infect. While some phages can only infect one or a few bacterial strains, other phages can infect many species or even bacteria from different genera. Different methods for determining host range may give different results, reflecting the multiple mechanisms bacteria have to resist phage infection and reflecting the different steps of infection each method depends on. This makes defining host range difficult. Another difficulty in describing host range arises from the inconsistent use of the words "narrow" and especially "broad" when describing the breadth of the host range. Nearly all bacteriophages have been isolated using a single host strain of bacteria. While this procedure is fairly standard, it may more likely produce narrow rather than broad host range phage. Our results and those of others suggest that using multiple host strains during isolation can more reliably produce broader host range phages. This challenges the common belief that most bacteriophages have a narrow host range. We highlight the implications of this for several areas that are affected by host range including horizontal gene transfer and phage therapy.
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http://dx.doi.org/10.3389/fmicb.2016.01352 | DOI Listing |
Bioinformatics
January 2025
Bioinformatics Lab, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, 1004, Philippines.
Motivation: Recent computational approaches for predicting phage-host interaction have explored the use of sequence-only protein language models to produce embeddings of phage proteins without manual feature engineering. However, these embeddings do not directly capture protein structure information and structure-informed signals related to host specificity.
Results: We present PHIStruct, a multilayer perceptron that takes in structure-aware embeddings of receptor-binding proteins, generated via the structure-aware protein language model SaProt, and then predicts the host from among the ESKAPEE genera.
Emerg Microbes Infect
January 2025
The Pirbright Institute, Pirbright, Woking, United Kingdom.
Clade 2.3.4.
View Article and Find Full Text PDFJ Helminthol
January 2025
Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii Prospect 33, 117071, Moscow, Russia.
Studying complexes of cryptic or pseudocryptic species opens new horizons for the understanding of speciation processes, an important yet vague issue for the digeneans. We investigated a hemiuroidean trematode across a wide geographic range including the northern European seas (White, Barents, and Pechora), East Siberian Sea, and the Pacific Northwest (Sea of Okhotsk and Sea of Japan). The goals were to explore the genetic diversity within through mitochondrial ( and genes) and ribosomal (ITS1, ITS2, 28S rDNA) marker sequences, to study morphometry of maritae, and to revise the life cycle data.
View Article and Find Full Text PDFBats are reservoir hosts for numerous well-known zoonotic viruses, but their broader virus-hosting capacities remain understudied. are an order of enteric viruses known to cause disease across a wide range of mammalian hosts, including Hepatitis A in humans and foot-and-mouth disease in ungulates. Host-switching and recombination drive the diversification of worldwide.
View Article and Find Full Text PDFMicrobial eukaryotes (aka protists) are known for their important roles in nutrient cycling across different ecosystems. However, the composition and function of protist-associated microbiomes remains largely elusive. Here, we employ cultivation-independent single-cell isolation and genome-resolved metagenomics to provide detailed insights into underexplored microbiomes and viromes of over 100 currently uncultivable ciliates and amoebae isolated from diverse environments.
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