Pharokka: a fast scalable bacteriophage annotation tool

Bioinformatics, Год журнала: 2022, Номер 39(1)

Опубликована: Дек. 1, 2022

Abstract Summary In recent years, there has been an increasing interest in bacteriophages, which led to growing numbers of bacteriophage genomic sequences becoming available. Consequently, is a need for rapid and consistent annotation tool dedicated bacteriophages. Existing tools either are not designed specifically bacteriophages or web- email-based require significant manual curation, makes their integration into bioinformatic pipelines challenging. Pharokka was created provide that annotates genomes easily, rapidly consistently with standards compliant outputs. Moreover, requires only two lines code install use takes under 5 min run average 50-kb genome. Availability implementation implemented Python available as bioconda package using ‘conda -c pharokka’. The source on GitHub (https://github.com/gbouras13/pharokka). tested Linux-64 MacOSX machines Windows Linux Virtual Machine.

Язык: Английский

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iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria

PLoS Biology, Год журнала: 2023, Номер 21(4), С. e3002083 - e3002083

Опубликована: Апрель 21, 2023

The extraordinary diversity of viruses infecting bacteria and archaea is now primarily studied through metagenomics. While metagenomes enable high-throughput exploration the viral sequence space, metagenome-derived sequences lack key information compared to isolated viruses, in particular host association. Different computational approaches are available predict host(s) uncultivated based on their genome sequences, but thus far individual limited either precision or recall, i.e., for a number they yield erroneous predictions no prediction at all. Here, we describe iPHoP, two-step framework that integrates multiple methods reliably taxonomy genus rank broad range archaea, while retaining low false discovery rate. Based large dataset virus genomes from IMG/VR database, illustrate how iPHoP can provide extensive guide further characterization viruses.

Язык: Английский

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Systematic exploration of Escherichia coli phage–host interactions with the BASEL phage collection

PLoS Biology, Год журнала: 2021, Номер 19(11), С. e3001424 - e3001424

Опубликована: Ноя. 16, 2021

Bacteriophages, the viruses infecting bacteria, hold great potential for treatment of multidrug-resistant bacterial infections and other applications due to their unparalleled diversity recent breakthroughs in genetic engineering. However, fundamental knowledge molecular mechanisms underlying phage–host interactions is mostly confined a few traditional model systems did not keep pace with massive expansion field. The true biology encoded by these has therefore remained largely untapped, phages therapy or are often still selected empirically. We sought promote systematic exploration composing well-assorted library 68 newly isolated organism Escherichia coli that we share community as BASEL (BActeriophage SElection your Laboratory) collection. This collection representative natural E . phage was intensively characterized phenotypically genomically alongside 10 well-studied phages. experimentally determined essential host receptors all phages, quantified sensitivity 11 defense across different layers immunity, matched results phages’ range panel pathogenic enterobacterial strains. Clear patterns distribution phenotypes genomic features highlighted differences potency immunity suggested basis receptor specificity several groups. Our also indicate strong trade-offs between fitness traits like broad recognition resistance might drive divergent adaptation groups specific ecological niches. envision will inspire future work exploring bacteriophages hosts facilitating discovery an effective translation into biotechnology therapeutic applications.

Язык: Английский

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Expanding known viral diversity in the healthy infant gut

Nature Microbiology, Год журнала: 2023, Номер 8(5), С. 986 - 998

Опубликована: Апрель 10, 2023

Abstract The gut microbiome is shaped through infancy and impacts the maturation of immune system, thus protecting against chronic disease later in life. Phages, or viruses that infect bacteria, modulate bacterial growth by lysis lysogeny, with latter being especially prominent infant gut. Viral metagenomes (viromes) are difficult to analyse because they span uncharted viral diversity, lacking marker genes standardized detection methods. Here we systematically resolved diversity faecal viromes from 647 1-year-olds belonging Copenhagen Prospective Studies on Asthma Childhood 2010, an unselected Danish cohort healthy mother–child pairs. By assembly curation uncovered 10,000 species 248 virus family-level clades (VFCs). Most (232 VFCs) were previously unknown, Caudoviricetes class. Hosts determined for 79% phage using clustered regularly interspaced short palindromic repeat spacers within same children. Typical Bacteroides -infecting crAssphages outnumbered undescribed families infecting Clostridiales Bifidobacterium . Phage lifestyles conserved at family level, 33 virulent 118 temperate families. Virulent phages more abundant, while ones prevalent diverse. Together, found this study expand existing taxonomy provide a resource aiding future virome research.

Язык: Английский

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Resolving the structure of phage–bacteria interactions in the context of natural diversity

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Янв. 18, 2022

Microbial communities are shaped by viral predators. Yet, resolving which viruses (phages) and bacteria interacting is a major challenge in the context of natural levels microbial diversity. Thus, fundamental features how phage-bacteria interactions structured evolve wild remain poorly resolved. Here we use large-scale isolation environmental marine Vibrio their phages to obtain estimates strain-level phage predator loads, all-by-all host range assays discover genomic diversity shape interactions. We show that lytic interaction networks (as observed agar overlay) sparse-with loads being low for most bacterial strains, host-strain-specific. Paradoxically, also find although overlap killing generally rare between tailed phages, recombination common. Together, these results suggest during cryptic co-infections an important mode evolution communities. In development bioengineering therapeutics it consider nucleic acids introduced may spread into local populations through recombination, likelihood transfer not predictable based on range.

Язык: Английский

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Genetic determinants of host tropism in Klebsiella phages

Cell Reports, Год журнала: 2023, Номер 42(2), С. 112048 - 112048

Опубликована: Фев. 1, 2023

Bacteriophages play key roles in bacterial ecology and evolution are potential antimicrobials. However, the determinants of phage-host specificity remain elusive. Here, we isolate 46 phages to challenge 138 representative clinical isolates Klebsiella pneumoniae, a widespread opportunistic pathogen. Spot tests show narrow host range for most phages, with <2% 6,319 combinations tested yielding detectable interactions. Bacterial capsule diversity is main factor restricting phage range. Consequently, phage-encoded depolymerases tropism, depolymerase sequence types associated ability infect specific capsular across families. all broader found do not encode canonical depolymerases, suggesting alternative modes entry. These findings expand our knowledge complex interactions between bacteria their viruses point out feasibility predicting first steps infection using genome sequences.

Язык: Английский

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Immunogenicity of bacteriophages

Trends in Microbiology, Год журнала: 2023, Номер 31(10), С. 1058 - 1071

Опубликована: Май 15, 2023

Язык: Английский

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The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies

Microbial Genomics, Год журнала: 2024, Номер 10(2)

Опубликована: Фев. 20, 2024

Viral metagenomics has fuelled a rapid change in our understanding of global viral diversity and ecology. Long-read sequencing hybrid assembly approaches that combine long- short-read technologies are now being widely implemented bacterial genomics metagenomics. However, the use long-read to investigate communities is still its infancy. While Nanopore PacBio have been applied metagenomics, it not known what extent different will impact reconstruction community. Thus, we constructed mock bacteriophage community previously sequenced phage genomes them using Illumina, tested number approaches. When single technology, Illumina assemblies were best at recovering genomes. Nanopore- PacBio-only performed poorly comparison both genome recovery error rates, which varied with assembler used. The had errors manifested as SNPs INDELs frequencies 41 157 % higher than found only assemblies, respectively. 12 78 Illumina-only Despite high-read coverage, long-read-only recovered maximum one complete from any assembly, unless reads down-sampled prior assembly. Overall approach was by combination reads, reduced rates levels comparable short-read-only assemblies. approach. differences between technology downstream impacts on gene prediction, subsequent estimates within sample. These findings provide starting point for others choice algorithms analysis viromes.

Язык: Английский

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CARD domains mediate anti-phage defence in bacterial gasdermin systems

Nature, Год журнала: 2025, Номер unknown

Опубликована: Янв. 29, 2025

Язык: Английский

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Phage therapy

Nature Reviews Methods Primers, Год журнала: 2025, Номер 5(1)

Опубликована: Фев. 13, 2025

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