A Method for Improving the Accuracy and Efficiency of Bacteriophage Genome Annotation

Salisbury, Alicia; Tsourkas, Philippos K.

doi:10.3390/ijms20143391

Cited by 36 publications

(53 citation statements)

References 31 publications

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“…Encoding multiple exonucleases could be a result of adaptive evolution conferring fitness advantage over other phages. However, it could just as well reflect some of the challenges to accurate phage genome annotation, including false negatives (undetected genes) and incorrect functional annotation 29,30 . Gene content variation has been shown to be related to recombination events resulting in acquisition or loss of gene(s) 31 .…”

Section: Discussionmentioning

confidence: 99%

New insights into the biodiversity of coliphages in the intestine of poultry

Sørensen

Broeck

Kiil

et al. 2020

Sci Rep

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Despite phages’ ubiquitous presence and great importance in shaping microbial communities, little is known about the diversity of specific phages in different ecological niches. Here, we isolated, sequenced, and characterized 38 Escherichia coli-infecting phages (coliphages) from poultry faeces to gain a better understanding of the coliphage diversity in the poultry intestine. All phages belonged to either the Siphoviridae or Myoviridae family and their genomes ranged between 44,324 and 173,384 bp, with a G+C content between 35.5 and 46.4%. Phylogenetic analysis was performed based on single “marker” genes; the terminase large subunit, portal protein, and exonucleases, as well as the full draft genomes. Single gene analysis resulted in six distinct clusters. Only minor differences were observed between the different phylogenetic analyses, including branch lengths and additional duplicate or triplicate subclustering. Cluster formation was according to genome size, G+C content and phage subfamily. Phylogenetic analysis based on the full genomes supported these clusters. Moreover, several of our Siphoviridae phages might represent a novel unclassified phage genus. This study allowed for identification of several novel coliphages and provides new insights to the coliphage diversity in the intestine of poultry. Great diversity was observed amongst the phages, while they were isolated from an otherwise similar ecosystem.

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Section: Discussionmentioning

confidence: 99%

New insights into the biodiversity of coliphages in the intestine of poultry

Sørensen

Broeck

Kiil

et al. 2020

Sci Rep

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“…Briefly, an ORF was called if at least two of the algorithms agreed or if it was called only by PHANOTATE with a score ≤−3. Prodigal was prioritized over Glimmer and PHASTER to assign start and end coordinates for CDSs as previously suggested [35]. Next, nucleotide sequences for each predicted ORF were extracted with seqtk subseq (https://github.com/lh3/seqtk) and used for functional annotation.…”

Section: Genome Annotationmentioning

confidence: 99%

Isolation of Four Lytic Phages Infecting Klebsiella pneumoniae K22 Clinical Isolates from Spain

Domingo‐Calap

Beamud

Vienne

et al. 2020

IJMS

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The emergence of multi-drug-resistant bacteria represents a major public-health threat. Phages constitute a promising alternative to chemical antibiotics due to their high host specificity, abundance in nature, and evolvability. However, phage host specificity means that highly diverse bacterial species are particularly difficult to target for phage therapy. This is the case of Klebsiella pneumoniae, which presents a hypervariable extracellular matrix capsule exhibiting dozens of variants. Here, we report four novel phages infecting K. pneumoniae capsular type K22 which were isolated from environmental samples in Valencia, Spain. Full genome sequencing showed that these phages belong to the Podoviridae family and encode putative depolymerases that allow digestion of specific K22 K. pneumoniae capsules. Our results confirm the capsular type-specificity of K. pneumoniae phages, as indicated by their narrow infectivity in a panel of K. pneumoniae clinical isolates. Nonetheless, this work represents a step forward in the characterization of phage diversity, which may culminate in the future use of large panels of phages for typing and/or for combating multi-drug-resistant K. pneumoniae.

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“…The assembled genomes were annotated with DNA Master version 5.23.2., as described in references 10 and 11 , by students enrolled in the BIOL 217 course in spring 2020. We identified 77 genes in Jung and 264 in Ronan, 34 of which are tRNAs.…”

Section: Announcementmentioning

confidence: 99%