PHAST: A Fast Phage Search Tool

Zhou, You‐Xing; Liang, Yongjie; Lynch, Karlene H.; Dennis, Jonathan J.; Wishart, David S.

doi:10.1093/nar/gkr485

Cited by 1,855 publications

(1,645 citation statements)

References 18 publications

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“…The element herein referred to as Roseobacter phage RDJL Φ 1 (Supplementary Table S9) (Huang et al, 2011) due to PHAST annotation (Zhou et al, 2011) has also been described as gene transfer agent (Zhao et al, 2009;Thole et al, 2012). Gene transfer agents have first been described in Rhodobacteraceae (Marrs, 1974) and are widespread within the family (Biers et al, 2008;Huang et al, 2011;Thole et al, 2012).…”

Section: Discussionmentioning

confidence: 99%

Global occurrence and heterogeneity of the Roseobacter-clade species Ruegeria mobilis

et al. 2016

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Tropodithietic acid (TDA)-producing Ruegeria mobilis strains of the Roseobacter clade have primarily been isolated from marine aquaculture and have probiotic potential due to inhibition of fish pathogens. We hypothesized that TDA producers with additional novel features are present in the oceanic environment. We isolated 42 TDA-producing R. mobilis strains during a global marine research cruise. While highly similar on the 16S ribosomal RNA gene level (99-100% identity), the strains separated into four sub-clusters in a multilocus sequence analysis. They were further differentiated to the strain level by average nucleotide identity using pairwise genome comparison. The four sub-clusters could not be associated with a specific environmental niche, however, correlated with the pattern of sub-typing using co-isolated phages, the number of prophages in the genomes and the distribution in ocean provinces. Major genomic differences within the sub-clusters include prophages and toxin-antitoxin systems. In general, the genome of R. mobilis revealed adaptation to a particle-associated life style and querying TARA ocean data confirmed that R. mobilis is more abundant in the particle-associated fraction than in the free-living fraction occurring in 40% and 6% of the samples, respectively. Our data and the TARA data, although lacking sufficient data from the polar regions, demonstrate that R. mobilis is a globally distributed marine bacterial species found primarily in the upper open oceans. It has preserved key phenotypic behaviors such as the production of TDA, but contains diverse sub-clusters, which could provide new capabilities for utilization in aquaculture.

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Section: Discussionmentioning

confidence: 99%

Global occurrence and heterogeneity of the Roseobacter-clade species Ruegeria mobilis

et al. 2016

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“…transmembrane, extracellular) was examined using Psortb v3.0 (Subcellular Localization Prediction Tool; Yu et al, 2010) and InterProScan v5.0 (Jones et al, 2014). The presence of bacteriophage elements within the bacterial genomes was analysed using PHAST (Phage Search Tool; Zhou et al, 2011). CRISPRFinder (Grissa et al, 2007) was used to search the genomes for clustered regularly interspaced short palindromic repeat (CRISPR) sequences.…”

Section: Methodsmentioning

confidence: 99%

Genomics of Weissella cibaria with an examination of its metabolic traits

et al. 2015

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“…bolletii CIP108541 T genome was made available (15). The prophage region was predicted using PHAST (PHAge Search Tool) (16). Open reading frames (ORFs) were predicted using the software program Prodigal (http://prodigal.ornl.gov/) (17) with default parameters.…”

Section: Methodsmentioning

confidence: 99%

The First Structure of a Mycobacteriophage, the Mycobacterium abscessus subsp. bolletii Phage Araucaria

Sassi

Bebeacua

Drancourt

et al. 2013

J Virol

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The unique characteristics of the waxy mycobacterial cell wall raise questions about specific structural features of their bacteriophages. No structure of any mycobacteriophage is available, although ϳ3,500 have been described to date. To fill this gap, we embarked in a genomic and structural study of a bacteriophage from Mycobacterium abscessus subsp. bolletii, a member of the Mycobacterium abscessus group. This opportunistic pathogen is responsible for respiratory tract infections in patients with lung disorders, particularly cystic fibrosis. M. abscessus subsp. bolletii was isolated from respiratory tract specimens, and bacteriophages were observed in the cultures. We report here the genome annotation and characterization of the M. abscessus subsp. bolletii prophage Araucaria, as well as the first single-particle electron microscopy reconstruction of the whole virion. Araucaria belongs to Siphoviridae and possesses a 64-kb genome containing 89 open reading frames (ORFs), among which 27 could be annotated with certainty. Although its capsid and connector share close similarity with those of several phages from Gram-negative (Gram ؊ ) or Gram ؉ bacteria, its most distinctive characteristic is the helical tail decorated by radial spikes, possibly host adhesion devices, according to which the phage name was chosen. Its host adsorption device, at the tail tip, assembles features observed in phages binding to protein receptors, such as phage SPP1. All together, these results suggest that Araucaria may infect its mycobacterial host using a mechanism involving adhesion to cell wall saccharides and protein, a feature that remains to be further explored.

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PHAST: A Fast Phage Search Tool

Cited by 1,855 publications

References 18 publications

Global occurrence and heterogeneity of the Roseobacter-clade species Ruegeria mobilis

Global occurrence and heterogeneity of the Roseobacter-clade species Ruegeria mobilis

Genomics of Weissella cibaria with an examination of its metabolic traits

The First Structure of a Mycobacteriophage, the Mycobacterium abscessus subsp. bolletii Phage Araucaria

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