PhaBOX: A web server for identifying and characterizing phage contigs in metagenomic data

Shang, Jiayu; Cheng, Peng; Liao, Herui; Tang, Xubo; Sun, Yi

doi:10.48550/arxiv.2303.15707

Cited by 2 publications

(2 citation statements)

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“…To identify viral sequences in assembled scaffolds, the PhaMer tool [ 35 ], available through the online server PhaBOX [ 36 ], was used with default parameters. Taxonomic classification of identified viral contigs at the family level was conducted using the semi-supervised learning model PhaGCN [ 37 ] with default parameters.…”

Section: Methodsmentioning

confidence: 99%

Deep Isolated Aquifer Brines Harbor Atypical Halophilic Microbial Communities in Quebec, Canada

Gagnon,

Beauregard-Tousignant,

Marcil

et al. 2023

Genes

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The deep terrestrial subsurface, hundreds of meters to kilometers below the surface, is characterized by oligotrophic conditions, dark and often anoxic settings, with fluctuating pH, salinity, and water availability. Despite this, microbial populations are detected and active, contributing to biogeochemical cycles over geological time. Because it is extremely difficult to access the deep biosphere, little is known about the identity and metabolisms of these communities, although they likely possess unknown pathways and might interfere with deep waste deposits. Therefore, we analyzed rock and groundwater microbial communities from deep, isolated brine aquifers in two regions dating back to the Ordovician and Devonian, using amplicon and whole genome sequencing. We observed significant differences in diversity and community structure between both regions, suggesting an impact of site age and composition. The deep hypersaline groundwater did not contain typical halophilic bacteria, and genomes suggested pathways involved in protein and hydrocarbon degradation, and carbon fixation. We identified mainly one strategy to cope with osmotic stress: compatible solute uptake and biosynthesis. Finally, we detected many bacteriophage families, potentially indicating that bacteria are infected. However, we also found auxiliary metabolic genes in the viral genomes, probably conferring an advantage to the infected hosts.

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Section: Methodsmentioning

confidence: 99%

Deep Isolated Aquifer Brines Harbor Atypical Halophilic Microbial Communities in Quebec, Canada

Gagnon,

Beauregard-Tousignant,

Marcil

et al. 2023

Genes

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“…In addition to A. veronii being predicted as host of the phages, other species of Aeromonas (A. australiensis, A. diversa, Aeromonas sp.) and Serratia marcescens could also serve as their hosts as determined by PhaBox (47,48), suggesting that these phages could infect multiple hosts (Table 2). Of note, the two pairs of isolates (NB-2/NB-4 and NB-178/NB-181) that were highly genetically related by SNP had the same phage content.…”

Section: Characterization Of the Mobile Genetic Elements Among The Se...mentioning

confidence: 99%

Phylogenomics of novel clones ofAeromonas veroniirecovered from a freshwater lake reveals unique biosynthetic gene clusters

Lawal,

Bryan,

Parreira

et al. 2024

Preprint

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Aquatic ecosystems are important reservoirs for clinically relevant pathogens and antimicrobial resistance genes, thus presenting a significant risk to global health. Here, we assessed the phylogenomics of Aeromonas veronii (A. veronii) recovered from Lake Wilcox in Ontario using a combination of morphological, biochemical, and whole-genome sequencing (WGS) techniques. Eleven distinct bacterial colonies were isolated and identified as A. veronii (n=9), and two other Aeromonas species (A. caviae and A. allosaccharophila), with significant discrepancies noted between biochemical and WGS identification methods. Of note, 67% (n=6/9) of A. veronii isolates were human pathogens (Pathogenicity score ≥ 0.50). The genomic analysis revealed high genetic diversity among the A. veronii isolates, including the discovery of 41 novel alleles and seven new sequence types (ST) suggesting the lake as a reservoir for multiple human pathogenic clones of this bacterium. The comparison of the newly isolated and sequenced A. veronii with 214 A. veronii genomes revealed significant genetic diversity and suggests potential broad geographical dissemination of strains. Chromosomal genes (OXA-912 and cphA [cphA3, cphA4, cphA7]) genes encoding resistance to β-lactamases were detected in all isolates. Human and non-human pathogenic strains of A. veronii differed in their virulence gene content, with type III secretion systems being associated with human pathogenic isolates. Mobilome analysis revealed the absence of plasmids in A. veronii isolates and the presence of 13 intact the great majority of which were P22-like (Peduoviridae) phages, and nine different insertion sequence families. Novel biosynthetic gene clusters were identified and characterized, indicating the potential for unique secondary metabolite production in A. veronii with different pathogenic potential. Overall, this study underscores the importance of continuous surveillance of aquatic ecosystems for the presence of pathogens, contributing to our understanding of their evolution, potential for human pathogenicity, and the ecological roles of their genetic elements.

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PhaBOX: A web server for identifying and characterizing phage contigs in metagenomic data

Cited by 2 publications

References 0 publications

Deep Isolated Aquifer Brines Harbor Atypical Halophilic Microbial Communities in Quebec, Canada

Deep Isolated Aquifer Brines Harbor Atypical Halophilic Microbial Communities in Quebec, Canada

Phylogenomics of novel clones ofAeromonas veroniirecovered from a freshwater lake reveals unique biosynthetic gene clusters

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