Mining bacterial NGS data vastly expands the complete genomes of temperate phages

Abstract

Temperate phages (active prophages induced from bacteria) help control pathogenicity, modulate community structure, and maintain gut homeostasis. Complete phage genome sequences are indispensable for understanding phage biology. Traditional plaque techniques are inapplicable to temperate phages due to their lysogenicity, curbing their identification and characterization. Existing bioinformatics tools for prophage prediction usually fail to detect accurate and complete temperate phage genomes. This study proposes a novel computational temperate phage detection method (TemPhD) mining both the integrated active prophages and their spontaneously induced forms (temperate phages) from next-generation sequencing raw data. Applying the method to the available dataset resulted in 192 326 complete temperate phage genomes with different host species, expanding the existing number of complete temperate phage genomes by more than 100-fold. The wet-lab experiments demonstrated that TemPhD can accurately determine the complete genome sequences of the temperate phages, with exact flanking sites, outperforming other state-of-the-art prophage prediction methods. Our analysis indicates that temperate phages are likely to function in the microbial evolution by (i) cross-infecting different bacterial host species; (ii) transferring antibiotic resistance and virulence genes and (iii) interacting with hosts through restriction-modification and CRISPR/anti-CRISPR systems. This work provides a comprehensively complete temperate phage genome database and relevant information, which can serve as a valuable resource for phage research.

Genetic characteristics and integration specificity of Salmonella enterica temperate phages

“…This study identified a total of 8,777 temperate phages specifically associated with S. enterica from the comprehensive public and compromised temperate phage database generated in our previous study ( Zhang et al, 2022 ). These temperate phages were detected from the bacterial next-generation sequencing data.…”

“…In a previous study, we observed that the Salmonella enterica genome contains the largest number of temperate phages compared to other sequenced bacterial species ( Zhang et al, 2022 ). Salmonella enterica is a zoonotic pathogen of substantial concern to global human and animal health ( Knodler and Elfenbein, 2019 ).…”

The low abundance of antimicrobial resistance genes (ARGs) in bacteriophages and their transfer bottlenecks limit the ability of phages to contribute to the spread of ARGs

“…In addition, temperate phage and prophage sequences were also screened for ARGs. A total of 66,823 temperate phage sequences were identified using the TemPhD [38] method (fetched from the PhageScope database [39]) and 49,254 prophage sequences extracted from the PhageClouds database [40] (Figure 1C).…”

“…In addition, temperate phage and prophage sequences were also screened for ARGs. A total of 66,823 temperate phage sequences were identified using the TemPhD [38] method (fetched from the PhageScope database [39]) and 49,254 prophage sequences extracted from the PhageClouds database [40] (Figure 1C). Interestingly, a maximum fraction of ARG-carrying phages were found in temperate and prophages sequences, 2.15% and 0.66%, in TemPhD and Phagecloud datasets, respectively, and the least occurrence was found in the MGV environmental database.…”

ProkBERT Family: Genomic Language Models for Microbiome Applications

“…Additionally, the categorization of viral taxonomy is still a topic of discussion (Walker et al, 2022). Though there have been recent efforts to expand databases (Camargo et al, 2023; Zhang et al, 2022), the overall understanding of viral diversity is still not complete (Yan et al, 2023). We have assembled a unique phage sequence database using recently published genomic data.…”