Mining of Thousands of Prokaryotic Genomes Reveals High Abundance of Prophages with a Strictly Narrow Host Range

López-Leal, Gamaliel; Camelo-Valera, Laura Carolina; Hurtado-Ramírez, Juan Manuel; Verleyen, Jérôme; Castillo-Ramírez, Santiago; Reyes-Muñoz, Alejandro

doi:10.1128/msystems.00326-22

Cited by 33 publications

(28 citation statements)

References 52 publications

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“…Comprehensive genomic analysis pointed out that prophages are common in bacterial genomes, especially in pathogens from the Enterobacterales order [ 39 ]. Indeed, putative prophage sequences are pervasive in the Erwinia spp., indicating that they could be relevant to bacterial evolution and environmental fitness.…”

Section: Discussionmentioning

confidence: 99%

Genomic Analysis Unveils the Pervasiveness and Diversity of Prophages Infecting Erwinia Species

et al. 2022

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Prophages are abundant elements integrated into bacterial genomes and contribute to inter-strain genetic variability and, in some cases, modulate the environmental behavior of bacteria, such as pathogen virulence. Here, we described prophage occurrence and diversity in publicly available Erwinia genome assemblies, a genus containing plant pathogens. Prophage-like sequences were identified and taxonomically classified. Sequence diversity was analyzed through intergenomic similarities. Furthermore, we searched for anti-phage defense systems in Erwinia spp., such as DISARM, BREX, and CRISPR-Cas systems, and identified the putative targets of CRISPR spacers. We identified 939 prophage-like sequences in 221 Erwinia spp. genome assemblies. Only 243 prophage-like sequences were classified, all belonging to the Caudoviricetes class. The set of putative Erwinia prophages was mostly unique since only three sequences showed more than 70% intergenomic similarities to known Erwinia phages. Overall, the number and type of CRISPR-Cas systems were conserved within Erwinia species, with many spacers directed to the putative prophages identified. This study increased the knowledge of the diversity and distribution of Erwinia prophages, contributing to the characterization of genetic and ecological factors influencing Erwinia spp. environmental fitness.

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Section: Discussionmentioning

confidence: 99%

Genomic Analysis Unveils the Pervasiveness and Diversity of Prophages Infecting Erwinia Species

et al. 2022

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“…From the taxonomical viewpoint, temperate phages may be particularly interesting, which, in the prophage form, are easy to overlook when relying on conventional cultivation-based approaches for phage identification. Prophages can contribute to the viability and adaptability of their bacterial host by altering some of its major characteristics such as antibiotic resistance, metabolic pathways, pathogenicity, and anti-phage resistance [ 17 , 18 ]. With the average Bacillus genome containing around five prophages [ 18 ], it is conceivable that an extensive exploration of prophage sequences paired with some experimental research to prove the prophages’ viability would very soon enable us to significantly increase the number of taxa comprising Bacillus -infecting viruses.…”

Section: Introductionmentioning

confidence: 99%

Novel Bacillus-Infecting Bacteriophage B13—The Founding Member of the Proposed New Genus Bunatrivirus

Kazantseva

Piligrimova

Shadrin

2022

Viruses

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In this work, we describe a novel temperate bacteriophage, Bacillus phage B13. Bacillus-infecting phages are widespread and abundant, though often overlooked including because of their temperate lifestyle. B13 was isolated from its bacterial host via mitomycin C induction. Its host range was determined, and its pH and thermal stability were evaluated. The whole genome of B13 was sequenced and annotated. The genome is 36,864 bp long and contains 53 genes. The tail genes of B13 suggest that the phage has a siphovirus morphotype. It was found both in vitro and in silico that the phage uses the 3′-cos DNA packaging strategy, and the phage genome termini were located. Comparative analyses revealed that B13 has no close relatives and should therefore be assigned to a new viral genus, for which we propose the name Bunatrivirus.

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“…These unfavorable conditions, together with the properties of surface materials, can drive taxonomic variations and functional shifts in the bacterial microbiome 8 . Ecological evidence also supports that environmental filtering can control the bacterial diversity in indoor environments 58 , which may in turn affect the diversity of phages that have a narrow host range 59 . Consistent with the differences in diversity and structure between bacterial communities in air and on surfaces 60 , the airborne and surfaceborne viromes in the present study were distinct.…”

Section: Discussionmentioning

confidence: 93%

Highly host-linked viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution

TONG

Mason

et al. 2022

Preprint

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Viruses in built environments (BEs) raise public health concerns, yet they are generally less studied than bacteria. To better understand viral dynamics in BEs, this study assessed viromes from 11 habitats across four types of BEs with low to high occupancy. The diversity, composition, metabolic functions, and lifestyles of the viromes were found to be habitat dependent. Caudovirales species were ubiquitous on surface habitats in the BEs, and some of them were distinct from those present in other environments. Antimicrobial resistance genes were identified in viruses inhabiting surfaces frequently touched by occupants and in viruses inhabiting occupants’ skin. Diverse CRISPR-Cas immunity systems and anti-CRISPR proteins were found in bacterial hosts and viruses, respectively, consistent with the strongly coupled virus–host links. Evidence of viruses potentially aiding host adaptation in a specific-habitat manner was identified through a unique gene insertion. This work illustrates that virus–host interactions occur frequently in BEs and that viruses are integral members of BE microbiomes.

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Mining of Thousands of Prokaryotic Genomes Reveals High Abundance of Prophages with a Strictly Narrow Host Range

Cited by 33 publications

References 52 publications

Genomic Analysis Unveils the Pervasiveness and Diversity of Prophages Infecting Erwinia Species

Genomic Analysis Unveils the Pervasiveness and Diversity of Prophages Infecting Erwinia Species

Novel Bacillus-Infecting Bacteriophage B13—The Founding Member of the Proposed New Genus Bunatrivirus

Highly host-linked viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution

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