Expanding the Diversity of Myoviridae Phages Infecting Lactobacillus Plantarum - A Novel Lineage of Lactobacillus Phages Comprising Five New Members

Kyrkou, Ifigeneia; Carstens, Alexander Byth; Ellegaard-Jensen, Lea; Kot, Witold; Zervas, Athanasios; Neve, Horst; Hansen, Lars Hestbjerg

doi:10.20944/preprints201812.0026.v1

Cited by 4 publications

(4 citation statements)

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“…The ferritin-like enzymes encoded by these phages belong to two families, namely, DNA protecting proteins (DPS) and manganese-catalases. Manganese-catalases have not been documented in phage genomes, and DPS-like enzymes have only been observed in seven Lactobacillus- infecting phages [ 97 ]. Both enzymes are involved in the tolerance of anaerobes to oxidative stress.…”

Section: Resultsmentioning

confidence: 99%

Thousands of previously unknown phages discovered in whole-community human gut metagenomes

et al. 2021

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Background Double-stranded DNA bacteriophages (dsDNA phages) play pivotal roles in structuring human gut microbiomes; yet, the gut virome is far from being fully characterized, and additional groups of phages, including highly abundant ones, continue to be discovered by metagenome mining. A multilevel framework for taxonomic classification of viruses was recently adopted, facilitating the classification of phages into evolutionary informative taxonomic units based on hallmark genes. Together with advanced approaches for sequence assembly and powerful methods of sequence analysis, this revised framework offers the opportunity to discover and classify unknown phage taxa in the human gut. Results A search of human gut metagenomes for circular contigs encoding phage hallmark genes resulted in the identification of 3738 apparently complete phage genomes that represent 451 putative genera. Several of these phage genera are only distantly related to previously identified phages and are likely to found new families. Two of the candidate families, “Flandersviridae” and “Quimbyviridae”, include some of the most common and abundant members of the human gut virome that infect Bacteroides, Parabacteroides, and Prevotella. The third proposed family, “Gratiaviridae,” consists of less abundant phages that are distantly related to the families Autographiviridae, Drexlerviridae, and Chaseviridae. Analysis of CRISPR spacers indicates that phages of all three putative families infect bacteria of the phylum Bacteroidetes. Comparative genomic analysis of the three candidate phage families revealed features without precedent in phage genomes. Some “Quimbyviridae” phages possess Diversity-Generating Retroelements (DGRs) that generate hypervariable target genes nested within defense-related genes, whereas the previously known targets of phage-encoded DGRs are structural genes. Several “Flandersviridae” phages encode enzymes of the isoprenoid pathway, a lipid biosynthesis pathway that so far has not been known to be manipulated by phages. The “Gratiaviridae” phages encode a HipA-family protein kinase and glycosyltransferase, suggesting these phages modify the host cell wall, preventing superinfection by other phages. Hundreds of phages in these three and other families are shown to encode catalases and iron-sequestering enzymes that can be predicted to enhance cellular tolerance to reactive oxygen species. Conclusions Analysis of phage genomes identified in whole-community human gut metagenomes resulted in the delineation of at least three new candidate families of Caudovirales and revealed diverse putative mechanisms underlying phage-host interactions in the human gut. Addition of these phylogenetically classified, diverse, and distinct phages to public databases will facilitate taxonomic decomposition and functional characterization of human gut viromes.

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Section: Resultsmentioning

confidence: 99%

Thousands of previously unknown phages discovered in whole-community human gut metagenomes

et al. 2021

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“…Two ORFs of vB_EcoA_RDN8.1 are encoded for HNH homing endonuclease proteins, which confer an advantage during mixed infections by specifically cleaving the DNA of a competing phage (Stoddard, 2011). These proteins are encoded as free-standing genes within introns or self-splicing intein (Kyrkou et al, 2019). It has been observed in an earlier study that nuclease-associated proteins like 'HNH proteins' are also crucial components of the terminase packaging reaction of E. coli phage HK97 (Kala et al, 2014).…”

Section: Citrobactermentioning

confidence: 99%

Characterization, genome analysis and in vitro activity of a novel phage vB_EcoA_RDN8.1 active against multi-drug resistant and extensively drug-resistant biofilm-forming uropathogenic Escherichia coli isolates, India

Chaudhary

Mohan

Mavuduru

et al. 2022

Journal of Applied Microbiology

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Aim:We aimed to study host range, stability, genome and antibiofilm activity of a novel phage vB_EcoA_RDN8.1 active against multi-drug resistant (MDR) and extensively drug-resistant (XDR) biofilm-forming uropathogenic Escherichia coli isolates. Methods and Results: A novel lytic phage vB_EcoA_RDN8.1 active against UPEC strains resistant to third-generation cephalosporins, fluoroquinolones, aminoglycosides, imipenem, beta-lactamase inhibitor combination and polymyxins was isolated from community raw sewage water of Chandigarh. It exhibited a clear plaque morphology and a burst size of 250. In the time-kill assay, the maximum amount of killing was achieved at MOI 1.0. vB_EcoA_RDN8.1 belongs to the family Autographiviridae, has a genome size of 39.5 kb with a GC content of 51.6%. It was stable over a wide range of temperatures and pH. It was able to inhibit biofilm formation which may be related to an endolysin encoded by ORF 19. Conclusions: The vB_EcoA_RDN8.1 is a novel lytic phage that has the potential for inclusion into phage cocktails being developed for the treatment of urinary tract infections (UTIs) caused by highly drug-resistant UPEC. Significance and Impact of the Study: We provide a detailed characterization of a novel lytic Escherichia phage with antibiofilm activity having a potential application against MDR and XDR UPEC causing UTIs.

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“…The ferritin-like enzymes encoded by these phages belong to two families, namely, DNA protecting proteins (DPS) and manganese-catalases. Manganese-catalases have not been documented in phage genomes and DPS-like enzymes have only been observed in seven Lactobacillus-infecting phages [96]. Both enzymes are involved in the tolerance of anaerobes to oxidative stress.…”

Section: Selection Of Candidate Families For Comparative Genomicsmentioning

confidence: 99%

Thousands of previously unknown phages discovered in whole-community human gut metagenomes

Benler

Yutin

Antipov

et al. 2021

Preprint

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Background: Double-stranded DNA bacteriophages (dsDNA phages) play pivotal roles in structuring human gut microbiomes; yet, the gut virome is far from being fully characterized, and additional groups of phages, including highly abundant ones, continue to be discovered by metagenome mining. A multilevel framework for taxonomic classification of viruses was recently adopted, facilitating the classification of phages into evolutionary informative taxonomic units based on hallmark genes. Together with advanced approaches for sequence assembly and powerful methods of sequence analysis, this revised framework offers the opportunity to discover and classify unknown phage taxa in the human gut.Results: A search of human gut metagenomes for circular contigs encoding phage hallmark genes resulted in the identification of 3,738 apparently complete phage genomes that represent 451 putative genera. Several of these phage genera are only distantly related to previously identified phages and are likely to found new families. Two of the candidate families, “Flandersviridae” and “Quimbyviridae”, include some of the most common and abundant members of the human gut virome that infect Bacteroides, Parabacteroides and Prevotella. The third proposed family, “Gratiaviridae”, consists of less abundant phages that are distantly related to the families Autographiviridae, Drexlerviridae and Chaseviridae. Analysis of CRISPR spacers indicates that phages of all three putative families infect bacteria of the phylum Bacteroidetes. Comparative genomic analysis of the three candidate phage families revealed features without precedent in phage genomes. Some “Quimbyviridae” phages possess Diversity-Generating Retroelements (DGRs) that generate hypervariable target genes nested within defense-related genes, whereas the previously known targets of phage-encoded DGRs are structural genes. Several “Flandersviridae” phages encode enzymes of the isoprenoid pathway, a lipid biosynthesis pathway that so far has not been known to be manipulated by phages. The “Gratiaviridae” phages encode a HipA-family protein kinase and glycosyltransferase, suggesting these phages modify the host cell wall, preventing superinfection by other phages. Hundreds of phages in these three and other families are shown to encode catalases and iron-sequestering enzymes that can be predicted to enhance cellular tolerance to reactive oxygen species.Conclusions: Analysis of phage genomes identified in whole-community human gut metagenomes resulted in the delineation of at least three new candidate families of Caudovirales and revealed diverse putative mechanisms underlying phage-host interactions in the human gut. Addition of these phylogenetically classified, diverse and distinct phages to public databases will facilitate taxonomic decomposition and functional characterization of human gut viromes.

show abstract

Expanding the Diversity of Myoviridae Phages Infecting Lactobacillus Plantarum - A Novel Lineage of Lactobacillus Phages Comprising Five New Members

Cited by 4 publications

References 77 publications

Thousands of previously unknown phages discovered in whole-community human gut metagenomes

Thousands of previously unknown phages discovered in whole-community human gut metagenomes

Characterization, genome analysis and in vitro activity of a novel phage vB_EcoA_RDN8.1 active against multi-drug resistant and extensively drug-resistant biofilm-forming uropathogenic Escherichia coli isolates, India

Thousands of previously unknown phages discovered in whole-community human gut metagenomes

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