Correction: Corrigendum: Lytic to temperate switching of viral communities

Knowles, Ben; Silveira, Cynthia B.; Bailey, Barbara; Barott, Katie L.; Cantu, Adrian; Cobián-Güemes, Ana G; Coutinho, Felipe H.; Dinsdale, Elizabeth A.; Felts, Ben; Furby, Kathryn A.; George, Emma E.; Green, K. T.; Gregoracci, Gustavo Bueno; Haas, Andreas F.; Haggerty, John M.; Hester, Eric R.; Hisakawa, Nao; Kelly, Linda Wegley; Lim, Yan-Wei; Little, Mark; Luque, Antoni; McDole-Somera, T.; McNair, Katelyn; Oliveira, Louisi Souza de; Quistad, Steven D.; Robinett, N. L.; Sala, Enric; Szűcs, Péter; Sanchez, Savannah E.; Sandin, Stuart A.; Silva, G. G. Z.; Smith, Jennifer E.; Sullivan, Christopher J.; Thompson, Cristiane C.; Vermeij, Mark J. A.; Youle, Merry; Young, Charles W.; Zgliczynski, Brian J.; Brainard, R. E.; Edwards, Robert A.; Nulton, James; Thompson, Fabiano L.; Rohwer, Forest

doi:10.1038/nature19335

Cited by 13 publications

(8 citation statements)

References 1 publication

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“…S20). A similar trend has been seen in other environments (43,44), including the water column of tropical coral reefs, and has been described as Piggyback-the-Winner dynamics (43). Piggyback-the-Winner posits that when VMRs are low, such as in interface and turf algal samples, there are more bacterial cells harboring lysogenic phage.…”

Section: Discussionsupporting

confidence: 59%

A multiomic analysis of in situ coral–turf algal interactions

Roach

Little

Arts

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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Viruses, microbes, and host macroorganisms form ecological units called holobionts. Here, a combination of metagenomic sequencing, metabolomic profiling, and epifluorescence microscopy was used to investigate how the different components of the holobiont including bacteria, viruses, and their associated metabolites mediate ecological interactions between corals and turf algae. The data demonstrate that there was a microbial assemblage unique to the coral-turf algae interface displaying higher microbial abundances and larger microbial cells. This was consistent with previous studies showing that turf algae exudates feed interface and coral-associated microbial communities, often at the detriment of the coral. Further supporting this hypothesis, when the metabolites were assigned a nominal oxidation state of carbon (NOSC), we found that the turf algal metabolites were significantly more reduced (i.e., have higher potential energy) compared to the corals and interfaces. The algae feeding hypothesis was further supported when the ecological outcomes of interactions (e.g., whether coral was winning or losing) were considered. For example, coral holobionts losing the competition with turf algae had higher Bacteroidetes-to-Firmicutes ratios and an elevated abundance of genes involved in bacterial growth and division. These changes were similar to trends observed in the obese human gut microbiome, where overfeeding of the microbiome creates a dysbiosis detrimental to the long-term health of the metazoan host. Together these results show that there are specific biogeochemical changes at coral–turf algal interfaces that predict the competitive outcomes between holobionts and are consistent with algal exudates feeding coral-associated microbes.

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Section: Discussionsupporting

confidence: 59%

A multiomic analysis of in situ coral–turf algal interactions

Roach

Little

Arts

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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“…It should be noted that establishment of lysogeny requires bacteriophage expression of integrase, while excision requires an additional phage-encoded protein called excisionase. Therefore, these two proteins are considered markers of lysogenic infection [15].…”

Section: Integrase/excisionase Identificationmentioning

confidence: 99%

Microbial Diversity and Phage–Host Interactions in the Georgian Coastal Area of the Black Sea Revealed by Whole Genome Metagenomic Sequencing

et al. 2020

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Viruses have the greatest abundance and highest genetic diversity in marine ecosystems. The interactions between viruses and their hosts is one of the hot spots of marine ecology. Besides their important role in various ecosystems, viruses, especially bacteriophages and their gene pool, are of enormous interest for the development of new gene products with high innovation value. Various studies have been conducted in diverse ecosystems to understand microbial diversity and phage–host interactions; however, the Black Sea, especially the Eastern coastal area, remains among the least studied ecosystems in this regard. This study was aimed at to fill this gap by analyzing microbial diversity and bacteriophage–host interactions in the waters of Eastern Black Sea using a metagenomic approach. To this end, prokaryotic and viral metagenomic DNA from two sampling sites, Poti and Gonio, were sequenced on the Illumina Miseq platform and taxonomic and functional profiles of the metagenomes were obtained using various bioinformatics tools. Our metagenomics analyses allowed us to identify the microbial communities, with Proteobacteria, Cyanobacteria, Actinibacteria, and Firmicutes found to be the most dominant bacterial phyla and Synechococcus and Candidatus Pelagibacter phages found to be the most dominant viral groups in the Black Sea. As minor groups, putative phages specific to human pathogens were identified in the metagenomes. We also characterized interactions between the phages and prokaryotic communities by determining clustered regularly interspaced short palindromic repeats (CRISPR), prophage-like sequences, and integrase/excisionase sequences in the metagenomes, along with identification of putative horizontally transferred genes in the viral contigs. In addition, in the viral contig sequences related to peptidoglycan lytic activity were identified as well. This is the first study on phage and prokaryote diversity and their interactions in the Eastern coastal area of the Black Sea using a metagenomic approach.

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“…Bacteriophages are known to be the most abundant biological entities on earth (50). Over billions of years of coevolution, more than 80% of bacterial genomes have become populated with at least one prophage (51,52), also known as molecular imprints, which serve as an untapped arsenal for the discovery of phage-related antimicrobial agents.…”

Section: Discussionmentioning

confidence: 99%

Dimer-monomer transition defines a hyper-thermostable peptidoglycan hydrolase mined from bacterial proteome by lysin-derived antimicrobial peptide-primed screening

Zhang,

Hu,

Zhao

et al. 2024

Preprint

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Phage-derived peptidoglycan hydrolases (i.e., lysins) are considered a promising alternative to traditional antibiotics due to their low risks of resistance and unique mechanisms of action. However, the discovery of these enzymes is often hampered by limited source of available phage genomes. Herein, we report a new strategy to mine novel peptidoglycan hydrolases from bacterial proteomes by lysin-derived antimicrobial peptide-primed screening. As a proof-of-concept, five novel peptidoglycan hydrolases from the Acinetobacter baumannii (PHAb7-PHAb11) were identified using PlyF307 lysin-derived peptide as a template. PHAb10 and PHAb11 showed potent bactericidal activity against a variety of pathogens even after treatment at 100 degrees C for 1 hour, while the other three were thermosensitive. We solved the crystal structures of PHAb8, PHAb10, and PHAb11 and unveiled that hyper-thermostable PHAb10 underwent a unique folding-refolding thermodynamic scheme mediated by the dimer-monomer transition, while thermosensitive PHAb8 formed a monomer. Two mouse models of bacterial infection further demonstrated the safety and efficacy of PHAb10. Altogether, our antimicrobial peptide-primed strategy provides new clues for the discovery of novel antimicrobial drugs with therapeutic promise.

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Correction: Corrigendum: Lytic to temperate switching of viral communities

Cited by 13 publications

References 1 publication

A multiomic analysis of in situ coral–turf algal interactions

A multiomic analysis of in situ coral–turf algal interactions

Microbial Diversity and Phage–Host Interactions in the Georgian Coastal Area of the Black Sea Revealed by Whole Genome Metagenomic Sequencing

Dimer-monomer transition defines a hyper-thermostable peptidoglycan hydrolase mined from bacterial proteome by lysin-derived antimicrobial peptide-primed screening

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