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Naknaen A, Samernate T, Saeju P, Nonejuie P, Chaikeeratisak V. Nucleus-forming jumbophage PhiKZ therapeutically outcompetes non-nucleus-forming jumbophage Callisto. iScience 2024; 27:109790. [PMID: 38726363 PMCID: PMC11079468 DOI: 10.1016/j.isci.2024.109790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 03/21/2024] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
With the recent resurgence of phage therapy in modern medicine, jumbophages are currently under the spotlight due to their numerous advantages as anti-infective agents. However, most significant discoveries to date have primarily focused on nucleus-forming jumbophages, not their non-nucleus-forming counterparts. In this study, we compare the biological characteristics exhibited by two genetically diverse jumbophages: 1) the well-studied nucleus-forming jumbophage, PhiKZ; and 2) the newly discovered non-nucleus-forming jumbophage, Callisto. Single-cell infection studies further show that Callisto possesses different replication machinery, resulting in a delay in phage maturation compared to that of PhiKZ. The therapeutic potency of both phages was examined in vitro and in vivo, demonstrating that PhiKZ holds certain superior characteristics over Callisto. This research sheds light on the importance of the subcellular infection machinery and the organized progeny maturation process, which could potentially provide valuable insight in the future development of jumbophage-based therapeutics.
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Affiliation(s)
- Ampapan Naknaen
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Thanadon Samernate
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Panida Saeju
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Poochit Nonejuie
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
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2
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Putzeys L, Wicke L, Boon M, van Noort V, Vogel J, Lavigne R. Refining the transcriptional landscapes for distinct clades of virulent phages infecting Pseudomonas aeruginosa. Microlife 2024; 5:uqae002. [PMID: 38444699 PMCID: PMC10914365 DOI: 10.1093/femsml/uqae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/24/2024] [Accepted: 02/27/2024] [Indexed: 03/07/2024]
Abstract
The introduction of high-throughput sequencing has resulted in a surge of available bacteriophage genomes, unveiling their tremendous genomic diversity. However, our current understanding of the complex transcriptional mechanisms that dictate their gene expression during infection is limited to a handful of model phages. Here, we applied ONT-cappable-seq to reveal the transcriptional architecture of six different clades of virulent phages infecting Pseudomonas aeruginosa. This long-read microbial transcriptomics approach is tailored to globally map transcription start and termination sites, transcription units, and putative RNA-based regulators on dense phage genomes. Specifically, the full-length transcriptomes of LUZ19, LUZ24, 14-1, YuA, PAK_P3, and giant phage phiKZ during early, middle, and late infection were collectively charted. Beyond pinpointing traditional promoter and terminator elements and transcription units, these transcriptional profiles provide insights in transcriptional attenuation and splicing events and allow straightforward validation of Group I intron activity. In addition, ONT-cappable-seq data can guide genome-wide discovery of novel regulatory element candidates, including noncoding RNAs and riboswitches. This work substantially expands the number of annotated phage-encoded transcriptional elements identified to date, shedding light on the intricate and diverse gene expression regulation mechanisms in Pseudomonas phages, which can ultimately be sourced as tools for biotechnological applications in phage and bacterial engineering.
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Affiliation(s)
- Leena Putzeys
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
| | - Laura Wicke
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
| | - Vera van Noort
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Jörg Vogel
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
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3
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Silva MD, Melo LDR. Phage-Host Interaction Analysis Using Flow Cytometry. Methods Mol Biol 2024; 2734:133-140. [PMID: 38066366 DOI: 10.1007/978-1-0716-3523-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Phage-host interactions are commonly evaluated by culture-based methods. However, these techniques are very laborious and time-consuming. Therefore, other time-efficient, not labor-intensive, and cost-effective methods have been developed.This chapter describes the methodology used to assess the susceptibility of planktonic cultures of bacteria to phage infection and to study their interactions over time by flow cytometry.
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Affiliation(s)
- Maria Daniela Silva
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga & Guimarães, Portugal
| | - Luís D R Melo
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal.
- LABBELS - Associate Laboratory, Braga & Guimarães, Portugal.
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4
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Putzeys L, Intizar D, Lavigne R, Boon M. Obtaining Detailed Phage Transcriptomes Using ONT-Cappable-Seq. Methods Mol Biol 2024; 2793:207-235. [PMID: 38526733 DOI: 10.1007/978-1-0716-3798-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Detailed transcription maps of bacteriophages are not usually explored, limiting our understanding of molecular phage biology and restricting their exploitation and engineering. The ONT-cappable-seq method described here brings phage transcriptomics to the accessible nanopore sequencing platform and provides an affordable and more detailed overview of transcriptional features compared to traditional RNA-seq experiments. With ONT-cappable-seq, primary transcripts are specifically capped, enriched, and prepared for long-read sequencing on the nanopore sequencing platform. This enables end-to-end sequencing of unprocessed transcripts covering both phage and host genome, thus providing insight on their operons. The subsequent analysis pipeline makes it possible to rapidly identify the most important transcriptional features such as transcription start and stop sites. The obtained data can thus provide a comprehensive overview of the transcription by your phage of interest.
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Affiliation(s)
- Leena Putzeys
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Danish Intizar
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium.
| | - Maarten Boon
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
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5
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Montso PK, Kropinski AM, Mokoena F, Pierneef RE, Mlambo V, Ateba CN. Comparative genomics and proteomics analysis of phages infecting multi-drug resistant Escherichia coli O177 isolated from cattle faeces. Sci Rep 2023; 13:21426. [PMID: 38052835 PMCID: PMC10698182 DOI: 10.1038/s41598-023-48788-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023] Open
Abstract
The increasing prevalence of antimicrobial-resistant (AMR) pathogens has become a major global health concern. To address this challenge, innovative strategies such as bacteriophage therapy must be optimised. Genomic characterisation is a crucial step in identifying suitable phage candidates for combating AMR pathogens. The aim of this study was to characterise seven phages that infect the Escherichia coli O177 strain using a whole genome sequencing. The analysis of genome sequences revealed that these phages had linear dsDNA, with genome sizes spanning from 136, 483 to 166,791 bp and GC content varying from 35.39 to 43.63%. Taxonomically, the phages were classified under three different subfamilies (Stephanstirmvirinae, Tevenvirinae, and Vequintavirinae) and three genera (Phapecoctavirus, Tequatrovirus, and Vequintavirus) within the class Caudoviricetes. In silico PhageAI analysis predicted that all the phages were virulent, with confidence levels between 96.07 and 97.26%. The phage genomes contained between 66 and 82 ORFs, which encode hypothetical and putative functional proteins. In addition, the phage genomes contained core genes associated with molecular processes such as DNA replication, transcription modulation, nucleotide metabolism, phage structure (capsid and tail), and lysis. None of the genomes carried genes associated with undesirable traits such as integrase, antimicrobial resistance, virulence, and toxins. The study revealed high genome and proteome homology among E. coli O177 phages and other known Escherichia phages. The results suggest that the seven phages are new members of the genera Phapecoctavirus, Tequatrovirus, and Vequintavirus under the subfamilies Stephanstirmvirinae, Tevenvirinae, and Vequintavirinae, respectively.
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Affiliation(s)
- Peter Kotsoana Montso
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa.
- Department of Microbiology, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa.
| | - Andrew M Kropinski
- Department Food Science, and Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Fortunate Mokoena
- Department of Biochemistry, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Rian Ewald Pierneef
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0001, South Africa
- Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, 0001, South Africa
- SARChI Chair: Marine Microbiomics, Microbiome@UP, Department of Biochemistry, Genetics and Microbiology, University of Pretoria (UP), Hatfield, Pretoria, South Africa
| | - Victor Mlambo
- Faculty of Agriculture and Natural Sciences, School of Agricultural Sciences, University of Mpumalanga, Mbombela, 1200, South Africa
| | - Collins Njie Ateba
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
- Department of Microbiology, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
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6
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Śliwka P, Weber-Dąbrowska B, Żaczek M, Kuźmińska-Bajor M, Dusza I, Skaradzińska A. Characterization and Comparative Genomic Analysis of Three Virulent E. coli Bacteriophages with the Potential to Reduce Antibiotic-Resistant Bacteria in the Environment. Int J Mol Sci 2023; 24:ijms24065696. [PMID: 36982770 PMCID: PMC10059673 DOI: 10.3390/ijms24065696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/26/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
The emerging global crisis of antibiotic resistance demands new alternative antibacterial solutions. Although bacteriophages have been used to combat bacterial infections for over a century, a dramatic boost in phage studies has recently been observed. In the development of modern phage applications, a scientific rationale is strongly required and newly isolated phages need to be examined in detail. In this study, we present the full characterization of bacteriophages BF9, BF15, and BF17, with lytic activity against extended-spectrum β-lactamases (ESBLs)- and AmpC β-lactamases (AmpC)-producing Escherichia coli, the prevalence of which has increased significantly in livestock in recent decades, representing a great hazard to food safety and a public health risk. Comparative genomic and phylogenetic analysis indicated that BF9, BF15, and BF17 represent the genera Dhillonvirus, Tequatrovirus, and Asteriusvirus, respectively. All three phages significantly reduced in vitro growth of their bacterial host and retained the ability to lyse bacteria after preincubation at wide ranges of temperature (−20–40 °C) and pH (5–9). The results described herein indicate the lytic nature of BF9, BF15, and BF17, which, along with the absence of genes encoding toxins and bacterial virulence factors, represents an undoubted asset in terms of future phage application.
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Affiliation(s)
- Paulina Śliwka
- Department of Biotechnology and Food Microbiology, Wrocław University of Environmental and Life Sciences, 50-375 Wrocław, Poland
| | - Beata Weber-Dąbrowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland
| | - Maciej Żaczek
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland
| | - Marta Kuźmińska-Bajor
- Department of Biotechnology and Food Microbiology, Wrocław University of Environmental and Life Sciences, 50-375 Wrocław, Poland
| | - Izabela Dusza
- Department of Biotechnology and Food Microbiology, Wrocław University of Environmental and Life Sciences, 50-375 Wrocław, Poland
| | - Aneta Skaradzińska
- Department of Biotechnology and Food Microbiology, Wrocław University of Environmental and Life Sciences, 50-375 Wrocław, Poland
- Correspondence: ; Tel.: +48-71-320-7791
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7
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Huiting E, Cao X, Ren J, Athukoralage JS, Luo Z, Silas S, An N, Carion H, Zhou Y, Fraser JS, Feng Y, Bondy-Denomy J. Bacteriophages inhibit and evade cGAS-like immune function in bacteria. Cell 2023; 186:864-876.e21. [PMID: 36750095 PMCID: PMC9975087 DOI: 10.1016/j.cell.2022.12.041] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 10/29/2022] [Accepted: 12/21/2022] [Indexed: 02/09/2023]
Abstract
A fundamental strategy of eukaryotic antiviral immunity involves the cGAS enzyme, which synthesizes 2',3'-cGAMP and activates the effector STING. Diverse bacteria contain cGAS-like enzymes that produce cyclic oligonucleotides and induce anti-phage activity, known as CBASS. However, this activity has only been demonstrated through heterologous expression. Whether bacteria harboring CBASS antagonize and co-evolve with phages is unknown. Here, we identified an endogenous cGAS-like enzyme in Pseudomonas aeruginosa that generates 3',3'-cGAMP during phage infection, signals to a phospholipase effector, and limits phage replication. In response, phages express an anti-CBASS protein ("Acb2") that forms a hexamer with three 3',3'-cGAMP molecules and reduces phospholipase activity. Acb2 also binds to molecules produced by other bacterial cGAS-like enzymes (3',3'-cUU/UA/UG/AA) and mammalian cGAS (2',3'-cGAMP), suggesting broad inhibition of cGAS-based immunity. Upon Acb2 deletion, CBASS blocks lytic phage replication and lysogenic induction, but rare phages evade CBASS through major capsid gene mutations. Altogether, we demonstrate endogenous CBASS anti-phage function and strategies of CBASS inhibition and evasion.
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Affiliation(s)
- Erin Huiting
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Xueli Cao
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jie Ren
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Januka S Athukoralage
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Zhaorong Luo
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Sukrit Silas
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Na An
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Héloïse Carion
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yu Zhou
- National Institute of Biological Sciences, Beijing 102206, China
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yue Feng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Innovative Genomics Institute, Berkeley, CA 94720, USA.
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8
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Zhang B, Xu J, He X, Tong Y, Ren H. Interactions between Jumbo Phage SA1 and Staphylococcus: A Global Transcriptomic Analysis. Microorganisms 2022; 10:1590. [PMID: 36014008 DOI: 10.3390/microorganisms10081590] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/30/2022] [Accepted: 08/02/2022] [Indexed: 01/21/2023] Open
Abstract
Staphylococcus aureus (S. aureus) is an important zoonotic pathogen that poses a serious health concern to humans and cattle worldwide. Although it has been proven that lytic phages may successfully kill S. aureus, the interaction between the host and the phage has yet to be thoroughly investigated, which will likely limit the clinical application of phage. Here, RNA sequencing (RNA-seq) was used to examine the transcriptomics of jumbo phage SA1 and Staphylococcus JTB1-3 during a high multiplicity of infection (MOI) and RT-qPCR was used to confirm the results. The RNA-seq analysis revealed that phage SA1 took over the transcriptional resources of the host cells and that the genes were categorized as early, middle, and late, based on the expression levels during infection. A minor portion of the resources of the host was employed to enable phage replication after infection because only 35.73% (997/2790) of the host genes were identified as differentially expressed genes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the phage infection mainly affected the nucleotide metabolism, protein metabolism, and energy-related metabolism of the host. Moreover, the expression of the host genes involved in anti-phage systems, virulence, and drug resistance significantly changed during infection. This research gives a fresh understanding of the relationship between jumbo phages and their Gram-positive bacteria hosts and provides a reference for studying phage treatment and antibiotics.
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9
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Finstrlová A, Mašlaňová I, Blasdel Reuter BG, Doškař J, Götz F, Pantůček R. Global Transcriptomic Analysis of Bacteriophage-Host Interactions between a Kayvirus Therapeutic Phage and Staphylococcus aureus. Microbiol Spectr 2022; 10:e0012322. [PMID: 35435752 PMCID: PMC9241854 DOI: 10.1128/spectrum.00123-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/28/2022] [Indexed: 11/20/2022] Open
Abstract
Kayviruses are polyvalent broad host range staphylococcal phages with a potential to combat staphylococcal infections. However, the implementation of rational phage therapy in medicine requires a thorough understanding of the interactions between bacteriophages and pathogens at omics level. To evaluate the effect of a phage used in therapy on its host bacterium, we performed differential transcriptomic analysis by RNA-Seq from bacteriophage K of genus Kayvirus infecting two Staphylococcus aureus strains, prophage-less strain SH1000 and quadruple lysogenic strain Newman. The temporal transcriptional profile of phage K was comparable in both strains except for a few loci encoding hypothetical proteins. Stranded sequencing revealed transcription of phage noncoding RNAs that may play a role in the regulation of phage and host gene expression. The transcriptional response of S. aureus to phage K infection resembles a general stress response with differential expression of genes involved in a DNA damage response. The host transcriptional changes involved upregulation of nucleotide, amino acid and energy synthesis and transporter genes and downregulation of host transcription factors. The interaction of phage K with variable genetic elements of the host showed slight upregulation of gene expression of prophage integrases and antirepressors. The virulence genes involved in adhesion and immune evasion were only marginally affected, making phage K suitable for therapy. IMPORTANCE Bacterium Staphylococcus aureus is a common human and veterinary pathogen that causes mild to life-threatening infections. As strains of S. aureus are becoming increasingly resistant to multiple antibiotics, the need to search for new therapeutics is urgent. A promising alternative to antibiotic treatment of staphylococcal infections is a phage therapy using lytic phages from the genus Kayvirus. Here, we present a comprehensive view on the phage-bacterium interactions on transcriptomic level that improves the knowledge of molecular mechanisms underlying the Kayvirus lytic action. The results will ensure safer usage of the phage therapeutics and may also serve as a basis for the development of new antibacterial strategies.
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Affiliation(s)
- Adéla Finstrlová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Ivana Mašlaňová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | | | - Jiří Doškař
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Friedrich Götz
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany
| | - Roman Pantůček
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
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10
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Zhang B, Sun H, Zhao F, Wang Q, Pan Q, Tong Y, Ren H. Characterization and Genomic Analysis of a Novel Jumbo Bacteriophage vB_StaM_SA1 Infecting Staphylococcus aureus With Two Lysins. Front Microbiol 2022; 13:856473. [PMID: 35572667 PMCID: PMC9096886 DOI: 10.3389/fmicb.2022.856473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/04/2022] [Indexed: 11/30/2022] Open
Abstract
The development of new antimicrobial agents is critically needed due to the alarming increase in antibiotic resistance in bacterial pathogens. Phages have been widely considered as effective alternatives to antibiotics. A novel phage vB_StaM_SA1 (hereinafter as SA1) that can infect multiple Staphylococcus strains was isolated from untreated sewage of a pig farm, which belonged to Myoviridae family. At MOI of 0.1, the latent period of phage SA1 was 55 min, and the final titer reached about 109 PFU/mL. The genome of phage SA1 was 260,727 bp, indicating that it can be classified as a jumbo phage. The genome of SA1 had 258 ORFs and a serine tRNA, while only 53 ORFs were annotated with functions. Phage SA1 contained a group of core genes that was characterized by multiple RNA polymerase subunits and also found in phiKZ-related jumbo phages. The phylogenetic tree showed that phage SA1 was a phiKZ-related phage and was closer to jumbo phages compared with Staphylococcus phages with small genome. Three proteins (lys4, lys210, and lys211) were predicted to be associated with lysins, and two proteins with lytic function were verified by recombinant expression and bacterial survival test. Both lys210 and lys211 possessed efficient bactericidal ability, and lys210 could lyse all test strains. The results show that phage SA1 and lys210/lys211 could be potentially used as antibiotic agents to treat Staphylococcus infection.
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Affiliation(s)
- Bingyan Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huzhi Sun
- Qingdao Phagepharm Bio-tech Co., Ltd., Qingdao, China
| | - Feiyang Zhao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Qian Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Qiang Pan
- Qingdao Phagepharm Bio-tech Co., Ltd., Qingdao, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huiying Ren
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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11
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Putzeys L, Boon M, Lammens EM, Kuznedelov K, Severinov K, Lavigne R. Development of ONT-cappable-seq to unravel the transcriptional landscape of Pseudomonas phages. Comput Struct Biotechnol J 2022; 20:2624-2638. [PMID: 35685363 PMCID: PMC9163698 DOI: 10.1016/j.csbj.2022.05.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/16/2022] [Accepted: 05/16/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Leena Putzeys
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Eveline-Marie Lammens
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | | | | | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
- Corresponding author.
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12
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Melo LDR, Monteiro R, Pires DP, Azeredo J. Phage-Host Interaction Analysis by Flow Cytometry Allows for Rapid and Efficient Screening of Phages. Antibiotics (Basel) 2022; 11:antibiotics11020164. [PMID: 35203767 PMCID: PMC8868278 DOI: 10.3390/antibiotics11020164] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 01/27/2023] Open
Abstract
Recently, phages have become popular as an alternative to antibiotics. This increased demand for phage therapy needs rapid and efficient methods to screen phages infecting specific hosts. Existing methods are time-consuming, and for clinical purposes, novel, quick, and reliable screening methods are highly needed. Flow cytometry (FC) allows a quick differentiation and enumeration of bacterial cell populations and has been used to assess in vitro the activity of antimicrobial compounds. In this work, we propose FC as a rapid and reliable method to assess the susceptibility of a bacterial population to phage infection. For that, the interaction of phages vB_PaeM_CEB_DP1 and vB_PaeP_PE3 with Pseudomonas aeruginosa PAO1 was characterized by FC. Synchronous infection assays were performed, and samples were collected at different time points and stained with SYTO BC and PI before analysis. Part of the collected samples was used to characterize the expression of early, middle, and late genes by qPCR. Both FC and qPCR results were correlated with phage propagation assays. Results showed that SYTO BC median fluorescence intensity (MFI) values increased in the first 25 min of PE3 and DP1 infection. The increase of fluorescence is due to the expression of phage genes observed by qPCR. Since SYTO BC MFI values increase with gene expression, it allows the determination of host susceptibility to a phage in a short period of time, avoiding false positives caused by lysis from without. In conclusion, this method may allow for a quick and high-throughput real-time screening of different phages to a specific host, which can be crucial for a quick phage selection in clinical practice.
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Affiliation(s)
- Luís D. R. Melo
- LIBRO—Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, Campus de Gualtar, University of Minho, 4700-057 Braga, Portugal; (R.M.); (D.P.P.)
- LABBELS—Associate Laboratory, Braga, 4800-122 Guimarães, Portugal
- Correspondence: (L.D.R.M.); (J.A.); Tel.: +351-253-601-989 (L.D.R.M.); +351-253-604-414 (J.A.)
| | - Rodrigo Monteiro
- LIBRO—Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, Campus de Gualtar, University of Minho, 4700-057 Braga, Portugal; (R.M.); (D.P.P.)
- LABBELS—Associate Laboratory, Braga, 4800-122 Guimarães, Portugal
| | - Diana P. Pires
- LIBRO—Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, Campus de Gualtar, University of Minho, 4700-057 Braga, Portugal; (R.M.); (D.P.P.)
- LABBELS—Associate Laboratory, Braga, 4800-122 Guimarães, Portugal
| | - Joana Azeredo
- LIBRO—Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, Campus de Gualtar, University of Minho, 4700-057 Braga, Portugal; (R.M.); (D.P.P.)
- LABBELS—Associate Laboratory, Braga, 4800-122 Guimarães, Portugal
- Correspondence: (L.D.R.M.); (J.A.); Tel.: +351-253-601-989 (L.D.R.M.); +351-253-604-414 (J.A.)
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13
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Lood C, Haas PJ, van Noort V, Lavigne R. Shopping for phages? Unpacking design rules for therapeutic phage cocktails. Curr Opin Virol 2021; 52:236-243. [PMID: 34971929 DOI: 10.1016/j.coviro.2021.12.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/06/2021] [Accepted: 12/10/2021] [Indexed: 12/11/2022]
Abstract
In bacteriophage therapy, the combination of different phages into a single cocktail is of critical importance to overcome the narrow host range of single phage isolates. Today, the design of therapeutic cocktails is often akin to a black box and relies largely on intuition and (pre-)availability of isolates in local collections. Here we show that straightforward host range analysis can disclose design rules and we propose to apply/translate a data mining approach, historically applied in the field of marketing ('shopping cart analysis') to explore patterns in phage combinations. The technique is broadly applicable to host range datasets and can serve in combination with other molecular-based approaches to propose rationales for phage cocktail design.
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Affiliation(s)
- Cédric Lood
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium; Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, Laboratory of Computational Systems Biology, KU Leuven, Leuven, Belgium.
| | - Pieter-Jan Haas
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Vera van Noort
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, Laboratory of Computational Systems Biology, KU Leuven, Leuven, Belgium; Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
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14
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Lood C, Boeckaerts D, Stock M, De Baets B, Lavigne R, van Noort V, Briers Y. Digital phagograms: predicting phage infectivity through a multilayer machine learning approach. Curr Opin Virol 2021; 52:174-181. [PMID: 34952265 DOI: 10.1016/j.coviro.2021.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/26/2021] [Accepted: 12/04/2021] [Indexed: 12/19/2022]
Abstract
Machine learning has been broadly implemented to investigate biological systems. In this regard, the field of phage biology has embraced machine learning to elucidate and predict phage-host interactions, based on receptor-binding proteins, (anti-)defense systems, prophage detection, and life cycle recognition. Here, we highlight the enormous potential of integrating information from omics data with insights from systems biology to better understand phage-host interactions. We conceptualize and discuss the potential of a multilayer model that mirrors the phage infection process, integrating adsorption, bacterial pan-immune components and hijacking of the bacterial metabolism to predict phage infectivity. In the future, this model can offer insights into the underlying mechanisms of the infection process, and digital phagograms can support phage cocktail design and phage engineering.
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Affiliation(s)
- Cédric Lood
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium; Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Dimitri Boeckaerts
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium; KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Michiel Stock
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium; BIOBIX, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Bernard De Baets
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium.
| | - Vera van Noort
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium; Institute of Biology, Leiden University, Leiden, The Netherlands.
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium.
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15
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Malone LM, Hampton HG, Morgan XC, Fineran PC. Type I CRISPR-Cas provides robust immunity but incomplete attenuation of phage-induced cellular stress. Nucleic Acids Res 2021; 50:160-174. [PMID: 34928385 PMCID: PMC8754663 DOI: 10.1093/nar/gkab1210] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/09/2021] [Accepted: 11/23/2021] [Indexed: 11/14/2022] Open
Abstract
During infection, phages manipulate bacteria to redirect metabolism towards viral proliferation. To counteract phages, some bacteria employ CRISPR-Cas systems that provide adaptive immunity. While CRISPR-Cas mechanisms have been studied extensively, their effects on both the phage and the host during phage infection remains poorly understood. Here, we analysed the infection of Serratia by a siphovirus (JS26) and the transcriptomic response with, or without type I-E or I-F CRISPR-Cas immunity. In non-immune Serratia, phage infection altered bacterial metabolism by upregulating anaerobic respiration and amino acid biosynthesis genes, while flagella production was suppressed. Furthermore, phage proliferation required a late-expressed viral Cas4 homologue, which did not influence CRISPR adaptation. While type I-E and I-F immunity provided robust defence against phage infection, phage development still impacted the bacterial host. Moreover, DNA repair and SOS response pathways were upregulated during type I immunity. We also discovered that the type I-F system is controlled by a positive autoregulatory feedback loop that is activated upon phage targeting during type I-F immunity, leading to a controlled anti-phage response. Overall, our results provide new insight into phage-host dynamics and the impact of CRISPR immunity within the infected cell.
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Affiliation(s)
- Lucia M Malone
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Hannah G Hampton
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Xochitl C Morgan
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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16
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Rangel-Pineros G, Millard A, Michniewski S, Scanlan D, Sirén K, Reyes A, Petersen B, Clokie MR, Sicheritz-Pontén T. From Trees to Clouds: PhageClouds for Fast Comparison of ∼640,000 Phage Genomic Sequences and Host-Centric Visualization Using Genomic Network Graphs. Phage (New Rochelle) 2021; 2:194-203. [PMID: 36147515 PMCID: PMC9041511 DOI: 10.1089/phage.2021.0008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Background: Fast and computationally efficient strategies are required to explore genomic relationships within an increasingly large and diverse phage sequence space. Here, we present PhageClouds, a novel approach using a graph database of phage genomic sequences and their intergenomic distances to explore the phage genomic sequence space. Methods: A total of 640,000 phage genomic sequences were retrieved from a variety of databases and public virome assemblies. Intergenomic distances were calculated with dashing, an alignment-free method suitable for handling massive data sets. These data were used to build a Neo4j® graph database. Results: PhageClouds supported the search of related phages among all complete phage genomes from GenBank for a single query phage in just 10 s. Moreover, PhageClouds expanded the number of closely related phage sequences detected for both finished and draft phage genomes, in comparison with searches exclusively targeting phage entries from GenBank. Conclusions: PhageClouds is a novel resource that will facilitate the analysis of phage genomic sequences and the characterization of assembled phage genomes.
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Affiliation(s)
- Guillermo Rangel-Pineros
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogota, Colombia
| | - Andrew Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Slawomir Michniewski
- Warwick Medical School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - David Scanlan
- Warwick Medical School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Kimmo Sirén
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogota, Colombia
| | - Bent Petersen
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Martha R.J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Thomas Sicheritz-Pontén
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Address correspondence to: Thomas Sicheritz-Pontén, PhD, Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, Bygning 7, Room 7.1.20a, Copenhagen 1353, Denmark
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17
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Abstract
The bacteriophages have been explored at a huge scale as a model system for their applications in many biological-related fields. Jumbo phages with a large genome size from 200 to 500 kbp were not previously assigned a great value, and characterized by complex structures coupled with large virions with a wide variety of hosts. The origin of most of the jumbo phages was not well understood; however, many other prominent features have been discovered recently. In the current review, we strive to unearth the most advanced characteristics of jumbo phages, particularly their significance and structural organization that holds immense value to the viral life cycle. The unique characteristics of jumbo phages are the basis of variations in different types of phages concerning their organization at the genomic level, virion structure, evolution, and progeny propagation. The presence of tRNA and additional translation-related genes along with chaperonin genes mark the ability of these phages for being independent of host molecular machinery enabling them to have wide host options. A large number of jumbo phages have been isolated from various sources through advanced standard screening methods. The current review has summarized the available data on jumbo phages and discussed the genome orientation of jumbo phages, translational machinery, diversity and evolution of jumbo phages. In the studies conducted, jumbo phages possessed special additional genes that helps to reduce the dependence of jumbo phages on their hosts. Furthermore, their genomes might have evolved from smaller genome phages.
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Affiliation(s)
- Amina Nazir
- Key Laboratory of Molecular Medicine and Biotherapy in the Ministry of Industry and Information Technology, Department of Biology, School of Life Sciences, Beijing Institute of Technology, Beijing, People’s Republic of China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Azam Ali
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
| | - Hong Qing
- Key Laboratory of Molecular Medicine and Biotherapy in the Ministry of Industry and Information Technology, Department of Biology, School of Life Sciences, Beijing Institute of Technology, Beijing, People’s Republic of China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
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18
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Lechuga A, Lood C, Berjón-Otero M, Del Prado A, Wagemans J, van Noort V, Lavigne R, Salas M, Redrejo-Rodríguez M. Unraveling Protein Interactions between the Temperate Virus Bam35 and Its Bacillus Host Using an Integrative Yeast Two Hybrid-High Throughput Sequencing Approach. Int J Mol Sci 2021; 22:11105. [PMID: 34681765 DOI: 10.3390/ijms222011105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/08/2021] [Accepted: 10/10/2021] [Indexed: 11/20/2022] Open
Abstract
Bacillus virus Bam35 is the model Betatectivirus and member of the family Tectiviridae, which is composed of tailless, icosahedral, and membrane-containing bacteriophages. Interest in these viruses has greatly increased in recent years as they are thought to be an evolutionary link between diverse groups of prokaryotic and eukaryotic viruses. Additionally, betatectiviruses infect bacteria of the Bacillus cereus group, which are known for their applications in industry and notorious since it contains many pathogens. Here, we present the first protein–protein interactions (PPIs) network for a tectivirus–host system by studying the Bam35–Bacillus thuringiensis model using a novel approach that integrates the traditional yeast two-hybrid system and high-throughput sequencing (Y2H-HTS). We generated and thoroughly analyzed a genomic library of Bam35′s host B. thuringiensis HER1410 and screened interactions with all the viral proteins using different combinations of bait–prey couples. Initial analysis of the raw data enabled the identification of over 4000 candidate interactions, which were sequentially filtered to produce 182 high-confidence interactions that were defined as part of the core virus–host interactome. Overall, host metabolism proteins and peptidases were particularly enriched within the detected interactions, distinguishing this host–phage system from the other reported host–phage PPIs. Our approach also suggested biological roles for several Bam35 proteins of unknown function, including the membrane structural protein P25, which may be a viral hub with a role in host membrane modification during viral particle morphogenesis. This work resulted in a better understanding of the Bam35–B. thuringiensis interaction at the molecular level and holds great potential for the generalization of the Y2H-HTS approach for other virus–host models.
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19
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Islam MR, Martinez-Soto CE, Lin JT, Khursigara CM, Barbut S, Anany H. A systematic review from basics to omics on bacteriophage applications in poultry production and processing. Crit Rev Food Sci Nutr 2021:1-33. [PMID: 34609270 DOI: 10.1080/10408398.2021.1984200] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The growing human population is currently facing an unprecedented challenge on global food production and sustainability. Despite recognizing poultry as one of the most successful and rapidly growing food industries to address this challenge; poultry health and safety remain major issues that entail immediate attention. Bacterial diseases including colibacillosis, salmonellosis, and necrotic enteritis have become increasingly prevalent during poultry production. Likewise, outbreaks caused by consumption of undercooked poultry products contaminated with zoonotic bacterial pathogens such as Salmonella, Campylobacter and Listeria, are a serious public health concern. With antimicrobial resistance problem and restricted use of antibiotics in food producing animals, bacteriophages are increasingly recognized as an attractive natural antibacterial alternative. Bacteriophages have recently shown promising results to treat diseases in poultry, reduce contamination of carcasses, and enhance the safety of poultry products. Omics technologies have been successfully employed to accurately characterize bacteriophages and their genes/proteins important for interaction with bacterial hosts. In this review, the potential of using lytic bacteriophages to mitigate the risk of major poultry-associated bacterial pathogens are explored. This study also explores challenges associated with the adoption of this technology by industries. Furthermore, the impact of omics approaches on studying bacteriophages, their host interaction and applications is discussed.
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Affiliation(s)
- Md Rashedul Islam
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada
| | - Carlos E Martinez-Soto
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada.,Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Janet T Lin
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada
| | - Cezar M Khursigara
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Shai Barbut
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Hany Anany
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada.,Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.,Department of Food Science, University of Guelph, Guelph, Ontario, Canada
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20
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Pappas N, Dutilh BE. Finding functional associations between prokaryotic virus orthologous groups: a proof of concept. BMC Bioinformatics 2021; 22:438. [PMID: 34525942 DOI: 10.1186/s12859-021-04343-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 08/27/2021] [Indexed: 02/02/2023] Open
Abstract
Background The field of viromics has greatly benefited from recent developments in metagenomics, with significant efforts focusing on viral discovery. However, functional annotation of the increasing number of viral genomes is lagging behind. This is highlighted by the degree of annotation of the protein clusters in the prokaryotic Virus Orthologous Groups (pVOGs) database, with 83% of its current 9518 pVOGs having an unknown function. Results In this study we describe a machine learning approach to explore potential functional associations between pVOGs. We measure seven genomic features and use them as input to a Random Forest classifier to predict protein–protein interactions between pairs of pVOGs. After systematic evaluation of the model’s performance on 10 different datasets, we obtained a predictor with a mean accuracy of 0.77 and Area Under Receiving Operation Characteristic (AUROC) score of 0.83. Its application to a set of 2,133,027 pVOG-pVOG interactions allowed us to predict 267,265 putative interactions with a reported probability greater than 0.65. At an expected false discovery rate of 0.27, we placed 95.6% of the previously unannotated pVOGs in a functional context, by predicting their interaction with a pVOG that is functionally annotated. Conclusions We believe that this proof-of-concept methodology, wrapped in a reproducible and automated workflow, can represent a significant step towards obtaining a more complete picture of bacteriophage biology. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04343-w.
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21
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Markwitz P, Lood C, Olszak T, van Noort V, Lavigne R, Drulis-Kawa Z. Genome-driven elucidation of phage-host interplay and impact of phage resistance evolution on bacterial fitness. ISME J 2021. [PMID: 34465897 DOI: 10.1038/s41396-021-01096-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 01/21/2023]
Abstract
When considering the interactions between bacteriophages and their host, the issue of phage-resistance emergence is a key element in understanding the ecological impact of phages on the bacterial population. It is also an essential parameter for the implementation of phage therapy to combat antibiotic-resistant pathogens. This study investigates the phenotypic and genetic responses of five Pseudomonas aeruginosa strains (PAO1, A5803, AA43, CHA, and PAK) to the infection by seven phages with distinct evolutionary backgrounds and recognised receptors (LPS/T4P). Emerging phage-insensitivity was generally accompanied by self and cross-resistance mechanisms. Significant differences were observed between the reference PAO1 responses compared to other clinical representatives. LPS-dependent phage infections in clinical strains selected for mutations in the "global regulatory" and "other" genes, rather than in the LPS-synthesis clusters detected in PAO1 clones. Reduced fitness, as proxied by the growth rate, was correlated with large deletion (20-500 kbp) and phage carrier state. Multi-phage resistance was significantly correlated with a reduced growth rate but only in the PAO1 population. In addition, we observed that the presence of prophages decreased the lytic phage maintenance seemingly protecting the host against carrier state and occasional lytic phage propagation, thus preventing a significant reduction in bacterial growth rate.
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22
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Lee Y, Son B, Cha Y, Ryu S. Characterization and Genomic Analysis of PALS2, a Novel Staphylococcus Jumbo Bacteriophage. Front Microbiol 2021; 12:622755. [PMID: 33763042 PMCID: PMC7982418 DOI: 10.3389/fmicb.2021.622755] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/09/2021] [Indexed: 12/30/2022] Open
Abstract
Staphylococcus aureus is an important human pathogen that can be frequently encountered in clinical and food-processing surroundings. Among the various countermeasures, bacteriophages have been considered to be promising alternatives to antibiotics. In this study, the bacteriophage PALS2 was isolated from bird feces, and the genomic and biological characteristics of this phage were investigated. PALS2 was determined to belong to the Myoviridae family and exhibited extended host inhibition that persisted for up to 24 h with repeated bursts of 12 plaque-forming units/cell. The complete genome of PALS2 measured 268,746 base pairs (bp), indicating that PALS2 could be classified as a jumbo phage. The PALS2 genome contained 279 ORFs and 1 tRNA covering asparagine, and the majority of predicted PALS2 genes encoded hypothetical proteins. Additional genes involved in DNA replication and repair, nucleotide metabolism, and genes encoding multisubunit RNA polymerase were identified in the PALS2 genome, which is a common feature of typical jumbo phages. Comparative genomic analysis indicated that PALS2 is a phiKZ-related virus and is more similar to typical jumbo phages than to staphylococcal phages. Additionally, the effective antimicrobial activities of phage PALS2 suggest its possible use as a biocontrol agent in various clinical and food processing environments.
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Affiliation(s)
- Yoona Lee
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Bokyung Son
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Yoyeon Cha
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea
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23
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Molina-Mora JA, García F. Molecular Determinants of Antibiotic Resistance in the Costa Rican Pseudomonas aeruginosa AG1 by a Multi-omics Approach: A Review of 10 Years of Study. Phenomics 2021; 1:129-142. [PMID: 35233560 PMCID: PMC8210740 DOI: 10.1007/s43657-021-00016-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 01/13/2023]
Abstract
Pseudomonas aeruginosa AG1 (PaeAG1) is a Costa Rican strain that was isolated in 2010 in a major Hospital. This strain has resistance to multiple antibiotics such as β-lactams (including carbapenems), aminoglycosides, and fluoroquinolones. PaeAG1 is considered critical (Priority 1) due to its resistance to carbapenems, and it was the first report of a P. aeruginosa isolate carrying both VIM-2 and IMP-18 genes encoding for metallo-β-lactamases (MBL) enzymes (both with carbapenemase activity). Owing to these traits, we have studied this model for 10 years using diverse approaches including multi-omics. In this review, we summarize the main points of the different steps that we have studied in PaeAG1: preliminary analyses of this strain at the genomic and phenomic levels revealed that this microorganism has particular features of antibiotic resistance. In the multi-omics approach, the genome assembly was the initial step to identify the genomic determinants of this strain, including virulence factors, antibiotic resistance genes, as well as a complex accessory genome. Second, a comparative genomic approach was implemented to define and update the phylogenetic relationship among complete P. aeruginosa genomes, the genomic island content in other strains, and the architecture of the two MBL-carrying integrons. Third, the proteomic profile of PaeAG1 was studied after exposure to antibiotics using 2-dimensional gel electrophoresis (2D-GE). Fourth, to study the central response to multiple perturbations in P. aeruginosa, i.e., the core perturbome, a machine learning approach was used. The analysis revealed biological functions and determinants that are shared by different disturbances. Finally, to evaluate the effects of ciprofloxacin (CIP) on PaeAG1, a growth curve comparison, differential expression analysis (RNA-Seq), and network analysis were performed. Using the results of the core perturbome (pathways that also were found in this perturbation with CIP), it was possible to identify the “exclusive” response and determinants of PaeAG1 after exposure to CIP. Altogether, after a decade of study using a multi-omics approach (at genomics, comparative genomics, perturbomics, transcriptomics, proteomics, and phenomics levels), we have provided new insights about the genomic and transcriptomic determinants associated with antibiotic resistance in PaeAG1. These results not only partially explain the high-risk condition of this strain that enables it to conquer nosocomial environments and its multi-resistance profile, but also this information may eventually be used as part of the strategies to fight this pathogen.
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Affiliation(s)
- Jose Arturo Molina-Mora
- Centro de Investigación en Enfermedades Tropicales (CIET) & Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Fernando García
- Centro de Investigación en Enfermedades Tropicales (CIET) & Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
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Abstract
Since their discovery more than 100 years ago, the viruses that infect bacteria (bacteriophages) have been widely studied as model systems. Largely overlooked, however, have been "jumbo phages," with genome sizes ranging from 200 to 500 kbp. Jumbo phages generally have large virions with complex structures and a broad host spectrum. While the majority of jumbo phage genes are poorly functionally characterized, recent work has discovered many unique biological features, including a conserved tubulin homolog that coordinates a proteinaceous nucleus-like compartment that houses and segregates phage DNA. The tubulin spindle displays dynamic instability and centers the phage nucleus within the bacterial host during phage infection for optimal reproduction. The shell provides robust physical protection for the enclosed phage genomes against attack from DNA-targeting bacterial immune systems, thereby endowing jumbo phages with broad resistance. In this review, we focus on the current knowledge of the cytoskeletal elements and the specialized nuclear compartment derived from jumbo phages, and we highlight their importance in facilitating spatial and temporal organization over the viral life cycle. Additionally, we discuss the evolutionary relationships between jumbo phages and eukaryotic viruses, as well as the therapeutic potential and drawbacks of jumbo phages as antimicrobial agents in phage therapy.
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Gambino M, Brøndsted L. Looking into the future of phage-based control of zoonotic pathogens in food and animal production. Curr Opin Biotechnol 2020; 68:96-103. [PMID: 33186799 DOI: 10.1016/j.copbio.2020.10.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/01/2020] [Accepted: 10/03/2020] [Indexed: 11/28/2022]
Abstract
Using bacteriophages (phages) to control zoonotic pathogens in food and animal production is a realistic and promising antimicrobial approach. Recent studies have demonstrated their efficacy and safety, yet bringing phage products on the market remains a challenge. Here we summarize the procedure for advancing phage applications from the laboratory to simplified model systems and testing in pilot scale, to farms and food industries. We highlight the most important contributions concerning phages in food matrices and animal guts, and propose directions for future research required to understand interactions in such complex systems. Finally, we propose a holistic approach combining a data repository with modelling, multi-omic techniques and data analysis to modernize phage-based control of zoonotic pathogens.
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Affiliation(s)
- Michela Gambino
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark.
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Wicke L, Ponath F, Coppens L, Gerovac M, Lavigne R, Vogel J. Introducing differential RNA-seq mapping to track the early infection phase for Pseudomonas phage ɸKZ. RNA Biol 2020; 18:1099-1110. [PMID: 33103565 PMCID: PMC8244752 DOI: 10.1080/15476286.2020.1827785] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
As part of the ongoing renaissance of phage biology, more phage genomes are becoming available through DNA sequencing. However, our understanding of the transcriptome architecture that allows these genomes to be expressed during host infection is generally poor. Transcription start sites (TSSs) and operons have been mapped for very few phages, and an annotated global RNA map of a phage – alone or together with its infected host – is not available at all. Here, we applied differential RNA-seq (dRNA-seq) to study the early, host takeover phase of infection by assessing the transcriptome structure of Pseudomonas aeruginosa jumbo phage ɸKZ, a model phage for viral genetics and structural research. This map substantially expands the number of early expressed viral genes, defining TSSs that are active ten minutes after ɸKZ infection. Simultaneously, we record gene expression changes in the host transcriptome during this critical metabolism conversion. In addition to previously reported upregulation of genes associated with amino acid metabolism, we observe strong activation of genes with functions in biofilm formation (cdrAB) and iron storage (bfrB), as well as an activation of the antitoxin ParD. Conversely, ɸKZ infection rapidly down-regulates complexes IV and V of oxidative phosphorylation (atpCDGHF and cyoABCDE). Taken together, our data provide new insights into the transcriptional organization and infection process of the giant bacteriophage ɸKZ and adds a framework for the genome-wide transcriptomic analysis of phage–host interactions.
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Affiliation(s)
- Laura Wicke
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany.,Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Falk Ponath
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Lucas Coppens
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Milan Gerovac
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Jörg Vogel
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
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Barth ZK, Netter Z, Angermeyer A, Bhardwaj P, Seed KD. A Family of Viral Satellites Manipulates Invading Virus Gene Expression and Can Affect Cholera Toxin Mobilization. mSystems 2020; 5:e00358-20. [PMID: 33051375 DOI: 10.1128/mSystems.00358-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many viruses possess temporally unfolding gene expression patterns aimed at subverting host defenses, commandeering host metabolism, and ultimately producing a large number of progeny virions. High-throughput omics tools, such as RNA sequencing (RNA-seq), have dramatically enhanced the resolution of expression patterns during infection. Less studied have been viral satellites, mobile genomes that parasitize viruses. By performing RNA-seq on infection time courses, we have obtained the first time-resolved transcriptomes for bacteriophage satellites during lytic infection. Specifically, we have acquired transcriptomes for the lytic Vibrio cholerae phage ICP1 and all five known variants of ICP1's parasite, the phage inducible chromosomal island-like elements (PLEs). PLEs rely on ICP1 for both DNA replication and mobilization and abolish production of ICP1 progeny in infected cells. We investigated PLEs' impact on ICP1 gene expression and found that PLEs did not broadly restrict or reduce ICP1 gene expression. A major exception occurred in ICP1's capsid morphogenesis operon, which was downregulated by each of the PLE variants. Surprisingly, PLEs were also found to alter the gene expression of CTXΦ, the integrative phage that encodes cholera toxin and is necessary for virulence of toxigenic V. cholerae One PLE, PLE1, upregulated CTXΦ genes involved in replication and integration and boosted CTXΦ mobility following induction of the SOS response.IMPORTANCE Viral satellites are found in all domains of life and can have profound fitness effects on both the viruses they parasitize and the cells they reside in. In this study, we have acquired the first RNA sequencing (RNA-seq) transcriptomes of viral satellites outside plants, as well as the transcriptome of the phage ICP1, a predominant predator of pandemic Vibrio cholerae Capsid downregulation, previously observed in an unrelated phage satellite, is conserved among phage inducible chromosomal island-like elements (PLEs), suggesting that viral satellites are under strong selective pressure to reduce the capsid expression of their larger host viruses. Despite conserved manipulation of capsid expression, PLEs exhibit divergent effects on CTXΦ transcription and mobility. Our results demonstrate that PLEs can influence both their hosts' resistance to phage and the mobility of virulence-encoding elements, suggesting that PLEs can play a substantial role in shaping Vibrio cholerae evolution.
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Zhong Q, Yang L, Li L, Shen W, Li Y, Xu H, Zhong Z, Chen M, Le S. Transcriptomic Analysis Reveals the Dependency of Pseudomonas aeruginosa Genes for Double-Stranded RNA Bacteriophage phiYY Infection Cycle. iScience 2020; 23:101437. [PMID: 32827855 PMCID: PMC7452160 DOI: 10.1016/j.isci.2020.101437] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/16/2020] [Accepted: 08/03/2020] [Indexed: 12/11/2022] Open
Abstract
Bacteriophage phiYY is currently the only double-stranded RNA (dsRNA) phage that infects Pseudomonas aeruginosa and is a potential candidate for phage therapy. Here we applied RNA-seq to investigate the lytic cycle of phiYY infecting P. aeruginosa strain PAO1r. About 12.45% (651/5,229) of the host genes were determined to be differentially expressed genes. Moreover, oxidative stress response genes katB and ahpB are upregulated 64- to 128-fold after phage infection, and the single deletion of each gene blocked phiYY infection, indicating that phiYY is extremely sensitive to oxidative stress. On the contrary, another upregulated gene PA0800 might constrain phage infection, because the deletion of PA0800 resulted in a 3.5-fold increase of the efficiency of plating. Our study highlights a complicated dsRNA phage-phage global interaction and raises new questions toward the host defense mechanisms against dsRNA phage and dsRNA phage-encoded hijacking mechanisms.
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Affiliation(s)
- Qiu Zhong
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, Chongqing 400038, China
- Department of Clinical Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing 400038, China
| | - Lan Yang
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Linlin Li
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Wei Shen
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing 400038, China
| | - Yang Li
- Medical Center of Trauma and War Injury, Daping Hospital, Army Medical University, Chongqing 400038, China
- State Key Laboratory of Trauma, Burns and Combined Injuries, Army Medical University, Chongqing 400038, China
| | - Huan Xu
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, Chongqing 400038, China
| | - Zhuojun Zhong
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing 400038, China
| | - Ming Chen
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, Chongqing 400038, China
- State Key Laboratory of Trauma, Burns and Combined Injuries, Army Medical University, Chongqing 400038, China
| | - Shuai Le
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing 400038, China
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Clokie MR, Blasdel BG, Demars BO, Sicheritz-Pontén T. Rethinking Phage Ecology by Rooting it Within an Established Plant Framework. Phage (New Rochelle) 2020; 1:121-136. [PMID: 36147824 PMCID: PMC9041459 DOI: 10.1089/phage.2020.0015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Despite the abundance and significance of bacteriophages to microbial ecosystems, no broad ecological frameworks exist within which to determine "bacteriophage types" that reflect their ecological strategies and ways in which they interact with bacterial cells. To address this, we repurposed the well-established Grime's triangular CSR framework, which classifies plants according to three axes: competitiveness (C), ability to tolerate stress (S), and capacity to cope with disturbance (R). This framework is distinguished from other accepted schemes, as it seeks to identify individual characteristics of plants to understand their biological strategies and roles within an ecosystem. Our repurposing of the CSR triangle is based on phage transcription and the observation that typically phages have three major distinguishable transcription phases: early, middle, and late. We hypothesize that the proportion of genes expressed in these phases reflects key information about the phage "ecological strategy," namely the C, S, and R strategies, allowing us to examine phages in a similar way to how plants are projected onto the triangle. In the "phage version" of this scheme, we suggest: (1) that some phages prioritize the early phase of transcription that shuts off host defense mechanisms, which reflects competitiveness; (2) other phages prioritize tuning resource management mechanisms in the cell such as nucleotide metabolism during their "mid" expression profile to tolerate stress; and (3) a further subset of phages (termed Ruderals) survive disturbance by investing significant resources into regeneration so they express a higher proportion of their genes during late infection. We examined 42 published phage transcriptomes and show that they fall into discrete CSR categories according to their expression profiles. We discuss these positions in the context of their biology, which is largely consistent with our predictions of specific phage characteristics. In this opinion article, we suggest a starting point to ascribe phages into different functional types and thus understand them in an ecological framework. We suggest that this may have far-reaching implications for the application of phages in therapy and their exploitation to manipulate bacterial communities. We invite further use of this framework via our online tool; www.PhageCSR.ml.
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Affiliation(s)
- Martha R.J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Address correspondence to: Martha R.J. Clokie, PhD, Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | | | | | - Thomas Sicheritz-Pontén
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Address correspondence to: Thomas Sicheritz Pontén, PhD, Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, Bygning 7, Copenhagen 1353, Denmark
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