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Peters TL, Schow J, Spencer E, Van Leuven JT, Wichman H, Miller C. Directed evolution of bacteriophages: impacts of prolific prophage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601269. [PMID: 38979301 PMCID: PMC11230397 DOI: 10.1101/2024.06.28.601269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Various directed evolution methods exist that seek to procure bacteriophages with expanded host ranges, typically targeting phage-resistant or non-permissive bacterial hosts. The general premise of these methods is to propagate phage on multiple bacterial hosts, pool the lysate, and repeat the propagation process until phage(s) can form plaques on the target host(s). In theory, this propagation process produces a phage lysate that contains input phages and their evolved phage progeny. However, in practice, this phage lysate can also include prophages originating from bacterial hosts. Here we describe our experience implementing one directed evolution method, the Appelmans protocol, to study phage evolution in the Pseudomonas aeruginosa phage-host system, in which we observed rapid host-range expansion of the phage cocktail. Further experimentation and sequencing analysis revealed that this observed host-range expansion was due to a Casadabanvirus prophage that originated from one of the Appelmans hosts. Host-range analysis of the prophage showed that it could infect five of eight bacterial hosts initially used, allowing it to proliferate and persist through the end of the experiment. This prophage was represented in half of the sequenced phage samples isolated from the Appelmans experiment. This work highlights the impact of prophages in directed evolution experiments and the importance of incorporating sequencing data in analyses to verify output phages, particularly for those attempting to procure phages intended for phage therapy applications. This study also notes the usefulness of intraspecies antagonism assays between bacterial host strains to establish a baseline for inhibitory activity and determine presence of prophage. IMPORTANCE Directed evolution is a common strategy for evolving phages to expand host range, often targeting pathogenic strains of bacteria. In this study we investigated phage host-range expansion using directed evolution in the Pseudomonas aeruginosa system. We show that prophage are active players in directed evolution and can contribute to observation of host-range expansion. Since prophage are prevalent in bacterial hosts, particularly pathogenic strains of bacteria, and all directed evolution approaches involve iteratively propagating phage on one or more bacterial hosts, the presence of prophage in phage preparations is a factor that needs to be considered in experimental design and interpretation of results. These results highlight the importance of screening for prophages either genetically or through intraspecies antagonism assays during selection of bacterial strains and will contribute to improving experimental design of future directed evolution studies.
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Feltin C, Garneau JR, Morris CE, Bérard A, Torres-Barceló C. Novel phages of Pseudomonas syringae unveil numerous potential auxiliary metabolic genes. J Gen Virol 2024; 105:001990. [PMID: 38833289 PMCID: PMC11256456 DOI: 10.1099/jgv.0.001990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/07/2024] [Indexed: 06/06/2024] Open
Abstract
Relatively few phages that infect plant pathogens have been isolated and investigated. The Pseudomonas syringae species complex is present in various environments, including plants. It can cause major crop diseases, such as bacterial canker on apricot trees. This study presents a collection of 25 unique phage genomes that infect P. syringae. These phages were isolated from apricot orchards with bacterial canker symptoms after enrichment with 21 strains of P. syringae. This collection comprises mostly virulent phages, with only three being temperate. They belong to 14 genera, 11 of which are newly discovered, and 18 new species, revealing great genetic diversity within this collection. Novel DNA packaging systems have been identified bioinformatically in one of the new phage species, but experimental confirmation is required to define the precise mechanism. Additionally, many phage genomes contain numerous potential auxiliary metabolic genes with diversified putative functions. At least three phages encode genes involved in bacterial tellurite resistance, a toxic metalloid. This suggests that viruses could play a role in bacterial stress tolerance. This research emphasizes the significance of continuing the search for new phages in the agricultural ecosystem to unravel novel ecological diversity and new gene functions. This work contributes to the foundation for future fundamental and applied research on phages infecting phytopathogenic bacteria.
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Affiliation(s)
- Chloé Feltin
- INRAE, Pathologie Végétale, F-84140, Montfavet, France
| | - Julian R. Garneau
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
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3
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Roughgarden J. Lytic/Lysogenic Transition as a Life-History Switch. Virus Evol 2024; 10:veae028. [PMID: 38756985 PMCID: PMC11097211 DOI: 10.1093/ve/veae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/15/2024] [Accepted: 03/27/2024] [Indexed: 05/18/2024] Open
Abstract
The transition between lytic and lysogenic life cycles is the most important feature of the life-history of temperate viruses. To explain this transition, an optimal life-history model is offered based a discrete-time formulation of phage/bacteria population dynamics that features infection of bacteria by Poisson sampling of virions from the environment. The time step is the viral latency period. In this model, density-dependent viral absorption onto the bacterial surface produces virus/bacteria coexistence and density dependence in bacterial growth is not needed. The formula for the transition between lytic and lysogenic phases is termed the 'fitness switch'. According to the model, the virus switches from lytic to lysogenic when its population grows faster as prophage than as virions produced by lysis of the infected cells, and conversely for the switch from lysogenic to lytic. A prophage that benefits the bacterium it infects automatically incurs lower fitness upon exiting the bacterial genome, resulting in its becoming locked into the bacterial genome in what is termed here as a 'prophage lock'. The fitness switch qualitatively predicts the ecogeographic rule that environmental enrichment leads to microbialization with a concomitant increase in lysogeny, fluctuating environmental conditions promote virus-mediated horizontal gene transfer, and prophage-containing bacteria can integrate into the microbiome of a eukaryotic host forming a functionally integrated tripartite holobiont. These predictions accord more with the 'Piggyback-the-Winner' hypothesis than with the 'Kill-the-Winner' hypothesis in virus ecology.
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Affiliation(s)
- Joan Roughgarden
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, HI 96744, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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4
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Piña-González AM, Castelán-Sánchez HG, Hurtado-Ramírez JM, López-Leal G. Campylobacter prophage diversity reveals pervasive recombination between prophages from different Campylobacter species. Microbiol Spectr 2024; 12:e0279523. [PMID: 38088548 PMCID: PMC10782988 DOI: 10.1128/spectrum.02795-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/12/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Prophages play an important role in shaping the genetic diversity and evolution of their hosts. Acquisition or loss of prophages can lead to genomic variations, including changes in the bacterial phenotype promoted by recombination events, genetic repertoire exchanges and dissemination of virulence factors, and antibiotic resistance. By studying prophages in Campylobacter species, scientists can gain insights into the evolutionary patterns, pathogenicity mechanisms, epidemiology, and population dynamics of these species. This has implications for public health, antibiotic resistance surveillance, and the development of targeted therapeutic approaches.
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Affiliation(s)
- Adán Manuel Piña-González
- Laboratorio de Biología Computacional y Virómica Integrativa, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Hugo G. Castelán-Sánchez
- Grupo de Genómica y Dinámica Evolutiva de Microorganismos Emergentes, Consejo Nacional de Humanidades, Ciudad de México, México
| | | | - Gamaliel López-Leal
- Laboratorio de Biología Computacional y Virómica Integrativa, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
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Dougherty PE, Nielsen TK, Riber L, Lading HH, Forero-Junco LM, Kot W, Raaijmakers JM, Hansen LH. Widespread and largely unknown prophage activity, diversity, and function in two genera of wheat phyllosphere bacteria. THE ISME JOURNAL 2023; 17:2415-2425. [PMID: 37919394 PMCID: PMC10689766 DOI: 10.1038/s41396-023-01547-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023]
Abstract
Environmental bacteria host an enormous number of prophages, but their diversity and natural functions remain largely elusive. Here, we investigate prophage activity and diversity in 63 Erwinia and Pseudomonas strains isolated from flag leaves of wheat grown in a single field. Introducing and validating Virion Induction Profiling Sequencing (VIP-Seq), we identify and quantify the activity of 120 spontaneously induced prophages, discovering that some phyllosphere bacteria produce more than 108 virions/mL in overnight cultures, with significant induction also observed in planta. Sequence analyses and plaque assays reveal E. aphidicola prophages contribute a majority of intraspecies genetic diversity and divide their bacterial hosts into antagonistic factions engaged in widespread microbial warfare, revealing the importance of prophage-mediated microdiversity. When comparing spontaneously active prophages with predicted prophages we also find insertion sequences are strongly correlated with non-active prophages. In conclusion, we discover widespread and largely unknown prophage diversity and function in phyllosphere bacteria.
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Affiliation(s)
- Peter Erdmann Dougherty
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Tue Kjærgaard Nielsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Leise Riber
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Helen Helgå Lading
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark.
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6
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Dikareva E, Matharu D, Lahtinen E, Kolho KL, De Vos WM, Salonen A, Ponsero AJ. An extended catalog of integrated prophages in the infant and adult fecal microbiome shows high prevalence of lysogeny. Front Microbiol 2023; 14:1254535. [PMID: 37731926 PMCID: PMC10508911 DOI: 10.3389/fmicb.2023.1254535] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/14/2023] [Indexed: 09/22/2023] Open
Abstract
Background and aims The acquisition and gradual maturation of gut microbial communities during early childhood is central to an individual's healthy development. Bacteriophages have the potential to shape the gut bacterial communities. However, the complex ecological interactions between phages and their bacterial host are still poorly characterized. In this study, we investigated the abundance and diversity of integrated prophages in infant and adult gut bacteria by detecting integrated prophages in metagenome assembled genomes (MAGs) of commensal bacteria. Methods Our study included 88 infants sampled at 3 weeks, 3 months, 6 months, and 12 months (n = 323 total samples), and their parents around delivery time (n = 138 total samples). Fecal DNA was extracted and characterized by using shotgun metagenomic sequencing, and a collection of prokaryotic MAGs was generated. The MAG collection was screened for the presence of integrated bacteriophage sequences, allowing their taxonomic and functional characterization. Results A large collection of 6,186 MAGs from infant and adult gut microbiota was obtained and screened for integrated prophages, allowing the identification of 7,165 prophage sequences longer than 10 kb. Strikingly, more than 70% of the near-complete MAGs were identified as lysogens. The prevalence of prophages in MAGs varied across bacterial families, with a lower prevalence observed among Coriobacteriaceae, Eggerthellaceae, Veillonellaceae and Burkholderiaceae, while a very high prevalence of lysogen MAGs were observed in Oscillospiraceae, Enterococcaceae, and Enterobacteriaceae. Interestingly for several bacterial families such as Bifidobacteriaceae and Bacteroidaceae, the prevalence of prophages in MAGs was higher in early infant time point (3 weeks and 3 months) than in later sampling points (6 and 12 months) and in adults. The prophage sequences were clustered into 5,616 species-like vOTUs, 77% of which were novel. Finally, we explored the functional repertoire of the potential auxiliary metabolic genes carried by these prophages, encoding functions involved in carbohydrate metabolism and degradation, amino acid metabolism and carbon metabolism. Conclusion Our study provides an enhanced understanding of the diversity and prevalence of lysogens in infant and adult gut microbiota and suggests a complex interplay between prophages and their bacterial hosts.
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Affiliation(s)
- Evgenia Dikareva
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Dollwin Matharu
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Emilia Lahtinen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kaija-Leena Kolho
- Children's Hospital, Paediatric Research Centre, University of Helsinki and HUS, Helsinki, Finland
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Willem M. De Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Anne Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Alise J. Ponsero
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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7
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Braetz S, Schwerk P, Figueroa-Bossi N, Tedin K, Fulde M. Prophage Gifsy-1 Induction in Salmonella enterica Serovar Typhimurium Reduces Persister Cell Formation after Ciprofloxacin Exposure. Microbiol Spectr 2023; 11:e0187423. [PMID: 37306609 PMCID: PMC10433948 DOI: 10.1128/spectrum.01874-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 05/28/2023] [Indexed: 06/13/2023] Open
Abstract
Persister cells are drug-tolerant bacteria capable of surviving antibiotic treatment despite the absence of heritable resistance mechanisms. It is generally thought that persister cells survive antibiotic exposure through the implementation of stress responses and/or energy-sparing strategies. Exposure to DNA gyrase-targeting antibiotics could be particularly detrimental for bacteria that carry prophages integrated in their genomes. Gyrase inhibitors are known to induce prophages to switch from their dormant lysogenic state into the lytic cycle, causing the lysis of their bacterial host. However, the influence of resident prophages on the formation of persister cells has only been recently appreciated. Here, we evaluated the effect of endogenous prophage carriage on the generation of bacterial persistence during Salmonella enterica serovar Typhimurium exposure to both gyrase-targeting antibiotics and other classes of bactericidal antibiotics. Results from the analysis of strain variants harboring different prophage combinations revealed that prophages play a major role in limiting the formation of persister cells during exposure to DNA-damaging antibiotics. In particular, we present evidence that prophage Gifsy-1 (and its encoded lysis proteins) are major factors limiting persister cell formation upon ciprofloxacin exposure. Resident prophages also appear to have a significant impact on the initial drug susceptibility, resulting in an alteration of the characteristic biphasic killing curve of persister cells into a triphasic curve. In contrast, a prophage-free derivative of S. Typhimurium showed no difference in the killing kinetics for β-lactam or aminoglycoside antibiotics. Our study demonstrates that induction of prophages increased the susceptibility toward DNA gyrase inhibitors in S. Typhimurium, suggesting that prophages have the potential for enhancing antibiotic efficacy. IMPORTANCE Bacterial infections resulting from antibiotic treatment failure can often be traced to nonresistant persister cells. Moreover, intermittent or single treatment of persister cells with β-lactam antibiotics or fluoroquinolones can lead to the formation of drug-resistant bacteria and to the emergence of multiresistant strains. It is therefore important to have a better understanding of the mechanisms that impact persister formation. Our results indicate that prophage-associated bacterial killing significantly reduces persister cell formation in lysogenic cells exposed to DNA-gyrase-targeting drugs. This suggests that therapies based on gyrase inhibitors should be favored over alternative strategies when dealing with lysogenic pathogens.
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Affiliation(s)
- Sebastian Braetz
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Peter Schwerk
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Nara Figueroa-Bossi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Karsten Tedin
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Marcus Fulde
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
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8
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Du S, Tong X, Lai ACK, Chan CK, Mason CE, Lee PKH. Highly host-linked viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution. Nat Commun 2023; 14:2676. [PMID: 37160974 PMCID: PMC10169181 DOI: 10.1038/s41467-023-38400-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 04/27/2023] [Indexed: 05/11/2023] Open
Abstract
Viruses in built environments (BEs) raise public health concerns, yet they are generally less studied than bacteria. To better understand viral dynamics in BEs, this study assesses viromes from 11 habitats across four types of BEs with low to high occupancy. The diversity, composition, metabolic functions, and lifestyles of the viromes are found to be habitat dependent. Caudoviricetes species are ubiquitous on surface habitats in the BEs, and some of them are distinct from those present in other environments. Antimicrobial resistance genes are identified in viruses inhabiting surfaces frequently touched by occupants and in viruses inhabiting occupants' skin. Diverse CRISPR/Cas immunity systems and anti-CRISPR proteins are found in bacterial hosts and viruses, respectively, consistent with the strongly coupled virus-host links. Evidence of viruses potentially aiding host adaptation in a specific-habitat manner is identified through a unique gene insertion. This work illustrates that virus-host interactions occur frequently in BEs and that viruses are integral members of BE microbiomes.
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Affiliation(s)
- Shicong Du
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, P. R. China
| | - Alvin C K Lai
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Chak K Chan
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China.
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McKerral JC, Papudeshi B, Inglis LK, Roach MJ, Decewicz P, McNair K, Luque A, Dinsdale EA, Edwards RA. The Promise and Pitfalls of Prophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.20.537752. [PMID: 37131798 PMCID: PMC10153245 DOI: 10.1101/2023.04.20.537752] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Phages dominate every ecosystem on the planet. While virulent phages sculpt the microbiome by killing their bacterial hosts, temperate phages provide unique growth advantages to their hosts through lysogenic conversion. Many prophages benefit their host, and prophages are responsible for genotypic and phenotypic differences that separate individual microbial strains. However, the microbes also endure a cost to maintain those phages: additional DNA to replicate and proteins to transcribe and translate. We have never quantified those benefits and costs. Here, we analysed over two and a half million prophages from over half a million bacterial genome assemblies. Analysis of the whole dataset and a representative subset of taxonomically diverse bacterial genomes demonstrated that the normalised prophage density was uniform across all bacterial genomes above 2 Mbp. We identified a constant carrying capacity of phage DNA per bacterial DNA. We estimated that each prophage provides cellular services equivalent to approximately 2.4 % of the cell's energy or 0.9 ATP per bp per hour. We demonstrate analytical, taxonomic, geographic, and temporal disparities in identifying prophages in bacterial genomes that provide novel targets for identifying new phages. We anticipate that the benefits bacteria accrue from the presence of prophages balance the energetics involved in supporting prophages. Furthermore, our data will provide a new framework for identifying phages in environmental datasets, diverse bacterial phyla, and from different locations.
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Affiliation(s)
- Jody C. McKerral
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Laura K. Inglis
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Michael J. Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warsaw, 02-096, Poland
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
- The Viral Information Institute, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
| | - Antoni Luque
- The Viral Information Institute, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
- Department of Mathematics and Statistics, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
| | - Elizabeth A. Dinsdale
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Robert A. Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
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10
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Klonowska A, Ardley J, Moulin L, Zandberg J, Patrel D, Gollagher M, Marinova D, Reddy TBK, Varghese N, Huntemann M, Woyke T, Seshadri R, Ivanova N, Kyrpides N, Reeve W. Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018. Front Microbiol 2023; 14:1082107. [PMID: 36925474 PMCID: PMC10011098 DOI: 10.3389/fmicb.2023.1082107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/24/2023] [Indexed: 03/08/2023] Open
Abstract
Integrated virus genomes (prophages) are commonly found in sequenced bacterial genomes but have rarely been described in detail for rhizobial genomes. Cupriavidus taiwanensis STM 6018 is a rhizobial Betaproteobacteria strain that was isolated in 2006 from a root nodule of a Mimosa pudica host in French Guiana, South America. Here we describe features of the genome of STM 6018, focusing on the characterization of two different types of prophages that have been identified in its genome. The draft genome of STM 6018 is 6,553,639 bp, and consists of 80 scaffolds, containing 5,864 protein-coding genes and 61 RNA genes. STM 6018 contains all the nodulation and nitrogen fixation gene clusters common to symbiotic Cupriavidus species; sharing >99.97% bp identity homology to the nod/nif/noeM gene clusters from C. taiwanensis LMG19424T and "Cupriavidus neocalidonicus" STM 6070. The STM 6018 genome contains the genomes of two prophages: one complete Mu-like capsular phage and one filamentous phage, which integrates into a putative dif site. This is the first characterization of a filamentous phage found within the genome of a rhizobial strain. Further examination of sequenced rhizobial genomes identified filamentous prophage sequences in several Beta-rhizobial strains but not in any Alphaproteobacterial rhizobia.
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Affiliation(s)
- Agnieszka Klonowska
- Université de Montpellier, IRD, CIRAD, INRAE, Institut AgroPHIM Plant Health Institute, Montpellier, France
| | - Julie Ardley
- Centre for Crop and Food Innovation, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Lionel Moulin
- Université de Montpellier, IRD, CIRAD, INRAE, Institut AgroPHIM Plant Health Institute, Montpellier, France
| | - Jaco Zandberg
- Centre for Crop and Food Innovation, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Delphine Patrel
- Université de Montpellier, IRD, CIRAD, INRAE, Institut AgroPHIM Plant Health Institute, Montpellier, France
| | - Margaret Gollagher
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA, Australia
| | - Dora Marinova
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA, Australia
| | - T B K Reddy
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Neha Varghese
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Marcel Huntemann
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Rekha Seshadri
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nikos Kyrpides
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Wayne Reeve
- Centre for Crop and Food Innovation, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
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11
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Kupczok A, Bailey ZM, Refardt D, Wendling CC. Co-transfer of functionally interdependent genes contributes to genome mosaicism in lambdoid phages. Microb Genom 2022; 8:mgen000915. [PMID: 36748576 PMCID: PMC9836094 DOI: 10.1099/mgen.0.000915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Lambdoid (or Lambda-like) phages are a group of related temperate phages that can infect Escherichia coli and other gut bacteria. A key characteristic of these phages is their mosaic genome structure, which served as the basis for the 'modular genome hypothesis'. Accordingly, lambdoid phages evolve by transferring genomic regions, each of which constitutes a functional unit. Nevertheless, it is unknown which genes are preferentially transferred together and what drives such co-transfer events. Here we aim to characterize genome modularity by studying co-transfer of genes among 95 distantly related lambdoid (pro-)phages. Based on gene content, we observed that the genomes cluster into 12 groups, which are characterized by a highly similar gene content within the groups and highly divergent gene content across groups. Highly similar proteins can occur in genomes of different groups, indicating that they have been transferred. About 26 % of homologous protein clusters in the four known operons (i.e. the early left, early right, immunity and late operon) engage in gene transfer, which affects all operons to a similar extent. We identified pairs of genes that are frequently co-transferred and observed that these pairs tend to be near one another on the genome. We find that frequently co-transferred genes are involved in related functions and highlight interesting examples involving structural proteins, the cI repressor and Cro regulator, proteins interacting with DNA, and membrane-interacting proteins. We conclude that epistatic effects, where the functioning of one protein depends on the presence of another, play an important role in the evolution of the modular structure of these genomes.
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Affiliation(s)
- Anne Kupczok
- Bioinformatics Group, Wageningen University & Research, Wageningen, Netherlands,*Correspondence: Anne Kupczok,
| | - Zachary M. Bailey
- ETH Zürich, Institute of Integrative Biology, Universitätstrasse 16, Zürich, Switzerland
| | - Dominik Refardt
- Institute of Natural Resource Sciences, Zürich University of Applied Sciences, Campus Grüental, Wädenswil, Switzerland
| | - Carolin C. Wendling
- ETH Zürich, Institute of Integrative Biology, Universitätstrasse 16, Zürich, Switzerland
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