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Laguna-Castro M, Rodríguez-Moreno A, Llorente E, Lázaro E. The balance between fitness advantages and costs drives adaptation of bacteriophage Qβ to changes in host density at different temperatures. Front Microbiol 2023; 14:1197085. [PMID: 37303783 PMCID: PMC10248866 DOI: 10.3389/fmicb.2023.1197085] [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: 03/30/2023] [Accepted: 05/12/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction Host density is one of the main factors affecting the infective capacity of viruses. When host density is low, it is more difficult for the virus to find a susceptible cell, which increases its probability of being damaged by the physicochemical agents of the environment. Nevertheless, viruses can adapt to variations in host density through different strategies that depend on the particular characteristics of the life cycle of each virus. In a previous work, using the bacteriophage Qβ as an experimental model, we found that when bacterial density was lower than optimal the virus increased its capacity to penetrate into the bacteria through a mutation in the minor capsid protein (A1) that is not described to interact with the cell receptor. Results Here we show that the adaptive pathway followed by Qβ in the face of similar variations in host density depends on environmental temperature. When the value for this parameter is lower than optimal (30°C), the mutation selected is the same as at the optimal temperature (37°C). However, when temperature increases to 43°C, the mutation selected is located in a different protein (A2), which is involved both in the interaction with the cell receptor and in the process of viral progeny release. The new mutation increases the entry of the phage into the bacteria at the three temperatures assayed. However, it also considerably increases the latent period at 30 and 37°C, which is probably the reason why it is not selected at these temperatures. Conclusion The conclusion is that the adaptive strategies followed by bacteriophage Qβ, and probably other viruses, in the face of variations in host density depend not only on their advantages at this selective pressure, but also on the fitness costs that particular mutations may present in function of the rest of environmental parameters that influence viral replication and stability.
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Hawley DM, Gibson AK, Townsend AK, Craft ME, Stephenson JF. Bidirectional interactions between host social behaviour and parasites arise through ecological and evolutionary processes. Parasitology 2021; 148:274-288. [PMID: 33092680 PMCID: PMC11010184 DOI: 10.1017/s0031182020002048] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 02/07/2023]
Abstract
An animal's social behaviour both influences and changes in response to its parasites. Here we consider these bidirectional links between host social behaviours and parasite infection, both those that occur from ecological vs evolutionary processes. First, we review how social behaviours of individuals and groups influence ecological patterns of parasite transmission. We then discuss how parasite infection, in turn, can alter host social interactions by changing the behaviour of both infected and uninfected individuals. Together, these ecological feedbacks between social behaviour and parasite infection can result in important epidemiological consequences. Next, we consider the ways in which host social behaviours evolve in response to parasites, highlighting constraints that arise from the need for hosts to maintain benefits of sociality while minimizing fitness costs of parasites. Finally, we consider how host social behaviours shape the population genetic structure of parasites and the evolution of key parasite traits, such as virulence. Overall, these bidirectional relationships between host social behaviours and parasites are an important yet often underappreciated component of population-level disease dynamics and host-parasite coevolution.
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Affiliation(s)
- Dana M. Hawley
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA24061, USA
| | - Amanda K. Gibson
- Department of Biology, University of Virginia, Charlottesville, VA22903, USA
| | | | - Meggan E. Craft
- Department of Veterinary Population Medicine and Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN55108, USA
| | - Jessica F. Stephenson
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA15260, USA
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Hitchhiking, collapse, and contingency in phage infections of migrating bacterial populations. ISME JOURNAL 2020; 14:2007-2018. [PMID: 32358533 DOI: 10.1038/s41396-020-0664-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 04/05/2020] [Accepted: 04/15/2020] [Indexed: 01/17/2023]
Abstract
Natural bacterial populations are subjected to constant predation pressure by bacteriophages. Bacteria use a variety of molecular mechanisms to defend themselves from phage predation. However, since phages are nonmotile, perhaps the simplest defense against phage is for bacteria to move faster than phages. In particular, chemotaxis, the active migration of bacteria up attractant gradients, may help the bacteria escape slowly diffusing phages. Here we study phage infection dynamics in migrating bacterial populations driven by chemotaxis through low viscosity agar plates. We find that expanding phage-bacteria populations supports two moving fronts, an outermost bacterial front driven by nutrient uptake and chemotaxis and an inner phage front at which the bacterial population collapses due to phage predation. We show that with increasing adsorption rate and initial phage population, the speed of the moving phage front increases, eventually overtaking the bacterial front and driving the system across a transition from a regime where bacterial front speed exceeds that of the phage front to one where bacteria must evolve phage resistance to survive. Our data support the claim that this process requires phage to hitchhike with moving bacteria. A deterministic model recapitulates the transition under the assumption that phage virulence declines with host growth rate which we confirm experimentally. Finally, near the transition between regimes we observe macroscopic fluctuations in bacterial densities at the phage front. Our work opens a new, spatio-temporal, line of investigation into the eco-evolutionary struggle between bacteria and phage.
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Abedon ST. Phage "delay" towards enhancing bacterial escape from biofilms: a more comprehensive way of viewing resistance to bacteriophages. AIMS Microbiol 2017; 3:186-226. [PMID: 31294157 PMCID: PMC6605007 DOI: 10.3934/microbiol.2017.2.186] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 03/17/2017] [Indexed: 12/15/2022] Open
Abstract
In exploring bacterial resistance to bacteriophages, emphasis typically is placed on those mechanisms which completely prevent phage replication. Such resistance can be detected as extensive reductions in phage ability to form plaques, that is, reduced efficiency of plating. Mechanisms include restriction-modification systems, CRISPR/Cas systems, and abortive infection systems. Alternatively, phages may be reduced in their “vigor” when infecting certain bacterial hosts, that is, with phages displaying smaller burst sizes or extended latent periods rather than being outright inactivated. It is well known, as well, that most phages poorly infect bacteria that are less metabolically active. Extracellular polymers such as biofilm matrix material also may at least slow phage penetration to bacterial surfaces. Here I suggest that such “less-robust” mechanisms of resistance to bacteriophages could serve bacteria by slowing phage propagation within bacterial biofilms, that is, delaying phage impact on multiple bacteria rather than necessarily outright preventing such impact. Related bacteria, ones that are relatively near to infected bacteria, e.g., roughly 10+ µm away, consequently may be able to escape from biofilms with greater likelihood via standard dissemination-initiating mechanisms including erosion from biofilm surfaces or seeding dispersal/central hollowing. That is, given localized areas of phage infection, so long as phage spread can be reduced in rate from initial points of contact with susceptible bacteria, then bacterial survival may be enhanced due to bacteria metaphorically “running away” to more phage-free locations. Delay mechanisms—to the extent that they are less specific in terms of what phages are targeted—collectively could represent broader bacterial strategies of phage resistance versus outright phage killing, the latter especially as require specific, evolved molecular recognition of phage presence. The potential for phage delay should be taken into account when developing protocols of phage-mediated biocontrol of biofilm bacteria, e.g., as during phage therapy of chronic bacterial infections.
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Affiliation(s)
- Stephen T Abedon
- Department of Microbiology, the Ohio State University, 1680 University Dr., Mansfield, OH 44906, USA
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5
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Sistrom M, Park D, O’Brien HE, Wang Z, Guttman DS, Townsend JP, Turner PE. Genomic and Gene-Expression Comparisons among Phage-Resistant Type-IV Pilus Mutants of Pseudomonas syringae pathovar phaseolicola. PLoS One 2015; 10:e0144514. [PMID: 26670219 PMCID: PMC4687649 DOI: 10.1371/journal.pone.0144514] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 11/19/2015] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas syringae pv. phaseolicola (Pph) is a significant bacterial pathogen of agricultural crops, and phage Φ6 and other members of the dsRNA virus family Cystoviridae undergo lytic (virulent) infection of Pph, using the type IV pilus as the initial site of cellular attachment. Despite the popularity of Pph/phage Φ6 as a model system in evolutionary biology, Pph resistance to phage Φ6 remains poorly characterized. To investigate differences between phage Φ6 resistant Pph strains, we examined genomic and gene expression variation among three bacterial genotypes that differ in the number of type IV pili expressed per cell: ordinary (wild-type), non-piliated, and super-piliated. Genome sequencing of non-piliated and super-piliated Pph identified few mutations that separate these genotypes from wild type Pph--and none present in genes known to be directly involved in type IV pilus expression. Expression analysis revealed that 81.1% of gene ontology (GO) terms up-regulated in the non-piliated strain were down-regulated in the super-piliated strain. This differential expression is particularly prevalent in genes associated with respiration--specifically genes in the tricarboxylic acid cycle (TCA) cycle, aerobic respiration, and acetyl-CoA metabolism. The expression patterns of the TCA pathway appear to be generally up and down-regulated, in non-piliated and super-piliated Pph respectively. As pilus retraction is mediated by an ATP motor, loss of retraction ability might lead to a lower energy draw on the bacterial cell, leading to a different energy balance than wild type. The lower metabolic rate of the super-piliated strain is potentially a result of its loss of ability to retract.
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Affiliation(s)
- Mark Sistrom
- School of Natural Sciences, University of California Merced, Merced, 95343, CA, United States of America
- * E-mail:
| | - Derek Park
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, United States of America
| | - Heath E. O’Brien
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
| | - Zheng Wang
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, United States of America
| | - David S. Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Ontario, M5S 3B2, Canada
| | - Jeffrey P. Townsend
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, United States of America
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06520, United States of America
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, United States of America
- Program in Microbiology, Yale University, New Haven, CT 06520, United States of America
| | - Paul E. Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, United States of America
- Program in Microbiology, Yale University, New Haven, CT 06520, United States of America
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Abstract
Why is it that some parasites cause high levels of host damage (i.e. virulence) whereas others are relatively benign? There are now numerous reviews of virulence evolution in the literature but it is nevertheless still difficult to find a comprehensive treatment of the theory and data on the subject that is easily accessible to non-specialists. Here we attempt to do so by distilling the vast theoretical literature on the topic into a set of relatively few robust predictions. We then provide a comprehensive assessment of the available empirical literature that tests these predictions. Our results show that there have been some notable successes in integrating theory and data but also that theory and empiricism in this field do not ‘speak’ to each other very well. We offer a few suggestions for how the connection between the two might be improved.
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Abstract
PHAGE TARGETS FOR ADSORPTION CAN INCLUDE: (1) individual bacteria; (2) bacterial cellular arrangements such as streptococci; (3) microcolonies consisting of bacterial clones as can make up bacterial lawns and biofilms; and (4) bacterial biofilms themselves. While much effort has gone into considering category 1, and some into category 4, substantially less has been put into the question of how bacterial association into clonal arrangements or microcolonies might affect phage-bacterial interactions. Recently I have been exploring just this issue-within a single-authored monograph published in 2011 and a theoretical article published in 2012 as part of a special issue of the journal, Viruses. For this commentary, I have been invited to summarize my thinking on how bacterial association into either cellular arrangements or microcolonies might affect their susceptibility to phages along with related issues of bacterial resistance to phages and phage propagation in the context of both plaques and biofilms.
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Affiliation(s)
- Stephen T Abedon
- Department of Microbiology; The Ohio State University; Mansfield, OH USA
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8
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Ally D, Wiss VR, Deckert GE, Green D, Roychoudhury P, Wichman HA, Brown CJ, Krone SM. The impact of spatial structure on viral genomic diversity generated during adaptation to thermal stress. PLoS One 2014; 9:e88702. [PMID: 24533140 PMCID: PMC3922989 DOI: 10.1371/journal.pone.0088702] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 01/10/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Most clinical and natural microbial communities live and evolve in spatially structured environments. When changes in environmental conditions trigger evolutionary responses, spatial structure can impact the types of adaptive response and the extent to which they spread. In particular, localized competition in a spatial landscape can lead to the emergence of a larger number of different adaptive trajectories than would be found in well-mixed populations. Our goal was to determine how two levels of spatial structure affect genomic diversity in a population and how this diversity is manifested spatially. METHODOLOGY/PRINCIPAL FINDINGS We serially transferred bacteriophage populations growing at high temperatures (40°C) on agar plates for 550 generations at two levels of spatial structure. The level of spatial structure was determined by whether the physical locations of the phage subsamples were preserved or disrupted at each passage to fresh bacterial host populations. When spatial structure of the phage populations was preserved, there was significantly greater diversity on a global scale with restricted and patchy distribution. When spatial structure was disrupted with passaging to fresh hosts, beneficial mutants were spread across the entire plate. This resulted in reduced diversity, possibly due to clonal interference as the most fit mutants entered into competition on a global scale. Almost all substitutions present at the end of the adaptation in the populations with disrupted spatial structure were also present in the populations with structure preserved. CONCLUSIONS/SIGNIFICANCE Our results are consistent with the patchy nature of the spread of adaptive mutants in a spatial landscape. Spatial structure enhances diversity and slows fixation of beneficial mutants. This added diversity could be beneficial in fluctuating environments. We also connect observed substitutions and their effects on fitness to aspects of phage biology, and we provide evidence that some substitutions exclude each other.
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Affiliation(s)
- Dilara Ally
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
| | - Valorie R. Wiss
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
| | - Gail E. Deckert
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, United States of America
| | - Danielle Green
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Pavitra Roychoudhury
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- Department of Mathematics, University of Idaho, Moscow, Idaho, United States of America
| | - Holly A. Wichman
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
| | - Celeste J. Brown
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
| | - Stephen M. Krone
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- Department of Mathematics, University of Idaho, Moscow, Idaho, United States of America
- * E-mail:
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9
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Keen EC. Tradeoffs in bacteriophage life histories. BACTERIOPHAGE 2014; 4:e28365. [PMID: 24616839 PMCID: PMC3942329 DOI: 10.4161/bact.28365] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 02/24/2014] [Accepted: 02/26/2014] [Indexed: 11/19/2022]
Abstract
Viruses are the most abundant biological entities on the planet, yet most classical principles of evolutionary biology and ecology were not developed with viruses in mind. Here, the concept of biological tradeoffs, a fundamental tenet of life history theory, is examined in the context of bacteriophage biology. Specifically, several important parameters of phage life histories-replication, persistence, host range, and adsorption-are evaluated for tradeoffs. Available data indicate that replication rate is strongly negatively correlated with both persistence and host range, suggesting that the well-documented tradeoff in macroorganisms between offspring production and offspring quality also applies to phages. The biological tradeoffs that appear to characterize viruses' life histories have potential importance for viral evolution, ecology, and pathogenesis.
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Affiliation(s)
- Eric C Keen
- Department of Biology; University of Miami; Coral Gables, FL USA
- Laboratory of Molecular Biology; Center for Cancer Research; National Cancer Institute; National Institutes of Health; Bethesda, MD USA
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10
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Taylor TB, Buckling A. Bacterial motility confers fitness advantage in the presence of phages. J Evol Biol 2013; 26:2154-60. [PMID: 23937523 DOI: 10.1111/jeb.12214] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 06/03/2013] [Accepted: 06/06/2013] [Indexed: 01/13/2023]
Abstract
Dispersal provides the opportunity to escape harm and colonize new patches, enabling populations to expand and persist. However, the benefits of dispersal associated with escaping harm will be dependent on the structure of the environment and the likelihood of escape. Here, we empirically investigate how the spatial distribution of a parasite influences the evolution of host dispersal. Bacteriophages are a strong and common threat for bacteria in natural environments and offer a good system with which to explore parasite-mediated selection on host dispersal. We used two transposon mutants of the opportunistic bacteria, Pseudomonas aeruginosa, which varied in their motility (a disperser and a nondisperser), and the lytic bacteriophage ФKZ. The phage was distributed either in the central point of colony inoculation only, thus offering an escape route for the dispersing bacteria; or, present throughout the agar, where benefits of dispersal might be lost. Surprisingly, we found dispersal to be equally advantageous under both phage conditions relative to when phages were absent. A general explanation is that dispersal decreased the spatial structuring of host population, reducing opportunities for parasite transmission, but other more idiosyncratic mechanisms may also have contributed. This study highlights the crucial role the parasites can play on the evolution of dispersal and, more specifically, that bacteriophages, which are ubiquitous, are likely to select for bacterial motility.
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Affiliation(s)
- T B Taylor
- Biological Sciences, University of Reading, Reading, UK
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11
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Brown CJ, Millstein J, Williams CJ, Wichman HA. Selection affects genes involved in replication during long-term evolution in experimental populations of the bacteriophage φX174. PLoS One 2013; 8:e60401. [PMID: 23533679 PMCID: PMC3606162 DOI: 10.1371/journal.pone.0060401] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 02/26/2013] [Indexed: 11/18/2022] Open
Abstract
Observing organisms that evolve in response to strong selection over very short time scales allows the determination of the molecular mechanisms underlying adaptation. Although dissecting these molecular mechanisms is expensive and time-consuming, general patterns can be detected from repeated experiments, illuminating the biological processes involved in evolutionary adaptation. The bacteriophage φX174 was grown for 50 days in replicate chemostats under two culture conditions: Escherichia coli C as host growing at 37°C and Salmonella typhimurium as host growing at 43.5°C. After 50 days, greater than 20 substitutions per chemostat had risen to detectable levels. Of the 97 substitutions, four occurred in all four chemostats, five arose in both culture conditions, eight arose in only the high temperature S. typhimurium chemostats, and seven arose only in the E. coli chemostats. The remaining substitutions were detected only in a single chemostat, however, almost half of these have been seen in other similar experiments. Our findings support previous studies that host recognition and capsid stability are two biological processes that are modified during adaptation to novel hosts and high temperature. Based upon the substitutions shared across both environments, it is apparent that genome replication and packaging are also affected during adaptation to the chemostat environment, rather than to temperature or host per se. This environment is characterized by a large number of phage and very few hosts, leading to competition among phage within the host. We conclude from these results that adaptation to a high density environment selects for changes in genome replication at both protein and DNA sequence levels.
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Affiliation(s)
- Celeste J Brown
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America.
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12
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Methicillin-resistant Staphylococcus aureus phage plaque size enhancement using sublethal concentrations of antibiotics. Appl Environ Microbiol 2012; 78:8227-33. [PMID: 23001655 DOI: 10.1128/aem.02371-12] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phage therapy presents an alternative approach against the emerging methicillin-resistant Staphylococcus aureus (MRSA) threat. Some of the problems encountered during isolation of MRSA phages include the high prevalence of enteric phages in natural sources, nonspecific absorption of viable phage, and the formation of pinpoint or tiny plaques. The phage isolated in this study, MR-5, also formed tiny plaques against its host S. aureus ATCC 43300 (MRSA), making its detection and enumeration difficult. An improved method of increasing the plaque size of MRSA phage by incorporating sublethal concentrations of three different classes of antibiotics (inhibitors of protein synthesis) in the classical double-layer agar (DLA) method was investigated. The β-lactam and quinolone antibiotics commonly employed in earlier studies for increasing the plaque size did not show any significant effect on the plaque size of isolated MR-5 phage. Linezolid (oxazolidinone class), tetracycline, and ketolide antibiotics brought significant enhancements (3 times the original size) in the plaque size of MR-5 phage. Prior treatment with these antibiotics resulted in significant reductions in the time of adsorption and the latent period of MR-5 phage. To rule out whether the action of linezolid (which brought the maximum increase in plaque size) was specific for a single phage only, its effect on the plaque size of seven other S. aureus-specific phages was also assessed. Significant enhancements in the plaque size of these phages were observed. These results indicate that this modification can therefore safely be incorporated in the traditional DLA overlay method to search for new MRSA-virulent phages.
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Turner PE, Draghi JA, Wilpiszeski R. High-throughput analysis of growth differences among phage strains. J Microbiol Methods 2012; 88:117-21. [DOI: 10.1016/j.mimet.2011.10.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 10/29/2011] [Accepted: 10/29/2011] [Indexed: 11/28/2022]
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14
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Al-Jarbou AN. Genomic library screening for viruses from the human dental plaque revealed pathogen-specific lytic phage sequences. Curr Microbiol 2011; 64:1-6. [PMID: 21969025 DOI: 10.1007/s00284-011-0025-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2011] [Accepted: 09/17/2011] [Indexed: 10/17/2022]
Abstract
Bacterial pathogenesis presents an astounding arsenal of virulence factors that allow them to conquer many different niches throughout the course of infection. Principally fascinating is the fact that some bacterial species are able to induce different diseases by expression of different combinations of virulence factors. Nevertheless, studies aiming at screening for the presence of bacteriophages in humans have been limited. Such screening procedures would eventually lead to identification of phage-encoded properties that impart increased bacterial fitness and/or virulence in a particular niche, and hence, would potentially be used to reverse the course of bacterial infections. As the human oral cavity represents a rich and dynamic ecosystem for several upper respiratory tract pathogens. However, little is known about virus diversity in human dental plaque which is an important reservoir. We applied the culture-independent approach to characterize virus diversity in human dental plaque making a library from a virus DNA fraction amplified using a multiple displacement method and sequenced 80 clones. The resulting sequence showed 44% significant identities to GenBank databases by TBLASTX analysis. TBLAST homology comparisons showed that 66% was viral; 18% eukarya; 10% bacterial; 6% mobile elements. These sequences were sorted into 6 contigs and 45 single sequences in which 4 contigs and a single sequence showed significant identity to a small region of a putative prophage in the Corynebacterium diphtheria genome. These findings interestingly highlight the uniqueness of over half of the sequences, whilst the dominance of a pathogen-specific prophage sequences imply their role in virulence.
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Affiliation(s)
- Ahmed Nasser Al-Jarbou
- Department of Pharmaceutics, College of Pharmacy, Qassim University, Buraidah, Saudi Arabia.
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15
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Gallet R, Kannoly S, Wang IN. Effects of bacteriophage traits on plaque formation. BMC Microbiol 2011; 11:181. [PMID: 21827665 PMCID: PMC3176204 DOI: 10.1186/1471-2180-11-181] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Accepted: 08/09/2011] [Indexed: 11/10/2022] Open
Abstract
Background The appearance of plaques on a bacterial lawn is one of the enduring imageries in modern day biology. The seeming simplicity of a plaque has invited many hypotheses and models in trying to describe and explain the details of its formation. However, until now, there has been no systematic experimental exploration on how different bacteriophage (phage) traits may influence the formation of a plaque. In this study, we constructed a series of isogenic λ phages that differ in their adsorption rate, lysis timing, or morphology so that we can determine the effects if these changes on three plaque properties: size, progeny productivity, and phage concentration within plaques. Results We found that the adsorption rate has a diminishing, but negative impact on all three plaque measurements. Interestingly, there exists a concave relationship between the lysis time and plaque size, resulting in an apparent optimal lysis time that maximizes the plaque size. Although suggestive in appearance, we did not detect a significant effect of lysis time on plaque productivity. Nonetheless, the combined effects of plaque size and productivity resulted in an apparent convex relationship between the lysis time and phage concentration within plaques. Lastly, we found that virion morphology also affected plaque size. We compared our results to the available models on plaque size and productivity. For the models in their current forms, a few of them can capture the qualitative aspects of our results, but not consistently in both plaque properties. Conclusions By using a collection of isogenic phage strains, we were able to investigate the effects of individual phage traits on plaque size, plaque productivity, and average phage concentration in a plaque while holding all other traits constant. The controlled nature of our study allowed us to test several model predictions on plaque size and plaque productivity. It seems that a more realistic theoretical approach to plaque formation is needed in order to capture the complex interaction between phage and its bacterium host in a spatially restricted environment.
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Affiliation(s)
- Romain Gallet
- Department of Biological Sciences, University at Albany, 1400 Washington Avenue, Albany, New York 12222, USA.
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16
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O'Keefe KJ, Silander OK, McCreery H, Weinreich DM, Wright KM, Chao L, Edwards SV, Remold SK, Turner PE. Geographic differences in sexual reassortment in RNA phage. Evolution 2010; 64:3010-23. [PMID: 20500219 DOI: 10.1111/j.1558-5646.2010.01040.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The genetic structure of natural bacteriophage populations is poorly understood. Recent metagenomic studies suggest that phage biogeography is characterized by frequent migration. Using virus samples mostly isolated in Southern California, we recently showed that very little population structure exists in segmented RNA phage of the Cystoviridae family due to frequent segment reassortment (sexual genetic mixis) between unrelated virus individuals. Here we use a larger genetic dataset to examine the structure of Cystoviridae phage isolated from three geographic locations in Southern New England. We document extensive natural variation in the physical sizes of RNA genome segments for these viruses. In addition, consistent with earlier findings, our phylogenetic analyses and calculations of linkage disequilibrium (LD) show no evidence of within-segment recombination in wild populations. However, in contrast to the prior study, our analysis finds that reassortment of segments between individual phage plays a lesser role among cystoviruses sampled in New England, suggesting that the evolutionary importance of genetic mixis in Cystoviridae phage may vary according to geography. We discuss possible explanations for these conflicting results across the studies, such as differing local ecology and its impact on phage growth, and geographic differences in selection against hybrid phage genotypes.
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Affiliation(s)
- Kara J O'Keefe
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520-8106, USA
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Bacteriophages as model organisms for virus emergence research. Trends Microbiol 2009; 17:450-7. [PMID: 19765997 PMCID: PMC7127698 DOI: 10.1016/j.tim.2009.07.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Revised: 06/29/2009] [Accepted: 07/10/2009] [Indexed: 12/18/2022]
Abstract
Viruses fully emerge by gaining the ability to sustainably infect new host populations. When the hosts are humans, emerging viruses can present major public health issues, as exemplified by the AIDS pandemic. Therefore, heuristic approaches to identify nascent diseases before they become pandemic would be valuable. Unfortunately, the current patient-based and epidemiological approaches are ill-suited in this regard because they are largely responsive and not predictive. Alternative approaches based on virus evolutionary ecology might have greater potential to predict virus emergence. However, given the difficulties encountered when studying metazoan viruses in this context, the development of new model systems is greatly desirable. Here, I highlight studies that show that bacteriophages are appropriate model organisms for virus emergence research because of the ease in which important population parameters can be manipulated. Ideally this research will permit identifying major factors determining the persistence or extinction of emerging viruses. If such viruses could be recognized in advance, patient-based and epidemiological strategies could be better mobilized to deal with them.
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Abstract
Laboratory characterization of bacteriophage growth traditionally is done either in broth cultures or in semisolid agar media. These two environments may be distinguished in terms of their spatial structure, i.e., the degree to which they limit diffusion, motility, and environmental mixing. Well-mixed broth, for example, represents the microbiological ideal of a non-spatially structured environment. Agar, by contrast, imposes significant limitations on phage and bacterial movement and therefore gives rise to spatial structure. The study of phage growth within spatially structured environments, such as that seen during phage plaque formation, is important for three reasons. First, a large fraction of environmental bacteria live within spatially structured environments such as within biofilms, within soil, or when growing in or on the tissues of plants and animals. Second, phage growth as plaques is a central technique to phage studies, yet appears to be under appreciated by phage workers in terms of its complexity. Third, selective pressures acting on phage during plaque growth differ from those seen during broth growth. In this chapter we will discuss just what a plaque is, how one forms, and what can affect plaque size. We will describe methods, both experimental and theoretical, that have been employed to study plaque growth. As caveats we will discuss why plaque formation failure is not necessarily equivalent to virion inviability (Note 1). We also will consider problems with inferring phage broth growth fitness as a function of plaque characteristics (Note 2).
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Ecology and evolution in microbial systems: the generation and maintenance of diversity in phage–host interactions. Res Microbiol 2008; 159:382-9. [DOI: 10.1016/j.resmic.2008.05.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 05/14/2008] [Accepted: 05/15/2008] [Indexed: 11/24/2022]
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