1
|
Huisman JS, Bernhard A, Igler C. Should I stay or should I go: transmission trade-offs in phages and plasmids. Trends Microbiol 2025:S0966-842X(25)00007-1. [PMID: 39979200 DOI: 10.1016/j.tim.2025.01.007] [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: 11/04/2024] [Revised: 01/13/2025] [Accepted: 01/15/2025] [Indexed: 02/22/2025]
Abstract
Mobile genetic elements (MGEs), like temperate bacteriophages and conjugative plasmids, are major vectors of virulence and antibiotic resistance in bacterial populations. For reproductive success, MGEs must balance horizontal and vertical transmission. Yet, the cost of horizontal transmission (metabolic burden or host death) puts these transmission modes at odds. Using virulence-transmission trade-off (VTT) theory, we identify three groups of environmental variables affecting the balance between horizontal and vertical transmission: host density, host physiology, and competitors. We find that general theoretical predictions of the optimal response to environmental cues align with experimental evidence on the regulation of transmission by phages and plasmids. We further highlight gaps between theory and experiments, differences between phages and plasmids, and suggest areas for future research.
Collapse
Affiliation(s)
- Jana S Huisman
- Physics of Living Systems, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Andrina Bernhard
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Claudia Igler
- Division of Evolution, Infection, and Genomics, School of Biological Sciences, University of Manchester, Manchester, UK
| |
Collapse
|
2
|
Cordisco E, Serra DO. Moonlighting antibiotics: the extra job of modulating biofilm formation. Trends Microbiol 2025:S0966-842X(24)00327-5. [PMID: 39828459 DOI: 10.1016/j.tim.2024.12.011] [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: 10/07/2024] [Revised: 12/19/2024] [Accepted: 12/23/2024] [Indexed: 01/22/2025]
Abstract
The widespread use of antibiotics to treat bacterial infections has led to the common perception that their only function is to inhibit growth or kill bacteria. However, it has become clear that when antibiotics reach susceptible bacteria at non-lethal concentrations, they perform additional functions that significantly impact bacterial physiology, shaping both individual and collective behaviors. A key bacterial behavior influenced by sub-lethal antibiotic doses is biofilm formation, a multicellular, surface-associated mode of growth. This review explores different contexts in which natural and clinical antibiotics act as modulators of bacterial biofilm formation. We discuss cases that provide mechanistic insights into antibiotic modes of action, highlighting emerging common patterns and novel findings that pave the way for future research.
Collapse
Affiliation(s)
- Estefanía Cordisco
- Laboratorio de Estructura y Fisiología de Biofilms Microbianos, Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, Ocampo y Esmeralda, (2000) Rosario, Argentina
| | - Diego Omar Serra
- Laboratorio de Estructura y Fisiología de Biofilms Microbianos, Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, Ocampo y Esmeralda, (2000) Rosario, Argentina.
| |
Collapse
|
3
|
Dieppa-Colón E, Martin C, Kosmopoulos JC, Anantharaman K. Prophage-DB: a comprehensive database to explore diversity, distribution, and ecology of prophages. ENVIRONMENTAL MICROBIOME 2025; 20:5. [PMID: 39806487 PMCID: PMC11730488 DOI: 10.1186/s40793-024-00659-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2024] [Accepted: 12/17/2024] [Indexed: 01/16/2025]
Abstract
BACKGROUND Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact microbial community dynamics, microbial ecology, and evolution. Efforts to document the diversity, host range, infection dynamics, and effects of bacteriophage infection on host cell metabolism are extremely underexplored. Phages are classified as virulent or temperate based on their life cycles. Temperate phages adopt the lysogenic mode of infection, where the genome integrates into the host cell genome forming a prophage. Prophages enable viral genome replication without host cell lysis, and often contribute novel and beneficial traits to the host genome. Current phage research predominantly focuses on lytic phages, leaving a significant gap in knowledge regarding prophages, including their biology, diversity, and ecological roles. RESULTS Here we develop and describe Prophage-DB, a database of prophages, their proteins, and associated metadata that will serve as a resource for viral genomics and microbial ecology. To create the database, we identified and characterized prophages from genomes in three of the largest publicly available databases. We applied several state-of-the-art tools in our pipeline to annotate these viruses, cluster them, taxonomically classify them, and detect their respective auxiliary metabolic genes. In total, we identify and characterize over 350,000 prophages and 35,000 auxiliary metabolic genes. Our prophage database is highly representative based on statistical results and contains prophages from a diverse set of archaeal and bacterial hosts which show a wide environmental distribution. CONCLUSION Given that prophages are particularly overlooked and merit increased attention due to their vital implications for microbiomes and their hosts, we created Prophage-DB to advance our understanding of prophages in microbiomes through a comprehensive characterization of prophages in publicly available genomes. We propose that Prophage-DB will serve as a valuable resource for advancing phage research, offering insights into viral taxonomy, host relationships, auxiliary metabolic genes, and environmental distribution.
Collapse
Affiliation(s)
- Etan Dieppa-Colón
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Cody Martin
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - James C Kosmopoulos
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Data Science and AI, Indian Institute of Technology Madras, Chennai, TN, India.
| |
Collapse
|
4
|
Sargen MR, Helaine S. A prophage competition element protects Salmonella from lysis. Cell Host Microbe 2024; 32:2063-2079.e8. [PMID: 39515326 PMCID: PMC11840918 DOI: 10.1016/j.chom.2024.10.012] [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: 06/27/2024] [Revised: 09/11/2024] [Accepted: 10/16/2024] [Indexed: 11/16/2024]
Abstract
Most bacteria are polylysogens that carry multiple prophages integrated into the chromosome. These prophages confer advantages to their bacterial host, yet also pose a lethal threat as they can reactivate and enter a lytic cycle. DNA damage of the bacterial host is a common trigger of prophage lytic cycles. Because DNA damage is frequently experienced by bacterial pathogens exposed to host immune defenses, prophage activation may be common during infection. Investigating the consequences of prophage induction in Salmonella, we discover a prophage competition element in the Gifsy-1 prophage that we name ribonuclease effector module with ATPase, inhibitor, and nuclease (RemAIN) because it blocks the lytic cycles and release of viral particles of co-resident prophages. Intramacrophage Salmonella persisters, a subpopulation that incurs DNA damage, experience prophage reactivation and subsequent RemAIN activation, which influences Salmonella persisters and macrophage response to infection. Our findings reveal a multi-layered host-pathogen arms race in which prophage-prophage competition influences bacterial persistence and the mammalian immune response.
Collapse
Affiliation(s)
- Molly R Sargen
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Sophie Helaine
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
| |
Collapse
|
5
|
Richards VA, Ferrell BD, Polson SW, Wommack KE, Fuhrmann JJ. Soybean Bradyrhizobium spp. Spontaneously Produce Abundant and Diverse Temperate Phages in Culture. Viruses 2024; 16:1750. [PMID: 39599864 PMCID: PMC11599138 DOI: 10.3390/v16111750] [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: 10/07/2024] [Revised: 11/03/2024] [Accepted: 11/04/2024] [Indexed: 11/29/2024] Open
Abstract
Soybean bradyrhizobia (Bradyrhizobium spp.) are symbiotic root-nodulating bacteria that fix atmospheric nitrogen for the host plant. The University of Delaware Bradyrhizobium Culture Collection (UDBCC; 353 accessions) was created to study the diversity and ecology of soybean bradyrhizobia. Some UDBCC accessions produce temperate (lysogenic) bacteriophages spontaneously under routine culture conditions without chemical or other apparent inducing agents. Spontaneous phage production may promote horizontal gene transfer and shape bacterial genomes and associated phenotypes. A diverse subset (n = 98) of the UDBCC was examined for spontaneously produced virus-like particles (VLPs) using epifluorescent microscopy, with a majority (69%) producing detectable VLPs (>1 × 107 mL-1) in laboratory culture. Phages from the higher-producing accessions (>2.0 × 108 VLP mL-1; n = 44) were examined using transmission electron microscopy. Diverse morphologies were observed, including various tail types and lengths, capsid sizes and shapes, and the presence of collars or baseplates. In many instances, putative extracellular vesicles of a size similar to virions were also observed. Three of the four species examined (B. japonicum, B. elkanii, and B. diazoefficiens) produced apparently tailless phages. All species except B. ottawaense also produced siphovirus-like phages, while all but B. diazoefficiens additionally produced podovirus-like phages. Myovirus-like phages were restricted to B. japonicum and B. elkanii. At least three strains were polylysogens, producing up to three distinct morphotypes. These observations suggest spontaneously produced phages may play a significant role in the ecology and evolution of soybean bradyrhizobia.
Collapse
Affiliation(s)
- Vanessa A. Richards
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Barbra D. Ferrell
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
| | - Shawn W. Polson
- Department of Computer and Information Sciences, University of Delaware, Newark, DE 19713, USA
- Microbiology Graduate Program, University of Delaware, Newark, DE 19713, USA
| | - K. Eric Wommack
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
- Microbiology Graduate Program, University of Delaware, Newark, DE 19713, USA
| | - Jeffry J. Fuhrmann
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
- Microbiology Graduate Program, University of Delaware, Newark, DE 19713, USA
| |
Collapse
|
6
|
Warrell DL, Zarrella TM, Machalek C, Khare A. Interspecies surfactants serve as public goods enabling surface motility in Pseudomonas aeruginosa. J Bacteriol 2024; 206:e0028124. [PMID: 39235232 PMCID: PMC11500613 DOI: 10.1128/jb.00281-24] [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: 07/09/2024] [Accepted: 08/02/2024] [Indexed: 09/06/2024] Open
Abstract
In most natural environments, bacteria live in polymicrobial communities where secreted molecules from neighboring species alter bacterial behaviors, including motility, but such interactions are understudied. Pseudomonas aeruginosa is a motile opportunistic pathogen that exists in diverse multispecies environments, such as the soil, and is frequently found in human wound and respiratory tract co-infections with other bacteria, including Staphylococcus aureus. Here, we show that P. aeruginosa can co-opt secreted surfactants from other species for flagellar-based surface motility. We found that exogenous surfactants from S. aureus, other bacteria, and interkingdom species enabled P. aeruginosa to switch from swarming to an alternative surface spreading motility on semi-solid surfaces and allowed for the emergence of surface motility on hard agar where P. aeruginosa was otherwise unable to move. Although active flagellar function was required for surface spreading, known motility regulators were not essential, indicating that surface spreading may be regulated by an as yet unknown mechanism. This motility was distinct from the response of most other motile bacterial species in the presence of exogenous surfactants. Mutant analysis indicated that this P. aeruginosa motility was similar to a previously described mucin-based motility, "surfing," albeit with divergent regulation. Thus, our study demonstrates that secreted surfactants from the host as well as neighboring bacterial and interkingdom species act as public goods facilitating P. aeruginosa flagella-mediated surfing-like surface motility, thereby allowing it to access different environmental niches. IMPORTANCE Bacterial motility is an important determinant of bacterial fitness and pathogenesis, allowing expansion and invasion to access nutrients and adapt to new environments. Here, we demonstrate that secreted surfactants from a variety of foreign species, including other bacterial species, infection hosts, fungi, and plants, facilitate surface spreading motility in the opportunistic pathogen Pseudomonas aeruginosa that is distinct from established motility phenotypes. This response to foreign surfactants also occurs in Pseudomonas putida, but not in more distantly related bacterial species. Our systematic characterization of surfactant-based surface spreading shows that these interspecies surfactants serve as public goods to enable P. aeruginosa to move and explore environmental conditions when it would be otherwise immotile.
Collapse
Affiliation(s)
- Delayna L. Warrell
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Tiffany M. Zarrella
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
- Postdoctoral Research Associate Training Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, Maryland, USA
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Christopher Machalek
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Anupama Khare
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
7
|
Dieppa-Colón E, Martin C, Anantharaman K. Prophage-DB: A comprehensive database to explore diversity, distribution, and ecology of prophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.603044. [PMID: 39071402 PMCID: PMC11275716 DOI: 10.1101/2024.07.11.603044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Background Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact microbial community dynamics, microbial ecology, and evolution. Efforts to document the diversity, host range, infection dynamics, and effects of bacteriophage infection on host cell metabolism are extremely underexplored. Phages are classified as virulent or temperate based on their life cycles. Temperate phages adopt the lysogenic mode of infection, where the genome integrates into the host cell genome forming a prophage. Prophages enable viral genome replication without host cell lysis, and often contribute novel and beneficial traits to the host genome. Current phage research predominantly focuses on lytic phages, leaving a significant gap in knowledge regarding prophages, including their biology, diversity, and ecological roles. Results Here we develop and describe Prophage-DB, a database of prophages, their proteins, and associated metadata that will serve as a resource for viral genomics and microbial ecology. To create the database, we identified and characterized prophages from genomes in three of the largest publicly available databases. We applied several state-of-the-art tools in our pipeline to annotate these viruses, cluster and taxonomically classify them, and detect their respective auxiliary metabolic genes. In total, we identify and characterize over 350,000 prophages and 35,000 auxiliary metabolic genes. Our prophage database is highly representative based on statistical results and contains prophages from a diverse set of archaeal and bacterial hosts which show a wide environmental distribution. Conclusion Prophages are particularly overlooked in viral ecology and merit increased attention due to their vital implications for microbiomes and their hosts. Here, we created Prophage-DB to advance our comprehension of prophages in microbiomes through a comprehensive characterization of prophages in publicly available genomes. We propose that Prophage-DB will serve as a valuable resource for advancing phage research, offering insights into viral taxonomy, host relationships, auxiliary metabolic genes, and environmental distribution.
Collapse
Affiliation(s)
- Etan Dieppa-Colón
- Department of Bacteriology, University of Wisconsin-Madison
- Microbiology Doctoral Training Program, University of Wisconsin-Madison
| | - Cody Martin
- Department of Bacteriology, University of Wisconsin-Madison
- Microbiology Doctoral Training Program, University of Wisconsin-Madison
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison
- Department of Integrative Biology, University of Wisconsin-Madison
| |
Collapse
|
8
|
Bozidis P, Markou E, Gouni A, Gartzonika K. Does Phage Therapy Need a Pan-Phage? Pathogens 2024; 13:522. [PMID: 38921819 PMCID: PMC11206709 DOI: 10.3390/pathogens13060522] [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: 05/16/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024] Open
Abstract
The emergence of multidrug-resistant bacteria is undoubtedly one of the most serious global health threats. One response to this threat that has been gaining momentum over the past decade is 'phage therapy'. According to this, lytic bacteriophages are used for the treatment of bacterial infections, either alone or in combination with antimicrobial agents. However, to ensure the efficacy and broad applicability of phage therapy, several challenges must be overcome. These challenges encompass the development of methods and strategies for the host range manipulation and bypass of the resistance mechanisms developed by pathogenic bacteria, as has been the case since the advent of antibiotics. As our knowledge and understanding of the interactions between phages and their hosts evolves, the key issue is to define the host range for each application. In this article, we discuss the factors that affect host range and how this determines the classification of phages into different categories of action. For each host range group, recent representative examples are provided, together with suggestions on how the different groups can be used to combat certain types of bacterial infections. The available methodologies for host range expansion, either through sequential adaptation to a new pathogen or through genetic engineering techniques, are also reviewed.
Collapse
Affiliation(s)
- Petros Bozidis
- Department of Microbiology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece;
- Department of Microbiology, University Hospital of Ioannina, 45500 Ioannina, Greece; (E.M.); (A.G.)
| | - Eleftheria Markou
- Department of Microbiology, University Hospital of Ioannina, 45500 Ioannina, Greece; (E.M.); (A.G.)
| | - Athanasia Gouni
- Department of Microbiology, University Hospital of Ioannina, 45500 Ioannina, Greece; (E.M.); (A.G.)
| | - Konstantina Gartzonika
- Department of Microbiology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece;
- Department of Microbiology, University Hospital of Ioannina, 45500 Ioannina, Greece; (E.M.); (A.G.)
| |
Collapse
|
9
|
Svenningsen SL. Tactical terminase: How a Salmonella prophage navigates oxidative stress. Cell Host Microbe 2024; 32:781-783. [PMID: 38870894 DOI: 10.1016/j.chom.2024.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 06/15/2024]
Abstract
Stress-induced prophages commonly "jump ship" by inducing lysis via the host SOS response. In a recent work, Uppalapati et al. reports an alternate, stress-selective strategy. Instead of promoting lysis, the Salmonella Gifsy-1 prophage arrests growth specifically when the SOS response coincides with oxidative stress.
Collapse
|
10
|
Casters Y, Bäcker LE, Broux K, Aertsen A. Phage transmission strategies: are phages farming their host? Curr Opin Microbiol 2024; 79:102481. [PMID: 38677076 DOI: 10.1016/j.mib.2024.102481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/29/2024]
Abstract
Extensive coevolution has led to utterly intricate interactions between phages and their bacterial hosts. While both the (short-term) intracellular molecular host-subversion mechanisms during a phage infection cycle and the (long-term) mutational arms race between phages and host cells have traditionally received a lot of attention, there has been an underestimating neglect of (mid-term) transmission strategies by which phages manage to cautiously spread throughout their host population. However, recent findings underscore that phages encode mechanisms to avoid host cell scarcity and promote coexistence with the host, giving the impression that some phages manage to 'farm' their host population to ensure access to host cells for lytic consumption. Given the tremendous impact of phages on bacterial ecology, charting and understanding the complexity of such transmission strategies is of key importance.
Collapse
Affiliation(s)
- Yorben Casters
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 23 - bus 2457, 3001, Belgium
| | - Leonard E Bäcker
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 23 - bus 2457, 3001, Belgium
| | - Kevin Broux
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 23 - bus 2457, 3001, Belgium
| | - Abram Aertsen
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 23 - bus 2457, 3001, Belgium.
| |
Collapse
|
11
|
Gilman RT, Muldoon MR, Megremis S, Robertson DL, Chanishvili N, Papadopoulos NG. Lysogeny destabilizes computationally simulated microbiomes. Ecol Lett 2024; 27:e14464. [PMID: 38923281 DOI: 10.1111/ele.14464] [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: 01/03/2024] [Revised: 05/06/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
Microbiomes are ecosystems, and their stability can impact the health of their hosts. Theory predicts that predators influence ecosystem stability. Phages are key predators of bacteria in microbiomes, but phages are unusual predators because many have lysogenic life cycles. It has been hypothesized that lysogeny can destabilize microbiomes, but lysogeny has no direct analog in classical ecological theory, and no formal theory exists. We studied the stability of computationally simulated microbiomes with different numbers of temperate (lysogenic) and virulent (obligate lytic) phage species. Bacterial populations were more likely to fluctuate over time when there were more temperate phages species. After disturbances, bacterial populations returned to their pre-disturbance densities more slowly when there were more temperate phage species, but cycles engendered by disturbances dampened more slowly when there were more virulent phage species. Our work offers the first formal theory linking lysogeny to microbiome stability.
Collapse
Affiliation(s)
- R Tucker Gilman
- Department of Earth and Environmental Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, UK
| | - Mark R Muldoon
- Department of Mathematics, Faculty of Science and Engineering, University of Manchester, Manchester, UK
| | - Spyridon Megremis
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Department of Genetics and Genome Biology, Centre for Phage Research, Institute for Precision Health, University of Leicester, Leicester, UK
| | | | - Nina Chanishvili
- George Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, Georgia
- Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
- NewVision University, Tbilisi, Georgia
| | - Nikolaos G Papadopoulos
- Allergy Department, 2nd Pediatric Clinic, University of Athens, Athens, Greece
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK
| |
Collapse
|
12
|
Sprenger M, Siemers M, Krautwurst S, Papenfort K. Small RNAs direct attack and defense mechanisms in a quorum sensing phage and its host. Cell Host Microbe 2024; 32:727-738.e6. [PMID: 38579715 DOI: 10.1016/j.chom.2024.03.010] [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: 11/21/2023] [Revised: 02/02/2024] [Accepted: 03/13/2024] [Indexed: 04/07/2024]
Abstract
Many, if not all, bacteria use quorum sensing (QS) to control collective behaviors, and more recently, QS has also been discovered in bacteriophages (phages). Phages can produce communication molecules of their own, or "listen in" on the host's communication processes, to switch between lytic and lysogenic modes of infection. Here, we study the interaction of Vibrio cholerae with the lysogenic phage VP882, which is activated by the QS molecule DPO. We discover that induction of VP882 results in the binding of phage transcripts to the major RNA chaperone Hfq, which in turn outcompetes and downregulates host-encoded small RNAs (sRNAs). VP882 itself also encodes Hfq-binding sRNAs, and we demonstrate that one of these sRNAs, named VpdS, promotes phage replication by regulating host and phage mRNA levels. We further show that host-encoded sRNAs can antagonize phage replication by downregulating phage mRNA expression and thus might be part of the host's phage defense arsenal.
Collapse
Affiliation(s)
- Marcel Sprenger
- Friedrich Schiller University, Institute of Microbiology, 07745 Jena, Germany
| | - Malte Siemers
- Friedrich Schiller University, Institute of Microbiology, 07745 Jena, Germany; Microverse Cluster, Friedrich Schiller University Jena, 07743 Jena, Germany
| | | | - Kai Papenfort
- Friedrich Schiller University, Institute of Microbiology, 07745 Jena, Germany; Microverse Cluster, Friedrich Schiller University Jena, 07743 Jena, Germany.
| |
Collapse
|
13
|
Warrell DL, Zarrella TM, Machalek C, Khare A. Interspecies surfactants serve as public goods enabling surface motility in Pseudomonas aeruginosa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.573969. [PMID: 38260674 PMCID: PMC10802355 DOI: 10.1101/2024.01.03.573969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
In most natural environments, bacteria live in polymicrobial communities where secreted molecules from neighboring species alter bacterial behaviors including motility, but such interactions are understudied. Pseudomonas aeruginosa is a motile opportunistic pathogen that exists in diverse multispecies environments such as the soil and is frequently found in human wound and respiratory tract co-infections with other bacteria including Staphylococcus aureus. Here we show that P. aeruginosa can co-opt secreted surfactants from other species for flagellar-based surface motility. We found that exogenous surfactants from S. aureus, other bacteria, and interkingdom species enabled P. aeruginosa to switch from swarming to an alternative surface spreading motility on semi-solid surfaces and allowed for the emergence of surface motility on hard agar where P. aeruginosa was otherwise unable to move. This motility was distinct from the response of other motile bacteria in the presence of exogenous surfactants. Mutant analysis indicated that this P. aeruginosa motility was similar to a previously described mucin-based motility, 'surfing', albeit with divergent regulation. Thus, our study demonstrates that secreted surfactants from the host as well as neighboring bacterial and interkingdom species act as public goods facilitating P. aeruginosa flagella-mediated surfing-like surface motility, thereby allowing it to access different environmental niches.
Collapse
Affiliation(s)
- Delayna L. Warrell
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tiffany M. Zarrella
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Postdoctoral Research Associate Training Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD, USA
- Current address: Department of Biology, Georgetown University, Washington, DC, USA
| | - Christopher Machalek
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Anupama Khare
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
14
|
Silpe JE, Duddy OP, Johnson GE, Beggs GA, Hussain FA, Forsberg KJ, Bassler BL. Small protein modules dictate prophage fates during polylysogeny. Nature 2023; 620:625-633. [PMID: 37495698 PMCID: PMC10432266 DOI: 10.1038/s41586-023-06376-y] [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: 09/16/2022] [Accepted: 06/27/2023] [Indexed: 07/28/2023]
Abstract
Most bacteria in the biosphere are predicted to be polylysogens harbouring multiple prophages1-5. In studied systems, prophage induction from lysogeny to lysis is near-universally driven by DNA-damaging agents6. Thus, how co-residing prophages compete for cell resources if they respond to an identical trigger is unknown. Here we discover regulatory modules that control prophage induction independently of the DNA-damage cue. The modules bear little resemblance at the sequence level but share a regulatory logic by having a transcription factor that activates the expression of a neighbouring gene that encodes a small protein. The small protein inactivates the master repressor of lysis, which leads to induction. Polylysogens that harbour two prophages exposed to DNA damage release mixed populations of phages. Single-cell analyses reveal that this blend is a consequence of discrete subsets of cells producing one, the other or both phages. By contrast, induction through the DNA-damage-independent module results in cells producing only the phage sensitive to that specific cue. Thus, in the polylysogens tested, the stimulus used to induce lysis determines phage productivity. Considering the lack of potent DNA-damaging agents in natural habitats, additional phage-encoded sensory pathways to lysis likely have fundamental roles in phage-host biology and inter-prophage competition.
Collapse
Affiliation(s)
- Justin E Silpe
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Olivia P Duddy
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Grace E Johnson
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Grace A Beggs
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Fatima A Hussain
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kevin J Forsberg
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| |
Collapse
|