51
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Schroven K, Aertsen A, Lavigne R. Bacteriophages as drivers of bacterial virulence and their potential for biotechnological exploitation. FEMS Microbiol Rev 2021; 45:5902850. [PMID: 32897318 DOI: 10.1093/femsre/fuaa041] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/03/2020] [Indexed: 12/20/2022] Open
Abstract
Bacteria-infecting viruses (phages) and their hosts maintain an ancient and complex relationship. Bacterial predation by lytic phages drives an ongoing phage-host arms race, whereas temperate phages initiate mutualistic relationships with their hosts upon lysogenization as prophages. In human pathogens, these prophages impact bacterial virulence in distinct ways: by secretion of phage-encoded toxins, modulation of the bacterial envelope, mediation of bacterial infectivity and the control of bacterial cell regulation. This review builds the argument that virulence-influencing prophages hold extensive, unexplored potential for biotechnology. More specifically, it highlights the development potential of novel therapies against infectious diseases, to address the current antibiotic resistance crisis. First, designer bacteriophages may serve to deliver genes encoding cargo proteins which repress bacterial virulence. Secondly, one may develop small molecules mimicking phage-derived proteins targeting central regulators of bacterial virulence. Thirdly, bacteria equipped with phage-derived synthetic circuits which modulate key virulence factors could serve as vaccine candidates to prevent bacterial infections. The development and exploitation of such antibacterial strategies will depend on the discovery of other prophage-derived, virulence control mechanisms and, more generally, on the dissection of the mutualistic relationship between temperate phages and bacteria, as well as on continuing developments in the synthetic biology field.
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Affiliation(s)
- Kaat Schroven
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
| | - Abram Aertsen
- Laboratory of Food Microbiology, KU Leuven, Kasteelpark Arenberg 23, 3001 Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
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52
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Dimitriu T, Szczelkun MD, Westra ER. Evolutionary Ecology and Interplay of Prokaryotic Innate and Adaptive Immune Systems. Curr Biol 2021; 30:R1189-R1202. [PMID: 33022264 DOI: 10.1016/j.cub.2020.08.028] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Like many organisms, bacteria and archaea have both innate and adaptive immune systems to defend against infection by viruses and other parasites. Innate immunity most commonly relies on the endonuclease-mediated cleavage of any incoming DNA that lacks a specific epigenetic modification, through a system known as restriction-modification. CRISPR-Cas-mediated adaptive immunity relies on the insertion of short DNA sequences from parasite genomes into CRISPR arrays on the host genome to provide sequence-specific protection. The discovery of each of these systems has revolutionised our ability to carry out genetic manipulations, and, as a consequence, the enzymes involved have been characterised in exquisite detail. In comparison, much less is known about the importance of these two arms of the defence for the ecology and evolution of prokaryotes and their parasites. Here, we review our current ecological and evolutionary understanding of these systems in isolation, and discuss the need to study how innate and adaptive immune responses are integrated when they coexist in the same cell.
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Affiliation(s)
- Tatiana Dimitriu
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK.
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.
| | - Edze R Westra
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK.
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53
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Chevallereau A, Pons BJ, van Houte S, Westra ER. Interactions between bacterial and phage communities in natural environments. Nat Rev Microbiol 2021; 20:49-62. [PMID: 34373631 DOI: 10.1038/s41579-021-00602-y] [Citation(s) in RCA: 176] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 06/28/2021] [Indexed: 12/20/2022]
Abstract
We commonly acknowledge that bacterial viruses (phages) shape the composition and evolution of bacterial communities in nature and therefore have important roles in ecosystem functioning. This view stems from studies in the 1990s to the first decade of the twenty-first century that revealed high viral abundance, high viral diversity and virus-induced microbial death in aquatic ecosystems as well as an association between collapses in bacterial density and peaks in phage abundance. The recent surge in metagenomic analyses has provided deeper insight into the abundance, genomic diversity and spatio-temporal dynamics of phages in a wide variety of ecosystems, ranging from deep oceans to soil and the mammalian digestive tract. However, the causes and consequences of variations in phage community compositions remain poorly understood. In this Review, we explore current knowledge of the composition and evolution of phage communities, as well as their roles in controlling the population and evolutionary dynamics of bacterial communities. We discuss the need for greater ecological realism in laboratory studies to capture the complexity of microbial communities that thrive in natural environments.
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Affiliation(s)
- Anne Chevallereau
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK. .,Department of Infection, Immunity and Inflammation, Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, Paris, France.
| | - Benoît J Pons
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK
| | - Stineke van Houte
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK
| | - Edze R Westra
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK.
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54
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Jacobson TB, Callaghan MM, Amador-Noguez D. Hostile Takeover: How Viruses Reprogram Prokaryotic Metabolism. Annu Rev Microbiol 2021; 75:515-539. [PMID: 34348026 DOI: 10.1146/annurev-micro-060621-043448] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To reproduce, prokaryotic viruses must hijack the cellular machinery of their hosts and redirect it toward the production of viral particles. While takeover of the host replication and protein synthesis apparatus has long been considered an essential feature of infection, recent studies indicate that extensive reprogramming of host primary metabolism is a widespread phenomenon among prokaryotic viruses that is required to fulfill the biosynthetic needs of virion production. In this review we provide an overview of the most significant recent findings regarding virus-induced reprogramming of prokaryotic metabolism and suggest how quantitative systems biology approaches may be used to provide a holistic understanding of metabolic remodeling during lytic viral infection. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Tyler B Jacobson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53726, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Melanie M Callaghan
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53726, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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55
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Correa AMS, Howard-Varona C, Coy SR, Buchan A, Sullivan MB, Weitz JS. Revisiting the rules of life for viruses of microorganisms. Nat Rev Microbiol 2021; 19:501-513. [PMID: 33762712 DOI: 10.1038/s41579-021-00530-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2021] [Indexed: 02/01/2023]
Abstract
Viruses that infect microbial hosts have traditionally been studied in laboratory settings with a focus on either obligate lysis or persistent lysogeny. In the environment, these infection archetypes are part of a continuum that spans antagonistic to beneficial modes. In this Review, we advance a framework to accommodate the context-dependent nature of virus-microorganism interactions in ecological communities by synthesizing knowledge from decades of virology research, eco-evolutionary theory and recent technological advances. We discuss that nuanced outcomes, rather than the extremes of the continuum, are particularly likely in natural communities given variability in abiotic factors, the availability of suboptimal hosts and the relevance of multitrophic partnerships. We revisit the 'rules of life' in terms of how long-term infections shape the fate of viruses and microbial cells, populations and ecosystems.
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Affiliation(s)
| | | | - Samantha R Coy
- BioSciences Department, Rice University, Houston, TX, USA
| | - Alison Buchan
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA.
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA. .,Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, USA.
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA. .,School of Physics, Georgia Institute of Technology, Atlanta, GA, USA.
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56
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Kirsch JM, Brzozowski RS, Faith D, Round JL, Secor PR, Duerkop BA. Bacteriophage-Bacteria Interactions in the Gut: From Invertebrates to Mammals. Annu Rev Virol 2021; 8:95-113. [PMID: 34255542 DOI: 10.1146/annurev-virology-091919-101238] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacteria and their viruses (bacteriophages or phages) interact antagonistically and beneficially in polymicrobial communities such as the guts of animals. These interactions are multifaceted and are influenced by environmental conditions. In this review, we discuss phage-bacteria interactions as they relate to the complex environment of the gut. Within the mammalian and invertebrate guts, phages and bacteria engage in diverse interactions including genetic coexistence through lysogeny, and phages directly modulate microbiota composition and the immune system with consequences that are becoming recognized as potential drivers of health and disease. With greater depth of understanding of phage-bacteria interactions in the gut and the outcomes, future phage therapies become possible. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Joshua M Kirsch
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA;
| | - Robert S Brzozowski
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA;
| | - Dominick Faith
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA;
| | - June L Round
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, Utah 84113, USA;
| | - Patrick R Secor
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA;
| | - Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA;
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57
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Abstract
Bacteriophages and bacterial biofilms are widely present in natural environments, a fact that has accelerated the evolution of phages and their bacterial hosts in these particular niches. Phage-host interactions in biofilm communities are rather complex, where phages are not always merely predators but also can establish symbiotic relationships that induce and strengthen biofilms. In this review we provide an overview of the main features affecting phage-biofilm interactions as well as the currently available methods of studying these interactions. In addition, we address the applications of phages for biofilm control in different contexts.
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Affiliation(s)
- Diana P Pires
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
| | - Luís D R Melo
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
| | - Joana Azeredo
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
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58
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Moderate Seasonal Dynamics Indicate an Important Role for Lysogeny in the Red Sea. Microorganisms 2021; 9:microorganisms9061269. [PMID: 34207938 PMCID: PMC8230703 DOI: 10.3390/microorganisms9061269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/08/2021] [Accepted: 05/13/2021] [Indexed: 11/17/2022] Open
Abstract
Viruses are the most abundant microorganisms in marine environments and viral infections can be either lytic (virulent) or lysogenic (temperate phage) within the host cell. The aim of this study was to quantify viral dynamics (abundance and infection) in the coastal Red Sea, a narrow oligotrophic basin with high surface water temperatures (22–32 °C degrees), high salinity (37.5–41) and continuous high insolation, thus making it a stable and relatively unexplored environment. We quantified viral and environmental changes in the Red Sea (two years) and the occurrence of lysogenic bacteria (induced by mitomycin C) on the second year. Water temperatures ranged from 24.0 to 32.5 °C, and total viral and bacterial abundances ranged from 1.5 to 8.7 × 106 viruses mL−1 and 1.9 to 3.2 × 105 bacteria mL−1, respectively. On average, 12.24% ± 4.8 (SE) of the prophage bacteria could be induced by mitomycin C, with the highest percentage of 55.8% observed in January 2018 when bacterial abundances were low; whereas no induction was measurable in spring when bacterial abundances were highest. Thus, despite the fact that the Red Sea might be perceived as stable, warm and saline, relatively modest changes in seasonal conditions were associated with large swings in the prevalence of lysogeny.
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59
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Abstract
Viruses play an essential role in shaping microbial community structures and serve as reservoirs for genetic diversity in many ecosystems. In hyperarid desert environments, where life itself becomes scarce and loses diversity, the interactions between viruses and host populations have remained elusive. Here, we resolved host-virus interactions in the soil metagenomes of the Atacama Desert hyperarid core, one of the harshest terrestrial environments on Earth. We show evidence of diverse viruses infecting a wide range of hosts found in sites up to 205 km apart. Viral genomes carried putative extremotolerance features (i.e., spore formation proteins) and auxiliary metabolic genes, indicating that viruses could mediate the spread of microbial resilience against environmental stress across the desert. We propose a mutualistic model of host-virus interactions in the hyperarid core where viruses seek protection in microbial cells as lysogens or pseudolysogens, while viral extremotolerance genes aid survival of their hosts. Our results suggest that the host-virus interactions in the Atacama Desert soils are dynamic and complex, shaping uniquely adapted microbiomes in this highly selective and hostile environment.IMPORTANCE Deserts are one of the largest and rapidly expanding terrestrial ecosystems characterized by low biodiversity and biomass. The hyperarid core of the Atacama Desert, previously thought to be devoid of life, is one of the harshest environments, supporting only scant biomass of highly adapted microbes. While there is growing evidence that viruses play essential roles in shaping the diversity and structure of nearly every ecosystem, very little is known about the role of viruses in desert soils, especially where viral contact with viable hosts is significantly reduced. Our results demonstrate that diverse viruses are widely dispersed across the desert, potentially spreading key stress resilience and metabolic genes to ensure host survival. The desertification accelerated by climate change expands both the ecosystem cover and the ecological significance of the desert virome. This study sheds light on the complex virus-host interplay that shapes the unique microbiome in desert soils.
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60
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Vallino M, Rossi M, Ottati S, Martino G, Galetto L, Marzachì C, Abbà S. Bacteriophage-Host Association in the Phytoplasma Insect Vector Euscelidius variegatus. Pathogens 2021; 10:pathogens10050612. [PMID: 34067814 PMCID: PMC8156552 DOI: 10.3390/pathogens10050612] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/26/2022] Open
Abstract
Insect vectors transmit viruses and bacteria that can cause severe diseases in plants and economic losses due to a decrease in crop production. Insect vectors, like all other organisms, are colonized by a community of various microorganisms, which can influence their physiology, ecology, evolution, and also their competence as vectors. The important ecological meaning of bacteriophages in various ecosystems and their role in microbial communities has emerged in the past decade. However, only a few phages have been described so far in insect microbiomes. The leafhopper Euscelidius variegatus is a laboratory vector of the phytoplasma causing Flavescence dorée, a severe grapevine disease that threatens viticulture in Europe. Here, the presence of a temperate bacteriophage in E. variegatus (named Euscelidius variegatus phage 1, EVP-1) was revealed through both insect transcriptome analyses and electron microscopic observations. The bacterial host was isolated in axenic culture and identified as the bacterial endosymbiont of E. variegatus (BEV), recently assigned to the genus Candidatus Symbiopectobacterium. BEV harbors multiple prophages that become active in culture, suggesting that different environments can trigger different mechanisms, finely regulating the interactions among phages. Understanding the complex relationships within insect vector microbiomes may help in revealing possible microbe influences on pathogen transmission, and it is a crucial step toward innovative sustainable strategies for disease management in agriculture.
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Affiliation(s)
- Marta Vallino
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy; (M.R.); (S.O.); (G.M.); (L.G.); (C.M.); (S.A.)
- Correspondence:
| | - Marika Rossi
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy; (M.R.); (S.O.); (G.M.); (L.G.); (C.M.); (S.A.)
| | - Sara Ottati
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy; (M.R.); (S.O.); (G.M.); (L.G.); (C.M.); (S.A.)
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Italy
| | - Gabriele Martino
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy; (M.R.); (S.O.); (G.M.); (L.G.); (C.M.); (S.A.)
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Italy
| | - Luciana Galetto
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy; (M.R.); (S.O.); (G.M.); (L.G.); (C.M.); (S.A.)
| | - Cristina Marzachì
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy; (M.R.); (S.O.); (G.M.); (L.G.); (C.M.); (S.A.)
| | - Simona Abbà
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy; (M.R.); (S.O.); (G.M.); (L.G.); (C.M.); (S.A.)
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61
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Jancheva M, Böttcher T. A Metabolite of Pseudomonas Triggers Prophage-Selective Lysogenic to Lytic Conversion in Staphylococcus aureus. J Am Chem Soc 2021; 143:8344-8351. [PMID: 33978401 PMCID: PMC8193634 DOI: 10.1021/jacs.1c01275] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Bacteriophages have
major impact on their microbial hosts and shape
entire microbial communities. The majority of these phages are latent
and reside as prophages integrated in the genomes of their microbial
hosts. A variety of intricate regulatory systems determine the switch
from a lysogenic to lytic life style, but so far strategies are lacking
to selectively control prophage induction by small molecules. Here
we show that Pseudomonas aeruginosa deploys a trigger
factor to hijack the lysogenic to lytic switch of a polylysogenic Staphylococcus aureus strain causing the selective production
of only one of its prophages. Fractionating extracts of P. aeruginosa identified the phenazine pyocyanin
as a highly potent prophage inducer of S. aureus that, in contrast to mitomycin C, displayed prophage
selectivity. Mutagenesis and biochemical investigations confirm the
existence of a noncanonical mechanism beyond SOS-response that is
controlled by the intracellular oxidation level and is prophage-selective.
Our results demonstrate that human pathogens can produce metabolites
triggering lysogenic to lytic conversion in a prophage-selective manner.
We anticipate our discovery to be the starting point of unveiling
metabolite-mediated microbe–prophage interactions and laying
the foundations for a selective small molecule controlled manipulation
of prophage activity. These could be for example applied to control
microbial communities by their built-in destruction mechanism in a
novel form of phage therapy or for the construction of small molecule-inducible
switches in synthetic biology.
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Affiliation(s)
- Magdalena Jancheva
- Department of Chemistry, Konstanz Research School Chemical Biology, Zukunftskolleg, University of Konstanz, 78457 Konstanz, Germany
| | - Thomas Böttcher
- Department of Chemistry, Konstanz Research School Chemical Biology, Zukunftskolleg, University of Konstanz, 78457 Konstanz, Germany.,Faculty of Chemistry, Department of Biological Chemistry & Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Vienna, Austria
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62
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Liu Z, Liang Z, Zhou Z, Li L, Meng D, Li X, Tao J, Jiang Z, Gu Y, Huang Y, Liu X, Yang Z, Drewniak L, Liu T, Liu Y, Liu S, Wang J, Jiang C, Yin H. Mobile genetic elements mediate the mixotrophic evolution of novel Alicyclobacillus species for acid mine drainage adaptation. Environ Microbiol 2021; 23:3896-3912. [PMID: 33913568 DOI: 10.1111/1462-2920.15543] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 04/12/2021] [Accepted: 04/24/2021] [Indexed: 12/25/2022]
Abstract
Alicyclobacillus species inhabit diverse environments and have adapted to broad ranges of pH and temperature. However, their adaptive evolutions remain elusive, especially regarding the role of mobile genetic elements (MGEs). Here, we characterized the distributions and functions of MGEs in Alicyclobacillus species across five environments, including acid mine drainage (AMD), beverages, hot springs, sediments, and soils. Nine Alicyclobacillus strains were isolated from AMD and possessed larger genome sizes and more genes than those from other environments. Four AMD strains evolved to be mixotrophic and fell into distinctive clusters in phylogenetic tree. Four types of MGEs including genomic island (GI), insertion sequence (IS), prophage, and integrative and conjugative element (ICE) were widely distributed in Alicyclobacillus species. Further, AMD strains did not possess CRISPR-Cas systems, but had more GI, IS, and ICE, as well as more MGE-associated genes involved in the oxidation of iron and sulfide and the resistance of heavy metal and low temperature. These findings highlight the differences in phenotypes and genotypes between strains isolated from AMD and other environments and the important role of MGEs in rapid environment niche expansions.
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Affiliation(s)
- Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410006, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410006, China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Zonglin Liang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhicheng Zhou
- College of Plant Protection, Hunan Agricultural University, Changsha, 410010, China
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410006, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410006, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410006, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410006, China
| | - Xiutong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiemeng Tao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410006, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410006, China
| | - Zhen Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yabing Gu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410006, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410006, China
| | - Ye Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410006, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410006, China
| | - Zhendong Yang
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, 02-096, Poland
| | - Lukasz Drewniak
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, 02-096, Poland
| | - Tianbo Liu
- Hunan Tobacco Science Institute, Changsha, 410010, China
| | - Yongjun Liu
- Hunan Tobacco Science Institute, Changsha, 410010, China
| | - Shuangjiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Chengying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410006, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, 410006, China
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63
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Characterization and Genomic Analysis of ɸSHP3, a New Transposable Bacteriophage Infecting Stenotrophomonas maltophilia. J Virol 2021; 95:JVI.00019-21. [PMID: 33536173 DOI: 10.1128/jvi.00019-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 01/29/2021] [Indexed: 01/21/2023] Open
Abstract
This study describes a novel transposable bacteriophage, ɸSHP3, continuously released by Stenotrophomonas maltophilia strain c31. Morphological observation and genomic analysis revealed that ɸSHP3 is a siphovirus with a 37,611-bp genome that encodes 51 putative proteins. Genomic comparisons indicated that ɸSHP3 is a B3-like transposable phage. Its genome configuration is similar to that of Pseudomonas phage B3, except for the DNA modification module. Similar to B3-like phages, the putative transposase B of ɸSHP3 is a homolog of the type two secretion component ExeA, which is proposed to serve as a potential virulence factor. Moreover, most proteins of ɸSHP3 have homologs in transposable phages, but only ɸSHP3 carries an RdgC-like protein encoded by gene 3, which exhibits exonuclease activity in vitro Two genes and their promoters coding for ɸSHP3 regulatory proteins were identified and appear to control the lytic-lysogenic switch. One of the proteins represses one promoter activity and confers immunity to ɸSHP3 superinfection in vivo The short regulatory region, in addition to the canonical bacterial promoter sequences, displays one LexA and two CpxR recognition sequences. This suggests that LexA and the CpxR/CpxA two-component system might be involved in the control of the ɸSHP3 genetic switch.IMPORTANCE S. maltophilia is an emerging global pathogenic bacterium that displays genetic diversity in both environmental and clinical strains. Transposable phages have long been known to improve the genetic diversity of bacterial strains by transposition. More than a dozen phages of S. maltophilia have been characterized. However, no transposable phage infecting S. maltophilia has been reported to date. Characterization of the first transposable phage, ɸSHP3, from S. maltophilia will contribute to our understanding of host-phage interactions and genetic diversity, especially the interchange of genetic materials among S. maltophilia.
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Fernández L, Duarte AC, Rodríguez A, García P. The relationship between the phageome and human health: are bacteriophages beneficial or harmful microbes? Benef Microbes 2021; 12:107-120. [PMID: 33789552 DOI: 10.3920/bm2020.0132] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In the context of the global antibiotic resistance crisis, bacteriophages are increasingly becoming promising antimicrobial agents against multi-resistant bacteria. Indeed, a huge effort is being made to bring phage-derived products to the market, a process that will also require revising the current regulations in order to facilitate their approval. However, despite the evidence supporting the safety of phages for humans, the general public would still be reluctant to use 'viruses' for therapeutic purposes. In this scenario, we consider that it is important to discuss the role of these microorganisms in the equilibrium of the microbiota and how this relates to human health. To do that, this review starts by examining the role of phages as key players in bacterial communities (including those that naturally inhabit the human body), modulating the species composition and contributing to maintain a 'healthy' status quo. Additionally, in specific situations, e.g. an infectious disease, bacteriophages can be used as target-specific antimicrobials against pathogenic bacteria (phage therapy), while being harmless to the desirable microbiota. Apart from that, incipient research shows the potential application of these viruses to treat diseases caused by bacterial dysbiosis. This latter application would be comparable to the use of probiotics or prebiotics, since bacteriophages can indirectly improve the growth of beneficial bacteria in the gastrointestinal tract by removing undesirable competitors. On the other hand, possible adverse effects do not appear to be an impediment to promote phage therapy. Nonetheless, it is important to remember their potentially negative impact, mainly concerning their immunogenicity or their potential spread of virulence and antibiotic resistance genes, especially by temperate phages. Overall, we believe that phages should be largely considered beneficial microbes, although it is paramount not to overlook their potential risks.
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Affiliation(s)
- L Fernández
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain.,DairySafe Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario s/n, 33011 Oviedo, Spain
| | - A C Duarte
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain.,DairySafe Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario s/n, 33011 Oviedo, Spain
| | - A Rodríguez
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain.,DairySafe Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario s/n, 33011 Oviedo, Spain
| | - P García
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain.,DairySafe Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario s/n, 33011 Oviedo, Spain
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65
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Yu Z, Schwarz C, Zhu L, Chen L, Shen Y, Yu P. Hitchhiking Behavior in Bacteriophages Facilitates Phage Infection and Enhances Carrier Bacteria Colonization. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:2462-2472. [PMID: 33381966 DOI: 10.1021/acs.est.0c06969] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Interactions between bacteriophages (phages) and biofilms remain poorly understood despite the broad implications for microbial ecology, water quality, and microbiome engineering. Here, we demonstrate that lytic coliphage PHH01 can hitchhike on carrier bacteria Bacillus cereus to facilitate its infection of host bacteria, Escherichia coli, in biofilms. Specifically, PHH01 could adsorb onto the flagella of B. cereus, and thus phage motility was increased, resulting in 4.36-fold more effective infection of E. coli in biofilm relative to free PHH01 alone. Moreover, phage infection mitigated interspecies competition and enhanced B. cereus colonization; the fraction of B. cereus in the final biofilm increased from 9% without phages to 43% with phages. The mutualistic relationship between the coliphage and carrier bacteria was substantiated by migration tests on an E. coli lawn: the conjugation of PHH01 and B. cereus enhanced B. cereus colonization by 6.54-fold compared to B. cereus alone (6.15 vs 0.94 cm2 in 24 h) and PHH01 migration by 5.15-fold compared to PHH01 alone (10.3 vs 2.0 mm in 24 h). Metagenomic and electron microscopic analysis revealed that the phages of diverse taxonomies and different morphologies could be adsorbed by the flagella of B. cereus, suggesting hitchhiking on flagellated bacteria might be a widespread strategy in aquatic phage populations. Overall, our study highlights that hitchhiking behavior in phages can facilitate phage infection of biofilm bacteria, promote carrier bacteria colonization, and thus significantly influence biofilm composition, which holds promise for mediating biofilm functions and moderating associated risks.
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Affiliation(s)
- Zhuodong Yu
- School of Environment and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Cory Schwarz
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
| | - Liang Zhu
- School of Environment and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Linlin Chen
- School of Environment and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yun Shen
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Pingfeng Yu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
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López-García P, Moreira D. Physical connections: prokaryotes parasitizing their kin. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:54-61. [PMID: 33225570 DOI: 10.1111/1758-2229.12910] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 06/11/2023]
Affiliation(s)
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, Orsay, AgroParisTech, 91400, France
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67
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Evolution along the parasitism-mutualism continuum determines the genetic repertoire of prophages. PLoS Comput Biol 2020; 16:e1008482. [PMID: 33275597 PMCID: PMC7744054 DOI: 10.1371/journal.pcbi.1008482] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 12/16/2020] [Accepted: 10/30/2020] [Indexed: 12/11/2022] Open
Abstract
Integrated into their bacterial hosts' genomes, prophage sequences exhibit a wide diversity of length and gene content, from highly degraded cryptic sequences to intact, functional prophages that retain a full complement of lytic-function genes. We apply three approaches-bioinformatics, analytical modelling and computational simulation-to understand the diverse gene content of prophages. In the bioinformatics work, we examine the distributions of over 50,000 annotated prophage genes identified in 1384 prophage sequences, comparing the gene repertoires of intact and incomplete prophages. These data indicate that genes involved in the replication, packaging, and release of phage particles have been preferentially lost in incomplete prophages, while tail fiber, transposase and integrase genes are significantly enriched. Consistent with these results, our mathematical and computational approaches predict that genes involved in phage lytic function are preferentially lost, resulting in shorter prophages that often retain genes that benefit the host. Informed by these models, we offer novel hypotheses for the enrichment of integrase and transposase genes in cryptic prophages. Overall, we demonstrate that functional and cryptic prophages represent a diversity of genetic sequences that evolve along a parasitism-mutualism continuum.
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68
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Compant S, Cambon MC, Vacher C, Mitter B, Samad A, Sessitsch A. The plant endosphere world - bacterial life within plants. Environ Microbiol 2020; 23:1812-1829. [PMID: 32955144 DOI: 10.1111/1462-2920.15240] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/11/2020] [Accepted: 09/16/2020] [Indexed: 12/23/2022]
Abstract
The plant endosphere is colonized by complex microbial communities and microorganisms, which colonize the plant interior at least part of their lifetime and are termed endophytes. Their functions range from mutualism to pathogenicity. All plant organs and tissues are generally colonized by bacterial endophytes and their diversity and composition depend on the plant, the plant organ and its physiological conditions, the plant growth stage as well as on the environment. Plant-associated microorganisms, and in particular endophytes, have lately received high attention, because of the increasing awareness of the importance of host-associated microbiota for the functioning and performance of their host. Some endophyte functions are known from mostly lab assays, genome prediction and few metagenome analyses; however, we have limited understanding on in planta activities, particularly considering the diversity of micro-environments and the dynamics of conditions. In our review, we present recent findings on endosphere environments, their physiological conditions and endophyte colonization. Furthermore, we discuss microbial functions, the interaction between endophytes and plants as well as methodological limitations of endophyte research. We also provide an outlook on needs of future research to improve our understanding on the role of microbiota colonizing the endosphere on plant traits and ecosystem functioning.
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Affiliation(s)
- Stéphane Compant
- Center for Health and Bioresources, Bioresources Unit, Konrad Lorenz Straße 24, AIT Austrian Institute of Technology, Tulln, A-3430, Austria
| | | | | | - Birgit Mitter
- Center for Health and Bioresources, Bioresources Unit, Konrad Lorenz Straße 24, AIT Austrian Institute of Technology, Tulln, A-3430, Austria
| | - Abdul Samad
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, G1V4C7, Canada
| | - Angela Sessitsch
- Center for Health and Bioresources, Bioresources Unit, Konrad Lorenz Straße 24, AIT Austrian Institute of Technology, Tulln, A-3430, Austria
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69
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Fiedoruk K, Zakrzewska M, Daniluk T, Piktel E, Chmielewska S, Bucki R. Two Lineages of Pseudomonas aeruginosa Filamentous Phages: Structural Uniformity over Integration Preferences. Genome Biol Evol 2020; 12:1765-1781. [PMID: 32658245 PMCID: PMC7549136 DOI: 10.1093/gbe/evaa146] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2020] [Indexed: 12/20/2022] Open
Abstract
Pseudomonas aeruginosa filamentous (Pf) bacteriophages are important factors contributing to the pathogenicity of this opportunistic bacterium, including biofilm formation and suppression of bacterial phagocytosis by macrophages. In addition, the capacity of Pf phages to form liquid crystal structures and their high negative charge density makes them potent sequesters of cationic antibacterial agents, such as aminoglycoside antibiotics or host antimicrobial peptides. Therefore, Pf phages have been proposed as a potential biomarker for risk of antibiotic resistance development. The majority of studies describing biological functions of Pf viruses have been performed with only three of them: Pf1, Pf4, and Pf5. However, our analysis revealed that Pf phages exist as two evolutionary lineages (I and II), characterized by substantially different structural/morphogenesis properties, despite sharing the same integration sites in the host chromosomes. All aforementioned model Pf phages are members of the lineage I. Hence, it is reasonable to speculate that their interactions with P. aeruginosa and impact on its pathogenicity may be not completely extrapolated to the lineage II members. Furthermore, in order to organize the present numerical nomenclature of Pf phages, we propose a more informative approach based on the insertion sites, that is, Pf-tRNA-Gly, -Met, -Sec, -tmRNA, and -DR (direct repeats), which are fully compatible with one of five types of tyrosine integrases/recombinases XerC/D carried by these viruses. Finally, we discuss possible evolutionary mechanisms behind this division and consequences from the perspective of virus-virus, virus-bacterium, and virus-human interactions.
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Affiliation(s)
- Krzysztof Fiedoruk
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Poland
| | - Magdalena Zakrzewska
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Poland
| | - Tamara Daniluk
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Poland
| | - Ewelina Piktel
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Poland
| | - Sylwia Chmielewska
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Poland
| | - Robert Bucki
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Poland
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70
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Cárdenas A, Ye J, Ziegler M, Payet JP, McMinds R, Vega Thurber R, Voolstra CR. Coral-Associated Viral Assemblages From the Central Red Sea Align With Host Species and Contribute to Holobiont Genetic Diversity. Front Microbiol 2020; 11:572534. [PMID: 33117317 PMCID: PMC7561429 DOI: 10.3389/fmicb.2020.572534] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 08/19/2020] [Indexed: 12/15/2022] Open
Abstract
Coral reefs are highly diverse marine ecosystems increasingly threatened on a global scale. The foundation species of reef ecosystems are stony corals that depend on their symbiotic microalgae and bacteria for aspects of their metabolism, immunity, and environmental adaptation. Conversely, the function of viruses in coral biology is less well understood, and we are missing an understanding of the diversity and function of coral viruses, particularly in understudied regions such as the Red Sea. Here we characterized coral-associated viruses using a large metagenomic and metatranscriptomic survey across 101 cnidarian samples from the central Red Sea. While DNA and RNA viral composition was different across coral hosts, biological traits such as coral life history strategy correlated with patterns of viral diversity. Coral holobionts were broadly associated with Mimiviridae and Phycodnaviridae that presumably infect protists and algal cells, respectively. Further, Myoviridae and Siphoviridae presumably target members of the bacterial phyla Actinobacteria, Firmicutes, and Proteobacteria, whereas Hepadnaviridae and Retroviridae might infect the coral host. Genes involved in bacterial virulence and auxiliary metabolic genes were common among the viral sequences, corroborating a contribution of viruses to the holobiont’s genetic diversity. Our work provides a first insight into Red Sea coral DNA and RNA viral assemblages and reveals that viral diversity is consistent with global coral virome patterns.
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Affiliation(s)
- Anny Cárdenas
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Jin Ye
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Maren Ziegler
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Jérôme P Payet
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
| | - Ryan McMinds
- Center of Modeling, Simulation and Interactions, Université Côte d'Azur, Nice, France
| | - Rebecca Vega Thurber
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Christian R Voolstra
- Department of Biology, University of Konstanz, Konstanz, Germany.,Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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71
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Tuttle MJ, Buchan A. Lysogeny in the oceans: Lessons from cultivated model systems and a reanalysis of its prevalence. Environ Microbiol 2020; 22:4919-4933. [PMID: 32935433 DOI: 10.1111/1462-2920.15233] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/19/2020] [Accepted: 08/23/2020] [Indexed: 12/12/2022]
Abstract
In the oceans, viruses that infect bacteria (phages) influence a variety of microbially mediated processes that drive global biogeochemical cycles. The nature of their influence is dependent upon infection mode, be it lytic or lysogenic. Temperate phages are predicted to be prevalent in marine systems where they are expected to execute both types of infection modes. Understanding the range and outcomes of temperate phage-host interactions is fundamental for evaluating their ecological impact. Here, we (i) review phage-mediated rewiring of host metabolism, with a focus on marine systems, (ii) consider the range and nature of temperate phage-host interactions, and (iii) draw on studies of cultivated model systems to examine the consequences of lysogeny among several dominant marine bacterial lineages. We also readdress the prevalence of lysogeny among marine bacteria by probing a collection of 1239 publicly available bacterial genomes, representing cultured and uncultivated strains, for evidence of complete prophages. Our conservative analysis, anticipated to underestimate true prevalence, predicts 18% of the genomes examined contain at least one prophage, the majority (97%) were found within genomes of cultured isolates. These results highlight the need for cultivation of additional model systems to better capture the diversity of temperate phage-host interactions in the oceans.
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Affiliation(s)
- Matthew J Tuttle
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Alison Buchan
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
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72
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Guerin E, Hill C. Shining Light on Human Gut Bacteriophages. Front Cell Infect Microbiol 2020; 10:481. [PMID: 33014897 PMCID: PMC7511551 DOI: 10.3389/fcimb.2020.00481] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/04/2020] [Indexed: 12/15/2022] Open
Abstract
The human gut is a complex environment that contains a multitude of microorganisms that are collectively termed the microbiome. Multiple factors have a role to play in driving the composition of human gut bacterial communities either toward homeostasis or the instability that is associated with many disease states. One of the most important forces are likely to be bacteriophages, bacteria-infecting viruses that constitute by far the largest portion of the human gut virome. Despite this, bacteriophages (phages) are the one of the least studied residents of the gut. This is largely due to the challenges associated with studying these difficult to culture entities. Modern high throughput sequencing technologies have played an important role in improving our understanding of the human gut phageome but much of the generated sequencing data remains uncharacterised. Overcoming this requires database-independent bioinformatic pipelines and even those phages that are successfully characterized only provide limited insight into their associated biological properties, and thus most viral sequences have been characterized as “viral dark matter.” Fundamental to understanding the role of phages in shaping the human gut microbiome, and in turn perhaps influencing human health, is how they interact with their bacterial hosts. An essential aspect is the isolation of novel phage-bacteria host pairs by direct isolation through various screening methods, which can transform in silico phages into a biological reality. However, this is also beset with multiple challenges including culturing difficulties and the use of traditional methods, such as plaquing, which may bias which phage-host pairs that can be successfully isolated. Phage-bacteria interactions may be influenced by many aspects of complex human gut biology which can be difficult to reproduce under laboratory conditions. Here we discuss some of the main findings associated with the human gut phageome to date including composition, our understanding of phage-host interactions, particularly the observed persistence of virulent phages and their hosts, as well as factors that may influence these highly intricate relationships. We also discuss current methodologies and bottlenecks hindering progression in this field and identify potential steps that may be useful in overcoming these hurdles.
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Affiliation(s)
- Emma Guerin
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
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73
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Evolutionary Stabilization of Cooperative Toxin Production through a Bacterium-Plasmid-Phage Interplay. mBio 2020; 11:mBio.00912-20. [PMID: 32694140 PMCID: PMC7374059 DOI: 10.1128/mbio.00912-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Colicins are toxins produced and released by Enterobacteriaceae to kill competitors in the gut. While group A colicins employ a division of labor strategy to liberate the toxin into the environment via colicin-specific lysis, group B colicin systems lack cognate lysis genes. In Salmonella enterica serovar Typhimurium (S. Tm), the group B colicin Ib (ColIb) is released by temperate phage-mediated bacteriolysis. Phage-mediated ColIb release promotes S. Tm fitness against competing Escherichia coli It remained unclear how prophage-mediated lysis is realized in a clonal population of ColIb producers and if prophages contribute to evolutionary stability of toxin release in S. Tm. Here, we show that prophage-mediated lysis occurs in an S. Tm subpopulation only, thereby introducing phenotypic heterogeneity to the system. We established a mathematical model to study the dynamic interplay of S. Tm, ColIb, and a temperate phage in the presence of a competing species. Using this model, we studied long-term evolution of phage lysis rates in a fluctuating infection scenario. This revealed that phage lysis evolves as bet-hedging strategy that maximizes phage spread, regardless of whether colicin is present or not. We conclude that the ColIb system, lacking its own lysis gene, is making use of the evolutionary stable phage strategy to be released. Prophage lysis genes are highly prevalent in nontyphoidal Salmonella genomes. This suggests that the release of ColIb by temperate phages is widespread. In conclusion, our findings shed new light on the evolution and ecology of group B colicin systems.IMPORTANCE Bacteria are excellent model organisms to study mechanisms of social evolution. The production of public goods, e.g., toxin release by cell lysis in clonal bacterial populations, is a frequently studied example of cooperative behavior. Here, we analyze evolutionary stabilization of toxin release by the enteric pathogen Salmonella The release of colicin Ib (ColIb), which is used by Salmonella to gain an edge against competing microbiota following infection, is coupled to bacterial lysis mediated by temperate phages. Here, we show that phage-dependent lysis and subsequent release of colicin and phage particles occurs only in part of the ColIb-expressing Salmonella population. This phenotypic heterogeneity in lysis, which represents an essential step in the temperate phage life cycle, has evolved as a bet-hedging strategy under fluctuating environments such as the gastrointestinal tract. Our findings suggest that prophages can thereby evolutionarily stabilize costly toxin release in bacterial populations.
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74
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Tan D, Hansen MF, de Carvalho LN, Røder HL, Burmølle M, Middelboe M, Svenningsen SL. High cell densities favor lysogeny: induction of an H20 prophage is repressed by quorum sensing and enhances biofilm formation in Vibrio anguillarum. THE ISME JOURNAL 2020; 14:1731-1742. [PMID: 32269377 PMCID: PMC7305317 DOI: 10.1038/s41396-020-0641-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 11/09/2022]
Abstract
Temperate ϕH20-like phages are repeatedly identified at geographically distinct areas as free phage particles or as prophages of the fish pathogen Vibrio anguillarum. We studied mutants of a lysogenic isolate of V. anguillarum locked in the quorum-sensing regulatory modes of low (ΔvanT) and high (ΔvanO) cell densities by in-frame deletion of key regulators of the quorum-sensing pathway. Remarkably, we find that induction of the H20-like prophage is controlled by the quorum-sensing state of the host, with an eightfold increase in phage particles per cell in high-cell-density cultures of the quorum-sensing-deficient ΔvanT mutant. Comparative studies with prophage-free strains show that biofilm formation is promoted at low cell density and that the H20-like prophage stimulates this behavior. In contrast, the high-cell-density state is associated with reduced prophage induction, increased proteolytic activity, and repression of biofilm. The proteolytic activity may dually function to disperse the biofilm and as a quorum-sensing-mediated antiphage strategy. We demonstrate an intertwined regulation of phage-host interactions and biofilm formation, which is orchestrated by host quorum-sensing signaling, suggesting that increased lysogeny at high cell density is not solely a strategy for phages to piggy-back the successful bacterial hosts but is also a host strategy evolved to take control of the lysis-lysogeny switch to promote host fitness.
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Affiliation(s)
- Demeng Tan
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Dalian SEM Bio-Engineering Technology Co. Ltd, Dalian, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mads Frederik Hansen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | | | - Mette Burmølle
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mathias Middelboe
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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75
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Pratama AA, van Elsas JD. Gene mobility in microbiomes of the mycosphere and mycorrhizosphere -role of plasmids and bacteriophages. FEMS Microbiol Ecol 2020; 95:5454738. [PMID: 30980672 DOI: 10.1093/femsec/fiz053] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/12/2019] [Indexed: 12/22/2022] Open
Abstract
Microbial activity in soil, including horizontal gene transfer (HGT), occurs in soil hot spots and at "hot moments". Given their capacities to explore soil for nutrients, soil fungi (associated or not with plant roots) can act as (1) selectors of myco(rrhizo)sphere-adapted organisms and (2) accelerators of HGT processes across the cell populations that are locally present. This minireview critically examines our current understanding of the drivers of gene mobility in the myco(rrhizo)sphere. We place a special focus on the role of two major groups of gene mobility agents, i.e. plasmids and bacteriophages. With respect to plasmids, there is mounting evidence that broad-host-range (IncP-1β and PromA group) plasmids are prominent drivers of gene mobility across mycosphere inhabitants. A role of IncP-1β plasmids in Fe uptake processes has been revealed. Moreover, a screening of typical mycosphere-inhabiting Paraburkholderia spp. revealed carriage of integrated plasmids, next to prophages, that presumably confer fitness enhancements. In particular, functions involved in biofilm formation and nutrient uptake were thus identified. The potential of the respective gene mobility agents to promote the movement of such genes is critically examined.
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Affiliation(s)
- Akbar Adjie Pratama
- Department of Microbial Ecology - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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76
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Molnár J, Magyar B, Schneider G, Laczi K, Valappil SK, Kovács ÁL, Nagy IK, Rákhely G, Kovács T. Identification of a novel archaea virus, detected in hydrocarbon polluted Hungarian and Canadian samples. PLoS One 2020; 15:e0231864. [PMID: 32302368 PMCID: PMC7164591 DOI: 10.1371/journal.pone.0231864] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/02/2020] [Indexed: 12/21/2022] Open
Abstract
Metagenomics is a helpful tool for the analysis of unculturable organisms and viruses. Viruses that target bacteria and archaea play important roles in the microbial diversity of various ecosystems. Here we show that Methanosarcina virus MV (MetMV), the second Methanosarcina sp. virus with a completely determined genome, is characteristic of hydrocarbon pollution in environmental (soil and water) samples. It was highly abundant in Hungarian hydrocarbon polluted samples and its genome was also present in the NCBI SRA database containing reads from hydrocarbon polluted samples collected in Canada, indicating the stability of its niche and the marker feature of this virus. MetMV, as the only currently identified marker virus for pollution in environmental samples, could contribute to the understanding of the complicated network of prokaryotes and their viruses driving the decomposition of environmental pollutants.
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Affiliation(s)
- János Molnár
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Pécs, Hungary
| | | | - György Schneider
- Institute of Medical Microbiology and Immunology, University of Pécs, Pécs, Hungary
| | - Krisztián Laczi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | | | - Árpád L. Kovács
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Pécs, Hungary
| | - Ildikó K. Nagy
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Pécs, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary
- Institute of Biophysics, Biological Research Center, Szeged, Hungary
| | - Tamás Kovács
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Pécs, Hungary
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77
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Sausset R, Petit MA, Gaboriau-Routhiau V, De Paepe M. New insights into intestinal phages. Mucosal Immunol 2020; 13:205-215. [PMID: 31907364 PMCID: PMC7039812 DOI: 10.1038/s41385-019-0250-5] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/13/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023]
Abstract
The intestinal microbiota plays important roles in human health. This last decade, the viral fraction of the intestinal microbiota, composed essentially of phages that infect bacteria, received increasing attention. Numerous novel phage families have been discovered in parallel with the development of viral metagenomics. However, since the discovery of intestinal phages by d'Hérelle in 1917, our understanding of the impact of phages on gut microbiota structure remains scarce. Changes in viral community composition have been observed in several diseases. However, whether these changes reflect a direct involvement of phages in diseases etiology or simply result from modifications in bacterial composition is currently unknown. Here we present an overview of the current knowledge in intestinal phages, their identity, lifestyles, and their possible effects on the gut microbiota. We also gather the main data on phage interactions with the immune system, with a particular emphasis on recent findings.
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Affiliation(s)
- R Sausset
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
- Myriade, 68 boulevard de Port Royal, 75005, Paris, France
| | - M A Petit
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - V Gaboriau-Routhiau
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
- Laboratory of Intestinal Immunity, INSERM UMR 1163, Institut Imagine, Paris, France
- Université Paris Descartes-Sorbonne Paris Cité, 75006, Paris, France
| | - M De Paepe
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
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78
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Taati Moghadam M, Amirmozafari N, Shariati A, Hallajzadeh M, Mirkalantari S, Khoshbayan A, Masjedian Jazi F. How Phages Overcome the Challenges of Drug Resistant Bacteria in Clinical Infections. Infect Drug Resist 2020; 13:45-61. [PMID: 32021319 PMCID: PMC6954843 DOI: 10.2147/idr.s234353] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/23/2019] [Indexed: 12/27/2022] Open
Abstract
Nowadays the most important problem in the treatment of bacterial infections is the appearance of MDR (multidrug-resistant), XDR (extensively drug-resistant) and PDR (pan drug-resistant) bacteria and the scarce prospects of producing new antibiotics. There is renewed interest in revisiting the use of bacteriophage to treat bacterial infections. The practice of phage therapy, the application of phages to treat bacterial infections, has been around for approximately a century. Phage therapy relies on using lytic bacteriophages and purified phage lytic proteins for treatment and lysis of bacteria at the site of infection. Current research indicates that phage therapy has the potential to be used as an alternative to antibiotic treatments. It is noteworthy that, whether phages are used on their own or combined with antibiotics, phages are still a promising agent to replace antibiotics. So, this review focuses on an understanding of challenges of MDR, XDR, and PDR bacteria and phages mechanism for treating bacterial infections and the most recent studies on potential phages, cocktails of phages, and enzymes of lytic phages in fighting these resistant bacteria.
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Affiliation(s)
- Majid Taati Moghadam
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Nour Amirmozafari
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Aref Shariati
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Student Research Committee, Iran University of Medical Sciences, Tehran, Iran
| | - Masoumeh Hallajzadeh
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shiva Mirkalantari
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Amin Khoshbayan
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Student Research Committee, Iran University of Medical Sciences, Tehran, Iran
| | - Faramarz Masjedian Jazi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Microbial Biotechnology Research Center, Iran University of Medical Science, Tehran, Iran
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79
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Huang T, Xiong T, Peng Z, Xiao YS, Liu ZG, Hu M, Xie MY. Genomic analysis revealed adaptive mechanism to plant-related fermentation of Lactobacillus plantarum NCU116 and Lactobacillus spp. Genomics 2020; 112:703-711. [DOI: 10.1016/j.ygeno.2019.05.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/23/2019] [Accepted: 05/08/2019] [Indexed: 11/26/2022]
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80
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Caflisch KM, Suh GA, Patel R. Biological challenges of phage therapy and proposed solutions: a literature review. Expert Rev Anti Infect Ther 2019; 17:1011-1041. [PMID: 31735090 DOI: 10.1080/14787210.2019.1694905] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Introduction: In light of the emergence of antibiotic-resistant bacteria, phage (bacteriophage) therapy has been recognized as a potential alternative or addition to antibiotics in Western medicine for use in humans.Areas covered: This review assessed the scientific literature on phage therapy published between 1 January 2007 and 21 October 2019, with a focus on the successes and challenges of this prospective therapeutic.Expert opinion: Efficacy has been shown in animal models and experimental findings suggest promise for the safety of human phagotherapy. Significant challenges remain to be addressed prior to the standardization of phage therapy in the West, including the development of phage-resistant bacteria; the pharmacokinetic complexities of phage; and any potential human immune response incited by phagotherapy.
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Affiliation(s)
- Katherine M Caflisch
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Gina A Suh
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Robin Patel
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN, USA.,Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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81
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Sutton TDS, Hill C. Gut Bacteriophage: Current Understanding and Challenges. Front Endocrinol (Lausanne) 2019; 10:784. [PMID: 31849833 PMCID: PMC6895007 DOI: 10.3389/fendo.2019.00784] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/28/2019] [Indexed: 12/13/2022] Open
Abstract
The gut microbiome is widely accepted to have a significant impact on human health yet, despite years of research on this complex ecosystem, the contributions of different forces driving microbial population structure remain to be fully elucidated. The viral component of the human gut microbiome is dominated by bacteriophage, which are known to play crucial roles in shaping microbial composition, driving bacterial diversity, and facilitating horizontal gene transfer. Bacteriophage are also one of the most poorly understood components of the human gut microbiome, with the vast majority of viral sequences sharing little to no homology to reference databases. If we are to understand the dynamics of bacteriophage populations, their interaction with the human microbiome and ultimately their influence on human health, we will depend heavily on sequence based approaches and in silico tools. This is complicated by the fact that, as with any research field in its infancy, methods of analyses vary and this can impede our ability to compare the outputs of different studies. Here, we discuss the major findings to date regarding the human virome and reflect on our current understanding of how gut bacteriophage shape the microbiome. We consider whether or not the virome field is built on unstable foundations and if so, how can we provide a solid basis for future experimentation. The virome is a challenging yet crucial piece of the human microbiome puzzle. In order to develop our understanding, we will discuss the need to underpin future studies with robust research methods and suggest some solutions to existing challenges.
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Affiliation(s)
| | - Colin Hill
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
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82
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Zimmerman AE, Howard-Varona C, Needham DM, John SG, Worden AZ, Sullivan MB, Waldbauer JR, Coleman ML. Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems. Nat Rev Microbiol 2019; 18:21-34. [PMID: 31690825 DOI: 10.1038/s41579-019-0270-x] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2019] [Indexed: 12/23/2022]
Abstract
Ecosystems are controlled by 'bottom-up' (resources) and 'top-down' (predation) forces. Viral infection is now recognized as a ubiquitous top-down control of microbial growth across ecosystems but, at the same time, cell death by viral predation influences, and is influenced by, resource availability. In this Review, we discuss recent advances in understanding the biogeochemical impact of viruses, focusing on how metabolic reprogramming of host cells during lytic viral infection alters the flow of energy and nutrients in aquatic ecosystems. Our synthesis revealed several emerging themes. First, viral infection transforms host metabolism, in part through virus-encoded metabolic genes; the functions performed by these genes appear to alleviate energetic and biosynthetic bottlenecks to viral production. Second, viral infection depends on the physiological state of the host cell and on environmental conditions, which are challenging to replicate in the laboratory. Last, metabolic reprogramming of infected cells and viral lysis alter nutrient cycling and carbon export in the oceans, although the net impacts remain uncertain. This Review highlights the need for understanding viral infection dynamics in realistic physiological and environmental contexts to better predict their biogeochemical consequences.
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Affiliation(s)
- Amy E Zimmerman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | | | - David M Needham
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Seth G John
- Department of Earth Science, University of Southern California, Los Angeles, CA, USA
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, USA.,Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA
| | - Jacob R Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Maureen L Coleman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA.
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83
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Carey JN, Mettert EL, Fishman-Engel DR, Roggiani M, Kiley PJ, Goulian M. Phage integration alters the respiratory strategy of its host. eLife 2019; 8:49081. [PMID: 31650957 PMCID: PMC6814406 DOI: 10.7554/elife.49081] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 09/23/2019] [Indexed: 12/11/2022] Open
Abstract
Temperate bacteriophages are viruses that can incorporate their genomes into their bacterial hosts, existing there as prophages that refrain from killing the host cell until induced. Prophages are largely quiescent, but they can alter host phenotype through factors encoded in their genomes (often virulence factors) or by disrupting host genes as a result of integration. Here we describe another mechanism by which a prophage can modulate host phenotype. We show that a temperate phage that integrates in Escherichia coli reprograms host regulation of an anaerobic respiratory system, thereby inhibiting a bet hedging strategy. The phage exerts this effect by upregulating a host-encoded signal transduction protein through transcription initiated from a phage-encoded promoter. We further show that this phenomenon occurs not only in a laboratory strain of E. coli, but also in a natural isolate that contains a prophage at this site. Animals and plants can all fall prey to viruses – and so can bacteria. The viruses that infect bacteria are called bacteriophages (or phages for short), and they are found everywhere bacteria live and probably outnumber bacteria by at least ten to one. While some phages quickly kill every bacterial cell they infect, others enter a dormant state by inserting their DNA into the DNA of their host cell. Here they lie in wait for a signal that reactivates them, triggering the production of more phages and the death of the host cell. While the phage lies dormant its DNA may harm the host by interfering with nearby bacterial genes, or it may actually provide new genes that benefit the host. In most cases the effects of dormant phages are unknown. A bacterium known as Escherichia coli is commonly found in the intestines of humans and other mammals. It can use a nutrient called trimethylamine oxide (TMAO) to help it survive rapid decreases in oxygen levels that can occur in its environment. When a phage called HK022 infects E. coli, the phage enters a dormant state by inserting its DNA between two genes that are critical for E. coli to use TMAO. However, it is not clear what effect, if any, HK022 has on E. coli’s behavior. To address this question, Carey et al. used genetic approaches to study E. coli cells carrying dormant HK022 phages. The experiments showed that the bacteria lost the ability to use TMAO to survive rapid decreases in oxygen because the dormant phages switched on one of the neighboring E. coli genes. Unexpectedly, the phage achieved this by neatly replacing the gene’s own promoter – the stretch of DNA that contains information about when the gene should be switched on, and how strongly – with a substitute promoter carried in the phage’s DNA. This substitute promoter is stronger than the normal version – meaning that the gene is more active than it should be. Phages are key players in every natural population of microbes and are therefore entwined in the health of humans and the environment. The findings of Carey et al. show a new mechanism through which phages modify their hosts. In the future it may be possible to develop this mechanism into a tool to manipulate bacteria in complex environments like infection sites, for example by introducing phages that block the mechanisms that allow bacteria to tolerate antibiotics.
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Affiliation(s)
- Jeffrey N Carey
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States
| | - Erin L Mettert
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, United States
| | | | - Manuela Roggiani
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Patricia J Kiley
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, United States
| | - Mark Goulian
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Biology, University of Pennsylvania, Philadelphia, United States.,Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, United States
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84
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Lysogeny in the Lactic Acid Bacterium Oenococcus oeni Is Responsible for Modified Colony Morphology on Red Grape Juice Agar. Appl Environ Microbiol 2019; 85:AEM.00997-19. [PMID: 31375489 DOI: 10.1128/aem.00997-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 07/24/2019] [Indexed: 11/20/2022] Open
Abstract
Oenococcus oeni is the lactic acid bacterium (LAB) that most commonly drives malolactic fermentation in wine. Although oenococcal prophages are highly prevalent, their implications on bacterial fitness have remained unexplored and more research is required in this field. An important step toward achieving this goal is the ability to produce isogenic pairs of strains that differ only by the lysogenic presence of a given prophage, allowing further comparisons of different phenotypic traits. A novel protocol for the rapid isolation of lysogens is presented. Bacteria were first picked from the center of turbid plaques produced by temperate oenophages on a sensitive nonlysogenic host. When streaked onto an agar medium containing red grape juice (RGJ), cells segregated into white and red colonies. PCR amplifications with phage-specific primers demonstrated that only lysogens underwent white-red morphotypic switching. The method proved successful for various oenophages irrespective of their genomic content and attachment site used for site-specific recombination in the bacterial chromosome. The color switch was also observed when a sensitive nonlysogenic strain was infected with an exogenously provided lytic phage, suggesting that intracolonial lysis triggers the change. Last, lysogens also produced red colonies on white grape juice agar supplemented with polyphenolic compounds. We posit that spontaneous prophage excision produces cell lysis events in lysogenic colonies growing on RGJ agar, which, in turn, foster interactions between lysed materials and polyphenolic compounds to yield colonies easily distinguishable by their red color. Furthermore, the technique was used successfully with other species of LAB.IMPORTANCE The presence of white and red colonies on red grape juice (RGJ) agar during enumeration of Oenococcus oeni in wine samples is frequently observed by stakeholders in the wine industry. Our study brings an explanation for this intriguing phenomenon and establishes a link between the white-red color switch and the lysogenic state of O. oeni It also provides a simple and inexpensive method to distinguish between lysogenic and nonlysogenic derivatives in O. oeni with a minimum of expended time and effort. Noteworthy, the protocol could be adapted to two other species of LAB, namely, Leuconostoc citreum and Lactobacillus plantarum It could be an effective tool to provide genetic, ecological, and functional insights into lysogeny and aid in improving biotechnological processes involving members of the lactic acid bacterium (LAB) family.
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85
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What is (not) known about the dynamics of the human gut virome in health and disease. Curr Opin Virol 2019; 37:52-57. [DOI: 10.1016/j.coviro.2019.05.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/28/2019] [Accepted: 05/29/2019] [Indexed: 01/21/2023]
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86
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Fillol-Salom A, Alsaadi A, de Sousa JAM, Zhong L, Foster KR, Rocha EPC, Penadés JR, Ingmer H, Haaber J. Bacteriophages benefit from generalized transduction. PLoS Pathog 2019; 15:e1007888. [PMID: 31276485 PMCID: PMC6636781 DOI: 10.1371/journal.ppat.1007888] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 07/17/2019] [Accepted: 06/03/2019] [Indexed: 01/26/2023] Open
Abstract
Temperate phages are bacterial viruses that as part of their life cycle reside in the bacterial genome as prophages. They are found in many species including most clinical strains of the human pathogens, Staphylococcus aureus and Salmonella enterica serovar Typhimurium. Previously, temperate phages were considered as only bacterial predators, but mounting evidence point to both antagonistic and mutualistic interactions with for example some temperate phages contributing to virulence by encoding virulence factors. Here we show that generalized transduction, one type of bacterial DNA transfer by phages, can create conditions where not only the recipient host but also the transducing phage benefit. With antibiotic resistance as a model trait we used individual-based models and experimental approaches to show that antibiotic susceptible cells become resistant to both antibiotics and phage by i) integrating the generalized transducing temperate phages and ii) acquiring transducing phage particles carrying antibiotic resistance genes obtained from resistant cells in the environment. This is not observed for non-generalized transducing temperate phages, which are unable to package bacterial DNA, nor for generalized transducing virulent phages that do not form lysogens. Once established, the lysogenic host and the prophage benefit from the existence of transducing particles that can shuffle bacterial genes between lysogens and for example disseminate resistance to antibiotics, a trait not encoded by the phage. This facilitates bacterial survival and leads to phage population growth. We propose that generalized transduction can function as a mutualistic trait where temperate phages cooperate with their hosts to survive in rapidly-changing environments. This implies that generalized transduction is not just an error in DNA packaging but is selected for by phages to ensure their survival. Viruses (phages) that only attack bacteria are highly common. Some of these phages naturally reside within the bacterial chromosome for extended periods of time. Upon release and propagation on phage susceptible cells, new phage particles are made but occasionally bacterial rather than phage DNA is packaged into phage heads. Transfer of random pieces of bacterial DNA between cells by such transducing particles has been termed generalized transduction and has long been used as a tool for genetic engineering. We show here that bacteria and generalized transducing phages cooperate to survive adverse conditions such as the presence of antibiotics by phage integration and transduction of antibiotic resistance genes from neighboring cells. The resulting cells are resistant to phage attack due to immunity provided by the integrated prophage and they are able to exchange bacterial DNA with other cells containing a similar prophage via the transducing particles. Previously, transduction has been considered an accident in phage biology. Here we propose that rather than being an accident, generalized transduction is an evolved trait selected by some temperate phages to persist in rapidly-changing environments.
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Affiliation(s)
- Alfred Fillol-Salom
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Ahlam Alsaadi
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Li Zhong
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Kevin R. Foster
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Eduardo P. C. Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France
| | - José R. Penadés
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
- * E-mail: (HI); (JH)
| | - Jakob Haaber
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
- * E-mail: (HI); (JH)
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87
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Müller J, Spriewald S, Stecher B, Stadler E, Fuchs TM. Evolutionary Stability of Salmonella Competition with the Gut Microbiota: How the Environment Fosters Heterogeneity in Exploitative and Interference Competition. J Mol Biol 2019; 431:4732-4748. [PMID: 31260689 DOI: 10.1016/j.jmb.2019.06.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/19/2019] [Accepted: 06/19/2019] [Indexed: 11/27/2022]
Abstract
Following ingestion, gastrointestinal pathogens compete against the gastrointestinal microbiota and overcome host immune defenses in order to cause infections. Besides employing direct killing mechanisms, the commensal microbiota occupies metabolic niches to outcompete invading pathogens. Salmonella enterica serovar Typhimurium (S. Typhimurium) uses several strategies to successfully colonize the gut and establish infection, of which an increasing number is based on phenotypic heterogeneity within the S. Typhimurium population. The utilization of myo-inositol (MI) and the production of colicin confer a selective advantage over the microbiota in terms of exploitative and interference competition, respectively. In this review, we summarize the genetic basis underlying bistability of MI catabolism and colicin production. As demonstrated by single-cell analyses, a stochastic switch in the expression of the genes responsible for colicin production and MI degradation constitutes the heterogeneity of the two phenotypes. Both genetic systems are tightly regulated to avoid their expression under non-appropriate conditions and possible detrimental effects on bacterial fitness. Moreover, evolutionary mechanisms underlying formation and stability of these phenotypes in S. Typhimurium are discussed. We propose that both MI catabolism and colicin production create a bet-hedging strategy, which provides an adaptive benefit for S. Typhimurium in the fluctuating environment of the mammalian gut.
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Affiliation(s)
- Johannes Müller
- Technische Universität München, Centre for Mathematical Sciences, Boltzmannstr. 3, 85747 Garching, Germany; Institute for Computational Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Stefanie Spriewald
- Max von Pettenkofer-Institute, LMU Munich, Pettenkoferstr. 9a, 80336 Munich, Germany
| | - Bärbel Stecher
- Max von Pettenkofer-Institute, LMU Munich, Pettenkoferstr. 9a, 80336 Munich, Germany
| | - Eva Stadler
- Technische Universität München, Centre for Mathematical Sciences, Boltzmannstr. 3, 85747 Garching, Germany
| | - Thilo M Fuchs
- Friedrich-Loeffler-Institut, Institut für Molekulare Pathogenese, Naumburger Str. 96a, 07743 Jena, Germany.
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88
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A phylogenetic test of the role of CRISPR-Cas in limiting plasmid acquisition and prophage integration in bacteria. Plasmid 2019; 104:102418. [PMID: 31195029 DOI: 10.1016/j.plasmid.2019.102418] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 06/01/2019] [Accepted: 06/05/2019] [Indexed: 12/17/2022]
Abstract
CRISPR-Cas is a prokaryotic defense system capable of protecting the cell from damaging foreign genetic elements. However, some genetic elements can be beneficial, which suggests the hypothesis that bacteria with CRISPR-Cas incur a cost of reduced intake of mutualistic plasmids and prophage. Here we present the first robust test of this hypothesis that controls for phylogenic and ecological biases in the distribution of CRISPR-Cas. We filtered the available genomic data (~7000 strains from ~2100 species) by first selecting all pairs of conspecific strains, one with and one without CRISPR-Cas (controlling ecological bias), and second by retaining only one such pair per bacterial family (controlling phylogenetic bias), resulting in pairs representing 38 bacterial families. Analysis of these pairs of bacterial strains showed that on average the CRISPR-Cas strain of each pair contained significantly fewer plasmids than its CRISPR-Cas negative partner (0.86 vs. 1.86). It also showed that the CRISPR-Cas positive strains had 31% fewer intact prophage (1.17 vs. 1.75), but the effect was highly variable and not significant. These results support the hypothesis that CRISPR-Cas reduces the rate of plasmid-mediated HGT and, given the abundant evidence of beneficial genes carried by plasmids, provide a clear example of a cost associated with the CRISPR-Cas system.
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89
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Diversity of CRISPR/Cas system in Clostridium perfringens. Mol Genet Genomics 2019; 294:1263-1275. [PMID: 31134321 DOI: 10.1007/s00438-019-01579-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 05/17/2019] [Indexed: 12/26/2022]
Abstract
Clostridium perfringens is an important pathogen of human and livestock infections, posing a threat to health. The horizontal gene transfer (HGT) of plasmids that carry toxin-related genes is involved in C. perfringens pathogenicity. The CRISPR/Cas system, which has been identified in a wide range of prokaryotes, provides acquired immunity against HGT. However, information about the CRISPR/Cas system in Clostridium perfringens is still limited. In this study, 111 C. perfringens strains with publicly available genomes were used to analyze the occurrence and diversity of CRISPR/Cas system and evaluate the potential of CRISPR-based genotyping in this multi-host pathogen. A total of 59 out of the 111 genomes harbored at least one confirmed CRISPR array. Four CRISPR/Cas system subtypes, including subtypes IB, IIA, IIC, and IIID systems, were identified in 32 strains. Subtype IB system was the most prevalent in this species, which was subdivided into four subgroups displaying subgroup specificity in terms of cas gene content, repeat sequence content, and PAM. We showed that the CRISPR spacer polymorphism can be used for evolutionary studies, and that it can provide discriminatory power for typing strains. Nevertheless, the application of this approach was largely limited to strains that contain the CRISPR/Cas system. Spacer origin analysis revealed that approximately one-fifth of spacers showed significant matches to plasmids and phages, thereby suggesting the implication of CRISPR/Cas systems in controlling HGT. Collectively, our results provide new insights into the diversity and evolution of CRISPR/Cas system in C. perfringens.
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90
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Torres-Barceló C, Gurney J, Gougat-Barberá C, Vasse M, Hochberg ME. Transient negative effects of antibiotics on phages do not jeopardise the advantages of combination therapies. FEMS Microbiol Ecol 2019; 94:5033398. [PMID: 29878184 DOI: 10.1093/femsec/fiy107] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 06/01/2018] [Indexed: 11/14/2022] Open
Abstract
Phages, the viruses of bacteria, have been proposed as antibacterial agents to complement or replace antibiotics due to the growing problem of resistance. In nature and in the clinic, antibiotics are ubiquitous and may affect phages indirectly via impacts on bacterial hosts. Even if the synergistic association of phages and antibiotics has been shown in several studies, the focus is often on bacteria with little known about the impact on phages. Evolutionary studies have demonstrated that time scale is an important factor in understanding the consequences of antimicrobial strategies, but this perspective is generally overlooked in phage-antibiotic combination studies. Here, we explore the effects of antibiotics on phages targeting the opportunistic pathogen Pseudomonas aeruginosa. We go beyond previous studies by testing the interaction between several types of antibiotics and phages, and evaluate the effects on several important phage parameters during 8 days of experimental co-evolution with bacteria. Our study reveals that antibiotics had a negative effect on phage density and efficacy early on, but not in the later stages of the experiment. The results indicate that antibiotics can affect phage adaptation, but that phages can nevertheless contribute to managing antibiotic resistance levels.
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Affiliation(s)
- Clara Torres-Barceló
- University of Reunion Island, UMR PVBMT, 7 chemin de l'Irat, F-97410 Saint-Pierre, La Réunion, France.,Institut des Sciences de l'Evolution, Université Montpellier, Place E Bataillon 34095, Montpellier, France
| | - James Gurney
- Institut des Sciences de l'Evolution, Université Montpellier, Place E Bataillon 34095, Montpellier, France
| | - Claire Gougat-Barberá
- Institut des Sciences de l'Evolution, Université Montpellier, Place E Bataillon 34095, Montpellier, France
| | - Marie Vasse
- Institut des Sciences de l'Evolution, Université Montpellier, Place E Bataillon 34095, Montpellier, France
| | - Michael E Hochberg
- Institut des Sciences de l'Evolution, Université Montpellier, Place E Bataillon 34095, Montpellier, France.,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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91
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Mathieu J, Yu P, Zuo P, Da Silva MLB, Alvarez PJJ. Going Viral: Emerging Opportunities for Phage-Based Bacterial Control in Water Treatment and Reuse. Acc Chem Res 2019; 52:849-857. [PMID: 30925037 DOI: 10.1021/acs.accounts.8b00576] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Water security to protect human lives and support sustainable development is one of the greatest global challenges of this century. While a myriad of water pollutants can impact public health, the greatest threat arises from pathogenic bacteria that can be harbored in different components of water treatment, distribution, and reuse systems. Bacterial biofilms can also promote water infrastructure corrosion and biofouling, which substantially increase the cost and complexity of many critical operations. Conventional disinfection and microbial control approaches are often insufficient to keep up with the increasing complexity and renewed relevance of this pressing challenge. For example, common disinfectants cannot easily penetrate and eradicate biofilms, and are also relatively ineffective against resistant microorganisms. The use of chemical disinfectants is also curtailed by regulations aimed at minimizing the formation of harmful disinfection byproducts. Furthermore, disinfectants cannot be used to kill problematic bacteria in biological treatment processes without upsetting system performance. This underscores the need for novel, more precise, and more sustainable microbial control technologies. Bacteriophages (phages), which are viruses that exclusively infect bacteria, are the most abundant (and perhaps the most underutilized) biological resource on Earth, and hold great promise for targeting problematic bacteria. Although phages should not replace broad-spectrum disinfectants in drinking water treatment, they offer great potential for applications where selective targeting of problematic bacteria is warranted and antimicrobial chemicals are either relatively ineffective or their use would result in unintended detrimental consequences. Promising applications for phage-based biocontrol include selectively suppressing bulking and foaming bacteria that hinder activated sludge clarification, mitigating proliferation of antibiotic resistant strains in biological wastewater treatment systems where broad-spectrum antimicrobials would impair pollutant biodegradation, and complementing biofilm eradication efforts to delay corrosion and biofouling. Phages could also mitigate harmful cyanobacteria blooms that produce toxins in source waters, and could also serve as substitutes for the prophylactic use of antibiotics and biocides in animal agriculture to reduce their discharge to source waters and the associated selective pressure for resistant bacteria. Here, we consider the phage life cycle and its implications for bacterial control, and elaborate on the biochemical basis of such potential application niches in the water supply and reuse cycle. We also discuss potential technological barriers for phage-based bacterial control and suggest strategies and research needs to overcome them.
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Affiliation(s)
- Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
| | - Pingfeng Yu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment, Houston, Texas 77005, United States
| | - Pengxiao Zuo
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
| | - Marcio L. B. Da Silva
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
| | - Pedro J. J. Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment, Houston, Texas 77005, United States
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92
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Lam TJ, Ye Y. CRISPRs for Strain Tracking and Their Application to Microbiota Transplantation Data Analysis. CRISPR J 2019; 2:41-50. [PMID: 30820491 PMCID: PMC6390457 DOI: 10.1089/crispr.2018.0046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/29/2018] [Accepted: 01/09/2019] [Indexed: 12/17/2022] Open
Abstract
CRISPR-Cas systems are adaptive immune systems naturally found in bacteria and archaea. Prokaryotes use these immune systems to defend against invaders, which include phages, plasmids, and other mobile genetic elements. Relying on the integration of spacers derived from invader sequences (protospacers) into CRISPR loci (forming spacers flanked by repeats), CRISPR-Cas systems are able to store the memory of past immunological encounters. While CRISPR-Cas systems have evolved in response to invading mobile genetic elements, invaders have also developed mechanisms to avoid detection. As a result of an arms race between CRISPR-Cas systems and their targets, CRISPR arrays typically undergo rapid turnover of spacers through the acquisition and loss events. Additionally, microbiomes of different individuals rarely share spacers. Here, we present a computational pipeline, CRISPRtrack, for strain tracking based on CRISPR spacer content, and we applied it to fecal transplantation microbiome data to study the retention of donor strains in recipients. Our results demonstrate the potential use of CRISPRs as a simple yet effective tool for donor-strain tracking in fecal transplantation and as a general purpose tool for quantifying microbiome similarity.
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Affiliation(s)
- Tony J Lam
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana
| | - Yuzhen Ye
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana
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93
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Ramisetty BCM, Sudhakari PA. Bacterial 'Grounded' Prophages: Hotspots for Genetic Renovation and Innovation. Front Genet 2019; 10:65. [PMID: 30809245 PMCID: PMC6379469 DOI: 10.3389/fgene.2019.00065] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/24/2019] [Indexed: 01/07/2023] Open
Abstract
Bacterial genomes are highly plastic allowing the generation of variants through mutations and acquisition of genetic information. The fittest variants are then selected by the econiche thereby allowing the bacterial adaptation and colonization of the habitat. Larger genomes, however, may impose metabolic burden and hence bacterial genomes are optimized by the loss of frivolous genetic information. The activity of temperate bacteriophages has acute consequences on the bacterial population as well as the bacterial genome through lytic and lysogenic cycles. Lysogeny is a selective advantage as the prophage provides immunity to the lysogen against secondary phage attack. Since the non-lysogens are eliminated by the lytic phages, lysogens multiply and colonize the habitat. Nevertheless, all lysogens have an imminent risk of lytic cycle activation and cell lysis. However, a mutation in the attachment sites or in the genes that encode the specific recombinase responsible for prophage excision could result in 'grounding' of the prophage. Since the lysogens with grounded prophage are immune to respective phage infection as well as dodge the induction of lytic cycle, we hypothesize that the selection of these mutant lysogens is favored relative to their normal lysogenic counterparts. These grounded prophages offer several advantages to the bacterial genome evolution through propensity for genetic variations including inversions, deletions, and insertions via horizontal gene transfer. We propose that the grounded prophages expedite bacterial genome evolution by acting as 'genetic buffer zones' thereby increasing the frequency as well as the diversity of variations on which natural selection favors the beneficial variants. The grounded prophages are also hotspots for horizontal gene transfer wherein several ecologically significant genes such as those involved in stress tolerance, antimicrobial resistance, and novel metabolic pathways, are integrated. Moreover, the high frequency of genetic changes within prophages also allows proportionate probability for the de novo genesis of genetic information. Through sequence analyses of well-characterized E. coli prophages we exemplify various roles of grounded prophages in E. coli ecology and evolution. Therefore, the temperate prophages are one of the most significant drivers of bacterial genome evolution and sites of biogenesis of genetic information.
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Affiliation(s)
- Bhaskar Chandra Mohan Ramisetty
- Laboratory of Molecular Biology and Evolution, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India
| | - Pavithra Anantharaman Sudhakari
- Laboratory of Molecular Biology and Evolution, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India
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94
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McDonald ND, Regmi A, Morreale DP, Borowski JD, Boyd EF. CRISPR-Cas systems are present predominantly on mobile genetic elements in Vibrio species. BMC Genomics 2019; 20:105. [PMID: 30717668 PMCID: PMC6360697 DOI: 10.1186/s12864-019-5439-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/08/2019] [Indexed: 12/11/2022] Open
Abstract
Background Bacteria are prey for many viruses that hijack the bacterial cell in order to propagate, which can result in bacterial cell lysis and death. Bacteria have developed diverse strategies to counteract virus predation, one of which is the clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR associated (Cas) proteins immune defense system. Species within the bacterial family Vibrionaceae are marine organisms that encounter large numbers of phages. Our goal was to determine the significance of CRISPR-Cas systems as a mechanism of defense in this group by investigating their prevalence, phylogenetic distribution, and genome context. Results Herein, we describe all the CRISPR-Cas system types and their distribution within the family Vibrionaceae. In Vibrio cholerae genomes, we identified multiple variant type I-F systems, which were also present in 41 additional species. In a large number of Vibrio species, we identified a mini type I-F system comprised of tniQcas5cas7cas6f, which was always associated with Tn7-like transposons. The Tn7-like elements, in addition to the CRISPR-Cas system, also contained additional cargo genes such as restriction modification systems and type three secretion systems. A putative hybrid CRISPR-Cas system was identified containing type III-B genes followed by a type I-F cas6f and a type I-F CRISPR that was associated with a prophage in V. cholerae and V. metoecus strains. Our analysis identified CRISPR-Cas types I-C, I-E, I-F, II-B, III-A, III-B, III-D, and the rare type IV systems as well as cas loci architectural variants among 70 species. All systems described contained a CRISPR array that ranged in size from 3 to 179 spacers. The systems identified were present predominantly within mobile genetic elements (MGEs) such as genomic islands, plasmids, and transposon-like elements. Phylogenetic analysis of Cas proteins indicated that the CRISPR-Cas systems were acquired by horizontal gene transfer. Conclusions Our data show that CRISPR-Cas systems are phylogenetically widespread but sporadic in occurrence, actively evolving, and present on MGEs within Vibrionaceae. Electronic supplementary material The online version of this article (10.1186/s12864-019-5439-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nathan D McDonald
- Department of Biological Sciences, University of Delaware, 328 Wolf Hall, Newark, DE, 19716, USA
| | - Abish Regmi
- Department of Biological Sciences, University of Delaware, 328 Wolf Hall, Newark, DE, 19716, USA
| | - Daniel P Morreale
- Department of Biological Sciences, University of Delaware, 328 Wolf Hall, Newark, DE, 19716, USA
| | - Joseph D Borowski
- Department of Biological Sciences, University of Delaware, 328 Wolf Hall, Newark, DE, 19716, USA
| | - E Fidelma Boyd
- Department of Biological Sciences, University of Delaware, 328 Wolf Hall, Newark, DE, 19716, USA.
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95
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De Sordi L, Lourenço M, Debarbieux L. The Battle Within: Interactions of Bacteriophages and Bacteria in the Gastrointestinal Tract. Cell Host Microbe 2019; 25:210-218. [DOI: 10.1016/j.chom.2019.01.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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96
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Keen EC, Dantas G. Close Encounters of Three Kinds: Bacteriophages, Commensal Bacteria, and Host Immunity. Trends Microbiol 2018; 26:943-954. [PMID: 29909042 PMCID: PMC6436384 DOI: 10.1016/j.tim.2018.05.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 05/08/2018] [Accepted: 05/17/2018] [Indexed: 12/22/2022]
Abstract
Recent years have witnessed an explosion of interest in the human microbiota. Although commensal bacteria have dominated research efforts to date, mounting evidence suggests that endogenous viral populations (the 'virome') play key roles in basic human physiology. The most numerous constituents of the human virome are not eukaryotic viruses but rather bacteriophages, viruses that infect bacteria. Here, we review phages' interactions with their immediate (prokaryotic) and extended (eukaryotic) hosts and with each other, with a particular emphasis on the temperate phages and prophages which dominate the human virome. We also discuss key outstanding questions in this emerging field and emphasize the urgent need for functional studies in animal models to complement previous in vitro work and current computational approaches.
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Affiliation(s)
- Eric C Keen
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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97
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Van Houdt R, Provoost A, Van Assche A, Leys N, Lievens B, Mijnendonckx K, Monsieurs P. Cupriavidus metallidurans Strains with Different Mobilomes and from Distinct Environments Have Comparable Phenomes. Genes (Basel) 2018; 9:genes9100507. [PMID: 30340417 PMCID: PMC6210171 DOI: 10.3390/genes9100507] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/11/2018] [Accepted: 10/15/2018] [Indexed: 12/16/2022] Open
Abstract
Cupriavidus metallidurans has been mostly studied because of its resistance to numerous heavy metals and is increasingly being recovered from other environments not typified by metal contamination. They host a large and diverse mobile gene pool, next to their native megaplasmids. Here, we used comparative genomics and global metabolic comparison to assess the impact of the mobilome on growth capabilities, nutrient utilization, and sensitivity to chemicals of type strain CH34 and three isolates (NA1, NA4 and H1130). The latter were isolated from water sources aboard the International Space Station (NA1 and NA4) and from an invasive human infection (H1130). The mobilome was expanded as prophages were predicted in NA4 and H1130, and a genomic island putatively involved in abietane diterpenoids metabolism was identified in H1130. An active CRISPR-Cas system was identified in strain NA4, providing immunity to a plasmid that integrated in CH34 and NA1. No correlation between the mobilome and isolation environment was found. In addition, our comparison indicated that the metal resistance determinants and properties are conserved among these strains and thus maintained in these environments. Furthermore, all strains were highly resistant to a wide variety of chemicals, much broader than metals. Only minor differences were observed in the phenomes (measured by phenotype microarrays), despite the large difference in mobilomes and the variable (shared by two or three strains) and strain-specific genomes.
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Affiliation(s)
- Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), B-2400 Mol, Belgium.
| | - Ann Provoost
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), B-2400 Mol, Belgium.
| | - Ado Van Assche
- Laboratory for Process Microbial Ecology and Bioinspirational Management, KU Leuven, B-2860 Sint-Katelijne-Waver, Belgium.
| | - Natalie Leys
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), B-2400 Mol, Belgium.
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management, KU Leuven, B-2860 Sint-Katelijne-Waver, Belgium.
| | - Kristel Mijnendonckx
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), B-2400 Mol, Belgium.
| | - Pieter Monsieurs
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), B-2400 Mol, Belgium.
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98
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Abstract
The human body is colonized by a diverse collective of microorganisms, including bacteria, fungi, protozoa and viruses. The smallest entity of this microbial conglomerate are the bacterial viruses. Bacteriophages, or phages for short, exert significant selective pressure on their bacterial hosts, undoubtedly influencing the human microbiome and its impact on our health and well-being. Phages colonize all niches of the body, including the skin, oral cavity, lungs, gut, and urinary tract. As such our bodies are frequently and continuously exposed to diverse collections of phages. Despite the prevalence of phages throughout our bodies, the extent of their interactions with human cells, organs, and immune system is still largely unknown. Phages physically interact with our mucosal surfaces, are capable of bypassing epithelial cell layers, disseminate throughout the body and may manipulate our immune system. Here, I establish the novel concept of an "intra-body phageome," which encompasses the collection of phages residing within the classically "sterile" regions of the body. This review will take a phage-centric view of the microbiota, human body, and immune system with the ultimate goal of inspiring a greater appreciation for both the indirect and direct interactions between bacteriophages and their mammalian hosts.
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Affiliation(s)
- Jeremy J Barr
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
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99
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Li XY, Lachnit T, Fraune S, Bosch TCG, Traulsen A, Sieber M. Temperate phages as self-replicating weapons in bacterial competition. J R Soc Interface 2018; 14:rsif.2017.0563. [PMID: 29263125 DOI: 10.1098/rsif.2017.0563] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/24/2017] [Indexed: 12/14/2022] Open
Abstract
Microbial communities are accompanied by a diverse array of viruses. Through infections of abundant microbes, these viruses have the potential to mediate competition within the community, effectively weakening competitive interactions and promoting coexistence. This is of particular relevance for host-associated microbial communities, because the diversity of the microbiota has been linked to host health and functioning. Here, we study the interaction between two key members of the microbiota of the freshwater metazoan Hydra vulgaris The two commensal bacteria Curvibacter sp. and Duganella sp. protect their host from fungal infections, but only if both of them are present. Coexistence of the two bacteria is thus beneficial for Hydra Intriguingly, Duganella sp. appears to be the superior competitor in vitro due to its higher growth rate when both bacteria are grown separately, but in co-culture the outcome of competition depends on the relative initial abundances of the two species. The presence of an inducible prophage in the Curvibacter sp. genome, which is able to lytically infect Duganella sp., led us to hypothesize that the phage modulates the interaction between these two key members of the Hydra microbiota. Using a mathematical model, we show that the interplay of the lysogenic life cycle of the Curvibacter phage and the lytic life cycle on Duganella sp. can explain the observed complex competitive interaction between the two bacteria. Our results highlight the importance of taking lysogeny into account for understanding microbe-virus interactions and show the complex role phages can play in promoting coexistence of their bacterial hosts.
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Affiliation(s)
- Xiang-Yi Li
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Tim Lachnit
- Zoological Institute, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Sebastian Fraune
- Zoological Institute, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Thomas C G Bosch
- Zoological Institute, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Arne Traulsen
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Michael Sieber
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
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100
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Chatterjee A, Duerkop BA. Beyond Bacteria: Bacteriophage-Eukaryotic Host Interactions Reveal Emerging Paradigms of Health and Disease. Front Microbiol 2018; 9:1394. [PMID: 29997604 PMCID: PMC6030379 DOI: 10.3389/fmicb.2018.01394] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 06/07/2018] [Indexed: 12/28/2022] Open
Abstract
For decades, a wealth of information has been acquired to define how host associated microbial communities contribute to health and disease. Within the human microbiota this has largely focused on bacteria, yet there is a myriad of viruses that occupy various tissue sites, the most abundant being bacteriophages that infect bacteria. Animal hosts are colonized with niche specific microbial communities where bacteria are continuously co-evolving with phages. Bacterial growth, metabolic activity, pathogenicity, antibiotic resistance, interspecies competition and evolution can all be influenced by phage infection and the beneficial nature of such interactions suggests that to an extent phages are tolerated by their hosts. With the understanding that phage-specific host–microbe interactions likely contribute to bacterial interactions with their mammalian hosts, phages and their communities may also impact aspects of mammalian health and disease that have gone unrecognized. Here, we review recent progress in understanding how bacteria acquire and tolerate phage in both pure culture and within complex communities. We apply these findings to discuss how intra-body phages interact with bacteria to influence their eukaryotic hosts through potential contributions to microbial homeostasis, mucosal immunity, immune tolerance and autoimmunity.
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Affiliation(s)
- Anushila Chatterjee
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
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