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Jackson M, Vineberg S, Theis KR. The Epistemology of Bacterial Virulence Factor Characterization. Microorganisms 2024; 12:1272. [PMID: 39065041 PMCID: PMC11278562 DOI: 10.3390/microorganisms12071272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024] Open
Abstract
The field of microbial pathogenesis seeks to identify the agents and mechanisms responsible for disease causation. Since Robert Koch introduced postulates that were used to guide the characterization of microbial pathogens, technological advances have substantially increased the capacity to rapidly identify a causative infectious agent. Research efforts currently focus on causation at the molecular level with a search for virulence factors (VFs) that contribute to different stages of the infectious process. We note that the quest to identify and characterize VFs sometimes lacks scientific rigor, and this suggests a need to examine the epistemology of VF characterization. We took this premise as an opportunity to explore the epistemology of VF characterization. In this perspective, we discuss how the characterization of various gene products that evolved to facilitate bacterial survival in the broader environment have potentially been prematurely mischaracterized as VFs that contribute to pathogenesis in the context of human biology. Examples of the reasoning that can affect misinterpretation, or at least a premature assignment of mechanistic causation, are provided. Our aim is to refine the categorization of VFs by emphasizing a broader biological view of their origin.
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Affiliation(s)
- Matthew Jackson
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Susan Vineberg
- Department of Philosophy, Wayne State University, Detroit, MI 48201, USA;
| | - Kevin R. Theis
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI 48201, USA
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2
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Gong C, Chakraborty D, Koudelka GB. A prophage encoded ribosomal RNA methyltransferase regulates the virulence of Shiga-toxin-producing Escherichia coli (STEC). Nucleic Acids Res 2024; 52:856-871. [PMID: 38084890 PMCID: PMC10810198 DOI: 10.1093/nar/gkad1150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 01/26/2024] Open
Abstract
Shiga toxin (Stx) released by Shiga toxin producing Escherichia coli (STEC) causes life-threatening illness. Its production and release require induction of Stx-encoding prophage resident within the STEC genome. We identified two different STEC strains, PA2 and PA8, bearing Stx-encoding prophage whose sequences primarily differ by the position of an IS629 insertion element, yet differ in their abilities to kill eukaryotic cells and whose prophages differ in their spontaneous induction frequencies. The IS629 element in ϕPA2, disrupts an ORF predicted to encode a DNA adenine methyltransferase, whereas in ϕPA8, this element lies in an intergenic region. Introducing a plasmid expressing the methyltransferase gene product into ϕPA2 bearing-strains increases both the prophage spontaneous induction frequency and virulence to those exhibited by ϕPA8 bearing-strains. However, a plasmid bearing mutations predicted to disrupt the putative active site of the methyltransferase does not complement either of these defects. When complexed with a second protein, the methyltransferase holoenzyme preferentially uses 16S rRNA as a substrate. The second subunit is responsible for directing the preferential methylation of rRNA. Together these findings reveal a previously unrecognized role for rRNA methylation in regulating induction of Stx-encoding prophage.
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Affiliation(s)
- Chen Gong
- Department of Biological Sciences University at Buffalo, Buffalo, NY 14260, USA
| | | | - Gerald B Koudelka
- Department of Biological Sciences University at Buffalo, Buffalo, NY 14260, USA
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3
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Liu Y, Koudelka G. O-Polysaccharides of LPS Modulate E. coli Uptake by Acanthamoeba castellanii. Microorganisms 2023; 11:1377. [PMID: 37374879 DOI: 10.3390/microorganisms11061377] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
Protozoan grazing is a major cause of bacterial mortality and controls bacterial population size and composition in the natural environment. To enhance their survival, bacteria evolved many defense strategies to avoid grazing by protists. Cell wall modification is one of the defense strategies that helps bacteria escape from recognition and/or internalization by its predators. Lipopolysaccharide (LPS) is the major component of Gram-negative bacterial cell wall. LPS is divided into three regions: lipid A, oligosaccharide core and O-specific polysaccharide. O-polysaccharide as the outermost region of E. coli LPS provides protection against predation by Acanthamoeba castellanii; however, the characteristics of O-polysaccharide contribute to this protection remain unknown. Here, we investigate how length, structure and composition of LPS affect E. coli recognition and internalization by A. castellanii. We found that length of O-antigen does not play a significant role in regulating bacterial recognition by A. castellanii. However, the composition and structure of O-polysaccharide play important roles in providing resistance to A. castellanii predation.
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Affiliation(s)
- Ying Liu
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Gerald Koudelka
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
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4
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The Oligosaccharide Region of LPS Governs Predation of E. coli by the Bacterivorous Protist, Acanthamoeba castellanii. Microbiol Spectr 2023; 11:e0293022. [PMID: 36648221 PMCID: PMC9927288 DOI: 10.1128/spectrum.02930-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Protozoan predation is a major cause of bacterial mortality. The first step of predation for phagocytic amoebae is the recognition of their prey. Lipopolysaccharide (LPS) is a major component of Gram-negative bacteria and is only present on the outer leaflet of the outer membrane lipid bilayer. LPS consists of three distinct regions: lipid A, an oligosaccharide core, and O-polysaccharide. Previous research in our lab determined that the oligosaccharide (OS) region of LPS mediates the recognition and internalization of Escherichia coli by Acanthamoeba castellanii. The oligosaccharide region is conceptually divided into the inner core and outer core. The LPS of any given E. coli strain contains only one of five different OS structures: K-12 and R1 to R4. All OSs contain the same inner core sugars but different outer core sugars. Here, we show that the Kdo2 moiety of the inner core is necessary and sufficient for E. coli recognition and internalization by A. castellanii. We also show that the precise composition of the variable outer core OS region modulates the efficiency with which A. castellanii consumes bacteria. The latter finding indicates that outer core OS composition plays a role in bacterial defense against phagocytic predators. IMPORTANCE Rather than being transmitted from host to host, most opportunistic bacterial pathogens reside in the environment for significant amounts of time. Protist predation is a major cause of bacterial mortality. To enhance their survival in the environment, bacteria have evolved various defense strategies such as filamentation, increased motility, biofilm formation, toxin release, and modification of cell wall structure; strategies which also enhance their virulence to humans. This work shows that the major component of the bacterial cell wall, LPS, also known as bacterial endotoxin, is a "dual use" factor, regulating amoeba predation of bacteria in addition to its well-known role as a human virulence factor. Both these functions are governed by the same parts of LPS. Thus, the structure and composition of this "dual use" factor likely evolved as a response to constant voracious protist grazing pressure in the environment, rather than during short-term infections of human and animals.
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5
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Montalbano Di Filippo M, Boni A, Chiani P, Marra M, Carollo M, Cristofari L, Minelli F, Knijn A, Morabito S. Exploring the nature of interaction between shiga toxin producing Escherichia coli (STEC) and free-living amoeba - Acanthamoeba sp. Front Cell Infect Microbiol 2022; 12:926127. [PMID: 36159652 PMCID: PMC9504058 DOI: 10.3389/fcimb.2022.926127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Free-living amoebae (FLA) are widely distributed protozoa in nature, known to cause severe eye infections and central nervous system disorders. There is growing attention to the potential role that these protozoa could act as reservoirs of pathogenic bacteria and, consequently, to the possibility that, the persistence and spread of the latter may be facilitated, by exploiting internalization into amoebae. Shiga toxin-producing strains of Escherichia coli (STEC) are zoonotic agents capable of causing serious diseases, such as hemorrhagic colitis (HC) and hemolytic uremic syndrome (HUS). Cattle represent the main natural reservoir of STEC, which are frequently found also in other domestic and wild ruminants, often without causing any evident symptoms of disease. The aspects related to the ecology of STEC strains in animal reservoirs and the environment are poorly known, including the persistence of these microorganisms within niches unfavorable to survival, such as soils or waters. In this study we investigated the interaction between STEC strains of serotype O157: H7 with different virulence gene profiles, and a genus of a wild free-living amoeba, Acanthamoeba sp. Our results confirm the ability of STEC strains to survive up to 20 days within a wild Acanthamoeba sp., in a quiescent state persisting in a non-cultivable form, until they reactivate following some stimulus of an unknown nature. Furthermore, our findings show that during their internalization, the E. coli O157 kept the set of the main virulence genes intact, preserving their pathogenetic potential. These observations suggest that the internalization in free-living amoebae may represent a means for STEC to resist in environments with non-permissive growth conditions. Moreover, by staying within the protozoa, STEC could escape their detection in the vehicles of infections and resist to the treatments used for the disinfection of the livestock environment.
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Affiliation(s)
- Margherita Montalbano Di Filippo
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
- *Correspondence: Margherita Montalbano Di Filippo,
| | - Arianna Boni
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Paola Chiani
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Manuela Marra
- Core Facilities, Istituto Superiore di Sanità, Rome, Italy
| | - Maria Carollo
- Core Facilities, Istituto Superiore di Sanità, Rome, Italy
| | - Lucrezia Cristofari
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Fabio Minelli
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Arnold Knijn
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Stefano Morabito
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
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6
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Shkoporov AN, Turkington CJ, Hill C. Mutualistic interplay between bacteriophages and bacteria in the human gut. Nat Rev Microbiol 2022; 20:737-749. [PMID: 35773472 DOI: 10.1038/s41579-022-00755-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 12/12/2022]
Abstract
Bacteriophages (phages) are often described as obligate predators of their bacterial hosts, and phage predation is one of the leading forces controlling the density and distribution of bacterial populations. Every 48 h half of all bacteria on Earth are killed by phages. Efficient killing also forms the basis of phage therapy in humans and animals and the use of phages as food preservatives. In turn, bacteria have a plethora of resistance systems against phage attack, but very few bacterial species, if any, have entirely escaped phage predation. However, in complex communities and environments such as the human gut, this antagonistic model of attack and counter-defence does not fully describe the scope of phage-bacterium interactions. In this Review, we explore some of the more mutualistic aspects of phage-bacterium interactions in the human gut, and we suggest that the relationship between phages and their bacterial hosts in the gut is best characterized not as a fight to the death between enemies but rather as a mutualistic relationship between partners.
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Affiliation(s)
- Andrey N Shkoporov
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland. .,Department of Medicine, University College Cork, Cork, Ireland.
| | | | - Colin Hill
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland.
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7
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Koskella B, Hernandez CA, Wheatley RM. Understanding the Impacts of Bacteriophage Viruses: From Laboratory Evolution to Natural Ecosystems. Annu Rev Virol 2022; 9:57-78. [PMID: 35584889 DOI: 10.1146/annurev-virology-091919-075914] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viruses of bacteriophages (phages) have broad effects on bacterial ecology and evolution in nature that mediate microbial interactions, shape bacterial diversity, and influence nutrient cycling and ecosystem function. The unrelenting impact of phages within the microbial realm is the result, in large part, of their ability to rapidly evolve in response to bacterial host dynamics. The knowledge gained from laboratory systems, typically using pairwise interactions between single-host and single-phage systems, has made clear that phages coevolve with their bacterial hosts rapidly, somewhat predictably, and primarily by counteradapting to host resistance. Recent advancement in metagenomics approaches, as well as a shifting focus toward natural microbial communities and host-associated microbiomes, is beginning to uncover the full picture of phage evolution and ecology within more complex settings. As these data reach their full potential, it will be critical to ask when and how insights gained from studies of phage evolution in vitro can be meaningfully applied to understanding bacteria-phage interactions in nature. In this review, we explore the myriad ways that phages shape and are themselves shaped by bacterial host populations and communities, with a particular focus on observed and predicted differences between the laboratory and complex microbial communities. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, California, USA;
| | - Catherine A Hernandez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
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8
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Králová S, Busse HJ, Bezdíček M, Sandoval-Powers M, Nykrýnová M, Staňková E, Krsek D, Sedláček I. Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov., Two Multidrug-Resistant Psychrotrophic Species Isolated From Antarctica. Front Microbiol 2021; 12:729977. [PMID: 34745033 PMCID: PMC8570120 DOI: 10.3389/fmicb.2021.729977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
Despite unfavorable Antarctic conditions, such as cold temperatures, freeze-thaw cycles, high ultraviolet radiation, dryness and lack of nutrients, microorganisms were able to adapt and surprisingly thrive in this environment. In this study, eight cold-adapted Flavobacterium strains isolated from a remote Antarctic island, James Ross Island, were studied using a polyphasic taxonomic approach to determine their taxonomic position. Phylogenetic analyses based on the 16S rRNA gene and 92 core genes clearly showed that these strains formed two distinct phylogenetic clusters comprising three and five strains, with average nucleotide identities significantly below 90% between both proposed species as well as between their closest phylogenetic relatives. Phenotyping revealed a unique pattern of biochemical and physiological characteristics enabling differentiation from the closest phylogenetically related Flavobacterium spp. Chemotaxonomic analyses showed that type strains P4023T and P7388T were characterized by the major polyamine sym-homospermidine and a quinone system containing predominantly menaquinone MK-6. In the polar lipid profile phosphatidylethanolamine, an ornithine lipid and two unidentified lipids lacking a functional group were detected as major lipids. These characteristics along with fatty acid profiles confirmed that these species belong to the genus Flavobacterium. Thorough genomic analysis revealed the presence of numerous cold-inducible or cold-adaptation associated genes, such as cold-shock proteins, proteorhodopsin, carotenoid biosynthetic genes or oxidative-stress response genes. Genomes of type strains surprisingly harbored multiple prophages, with many of them predicted to be active. Genome-mining identified biosynthetic gene clusters in type strain genomes with a majority not matching any known clusters which supports further exploratory research possibilities involving these psychrotrophic bacteria. Antibiotic susceptibility testing revealed a pattern of multidrug-resistant phenotypes that were correlated with in silico antibiotic resistance prediction. Interestingly, while typical resistance finder tools failed to detect genes responsible for antibiotic resistance, genomic prediction confirmed a multidrug-resistant profile and suggested even broader resistance than tested. Results of this study confirmed and thoroughly characterized two novel psychrotrophic Flavobacterium species, for which the names Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov. are proposed.
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Affiliation(s)
- Stanislava Králová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czechia
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Vienna, Austria
| | - Matěj Bezdíček
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czechia.,Department of Internal Medicine - Hematology and Oncology, Masaryk University, Brno, Czechia
| | | | - Markéta Nykrýnová
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Eva Staňková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czechia
| | - Daniel Krsek
- NRL for Diagnostic Electron Microscopy of Infectious Agents, National Institute of Public Health, Prague, Czechia
| | - Ivo Sedláček
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czechia
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9
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Ezzedine JA, Desdevises Y, Jacquet S. Bdellovibrio and like organisms: current understanding and knowledge gaps of the smallest cellular hunters of the microbial world. Crit Rev Microbiol 2021; 48:428-449. [PMID: 34595998 DOI: 10.1080/1040841x.2021.1979464] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Almost sixty years ago, Bdellovibrio and like organisms (BALOs) were discovered as the first obligate bacterial predators of other bacteria known to science. Since then, they were shown to be diverse and ubiquitous in the environment, and to bear astonishing ecological, physiological, and metabolic capabilities. The last decade has seen important strides made in understanding the mechanistic basis of their life cycle, the dynamics of their interactions with prey, along with significant developments towards their use in medicine, agriculture, and industry. This review details these achievements, identify current understanding and knowledge gaps to encourage and guide future BALO research.
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Affiliation(s)
- Jade A Ezzedine
- Université Savoie Mont-Blanc, INRAE, CARRTEL, Thonon-les-Bains, France.,Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, IRIG, Université Grenoble Alpes, Grenoble, France
| | - Yves Desdevises
- CNRS, Biologie Intégrative des Organismes Marins, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France
| | - Stéphan Jacquet
- Université Savoie Mont-Blanc, INRAE, CARRTEL, Thonon-les-Bains, France
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10
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Abstract
Bacteria harbor viruses called bacteriophages that, like all viruses, co-opt the host cellular machinery to replicate. Although this relationship is at first glance parasitic, there are social interactions among and between bacteriophages and their bacterial hosts. These social interactions can take on many forms, including cooperation, altruism, and cheating. Such behaviors among individuals in groups of bacteria have been well described. However, the social nature of some interactions between phages or phages and bacteria is only now becoming clear. Bacteria harbor viruses called bacteriophages that, like all viruses, co-opt the host cellular machinery to replicate. Although this relationship is at first glance parasitic, there are social interactions among and between bacteriophages and their bacterial hosts. These social interactions can take on many forms, including cooperation, altruism, and cheating. Such behaviors among individuals in groups of bacteria have been well described. However, the social nature of some interactions between phages or phages and bacteria is only now becoming clear. We are just beginning to understand how bacteriophages affect the sociobiology of bacteria, and we know even less about social interactions within bacteriophage populations. In this review, we discuss recent developments in our understanding of bacteriophage sociobiology, including how selective pressures influence the outcomes of social interactions between populations of bacteria and bacteriophages. We also explore how tripartite social interactions between bacteria, bacteriophages, and an animal host affect host-microbe interactions. Finally, we argue that understanding the sociobiology of bacteriophages will have implications for the therapeutic use of bacteriophages to treat bacterial infections.
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11
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Kavagutti VS, Andrei AŞ, Mehrshad M, Salcher MM, Ghai R. Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics. MICROBIOME 2019; 7:135. [PMID: 31630686 DOI: 10.1101/670067v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/24/2019] [Indexed: 05/22/2023]
Abstract
The persistent inertia in the ability to culture environmentally abundant microbes from aquatic ecosystems represents an obstacle in disentangling the complex web of ecological interactions spun by a diverse assortment of participants (pro- and eukaryotes and their viruses). In aquatic microbial communities, the numerically most abundant actors, the viruses, remain the most elusive, and especially in freshwaters their identities and ecology remain unknown. Here, using ultra-deep metagenomic sequencing from pelagic freshwater habitats, we recovered complete genomes of > 2000 phages, including small "miniphages" and large "megaphages" infecting iconic freshwater prokaryotic lineages. For instance, abundant freshwater Actinobacteria support infection by a very broad size range of phages (13-200 Kb). We describe many phages encoding genes that likely afford protection to their host from reactive oxygen species (ROS) in the aquatic environment and in the oxidative burst in protist phagolysosomes (phage-mediated ROS defense). Spatiotemporal abundance analyses of phage genomes revealed evanescence as the primary dynamic in upper water layers, where they displayed short-lived existences. In contrast, persistence was characteristic for the deeper layers where many identical phage genomes were recovered repeatedly. Phage and host abundances corresponded closely, with distinct populations displaying preferential distributions in different seasons and depths, closely mimicking overall stratification and mixis.
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Affiliation(s)
- Vinicius S Kavagutti
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Adrian-Ştefan Andrei
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Maliheh Mehrshad
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Michaela M Salcher
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
- Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic.
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12
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Kavagutti VS, Andrei AŞ, Mehrshad M, Salcher MM, Ghai R. Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics. MICROBIOME 2019; 7:135. [PMID: 31630686 PMCID: PMC6802176 DOI: 10.1186/s40168-019-0752-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/24/2019] [Indexed: 05/20/2023]
Abstract
The persistent inertia in the ability to culture environmentally abundant microbes from aquatic ecosystems represents an obstacle in disentangling the complex web of ecological interactions spun by a diverse assortment of participants (pro- and eukaryotes and their viruses). In aquatic microbial communities, the numerically most abundant actors, the viruses, remain the most elusive, and especially in freshwaters their identities and ecology remain unknown. Here, using ultra-deep metagenomic sequencing from pelagic freshwater habitats, we recovered complete genomes of > 2000 phages, including small "miniphages" and large "megaphages" infecting iconic freshwater prokaryotic lineages. For instance, abundant freshwater Actinobacteria support infection by a very broad size range of phages (13-200 Kb). We describe many phages encoding genes that likely afford protection to their host from reactive oxygen species (ROS) in the aquatic environment and in the oxidative burst in protist phagolysosomes (phage-mediated ROS defense). Spatiotemporal abundance analyses of phage genomes revealed evanescence as the primary dynamic in upper water layers, where they displayed short-lived existences. In contrast, persistence was characteristic for the deeper layers where many identical phage genomes were recovered repeatedly. Phage and host abundances corresponded closely, with distinct populations displaying preferential distributions in different seasons and depths, closely mimicking overall stratification and mixis.
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Affiliation(s)
- Vinicius S Kavagutti
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Adrian-Ştefan Andrei
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Maliheh Mehrshad
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Michaela M Salcher
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
- Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, České Budějovice, Czech Republic.
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13
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Seth-Smith HMB, Egli A. Whole Genome Sequencing for Surveillance of Diphtheria in Low Incidence Settings. Front Public Health 2019; 7:235. [PMID: 31497588 PMCID: PMC6713046 DOI: 10.3389/fpubh.2019.00235] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/06/2019] [Indexed: 12/29/2022] Open
Abstract
Corynebacterium diphtheriae (C. diphtheriae) is a relatively rare pathogen in most Western countries. While toxin producing strains can cause pharyngeal diphtheria with potentially fatal outcomes, the more common presentation is wound infections. The diphtheria toxin is encoded on a prophage and can also be carried by Corynebacterium ulcerans and Corynebacterium pseudotuberculosis. Currently, across Europe, infections are mainly diagnosed in travelers and refugees from regions where diphtheria is more endemic, patients from urban areas with poor hygiene, and intravenous drug users. About half of the cases are non-toxin producing isolates. Rapid identification of the bacterial pathogen and toxin production is a critical element of patient and outbreak management. Beside the immediate clinical management of the patient, public health agencies should be informed of toxigenic C. diphtheriae diagnoses as soon as possible. The collection of case-related epidemiological data from the patient is often challenging due to language barriers and social circumstances. However, information on patient contacts, vaccine status and travel/refugee route, where appropriate, is critical, and should be documented. In addition, isolates should be characterized using high resolution typing, in order to identify transmissions and outbreaks. In recent years, whole genome sequencing (WGS) has become the gold standard of high-resolution typing methods, allowing detailed investigations of pathogen transmissions. De-centralized sequencing strategies with redundancy in sequencing capacities, followed by data exchange may be a valuable future option, especially since WGS becomes more available and portable. In this context, the sharing of sequence data, using public available platforms, is essential. A close interaction between microbiology laboratories, treating physicians, refugee centers, social workers, and public health officials is a key element in successful management of suspected outbreaks. Analyzing bacterial isolates at reference centers may further help to provide more specialized microbiological techniques and to standardize information, but this is also more time consuming during an outbreak. Centralized communication strategies between public health agencies and laboratories helps considerably in establishing and coordinating effective surveillance and infection control. We review the current literature on high-resolution typing of C. diphtheriae and share our own experience with the coordination of a Swiss-German outbreak.
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Affiliation(s)
- Helena M. B. Seth-Smith
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Adrian Egli
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
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14
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Evolution of STEC virulence: Insights from the antipredator activities of Shiga toxin producing E. coli. Int J Med Microbiol 2018; 308:956-961. [DOI: 10.1016/j.ijmm.2018.07.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 06/29/2018] [Accepted: 07/10/2018] [Indexed: 11/17/2022] Open
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15
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Li C, Ju LK. Reclamation of wastewater organics via two-stage growth of bacteria-then-oleaginous phagotrophic algae. Bioprocess Biosyst Eng 2018; 41:1757-1766. [PMID: 30099623 DOI: 10.1007/s00449-018-1998-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/03/2018] [Indexed: 11/25/2022]
Abstract
A substantial amount of organic matter is wasted in current wastewater treatment processes. To reclaim the value of organic matter, a two-stage continuous-flow open process has been developed by utilizing the capability of phagotrophic algae in ingesting bacterial cells. In this process, wastewater is first pumped into a bacteria tank to grow bacterial cells, and then the effluent containing grown bacteria cells is fed to an algae tank to grow phagotrophic algae. The operation conditions such as dilution rate, pH, and dissolved oxygen level were comprehensively investigated and optimized with long-term tests. Results show that phagotrophic algae can be stably cultivated with wastewater organics through this open process without costly chemical/physical sterilization. The produced phagotrophic algae had high lipid content and can be potentially used as biofuel feedstock.
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Affiliation(s)
- Cong Li
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325-3906, USA.
| | - Lu-Kwang Ju
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325-3906, USA.
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16
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Predators and nutrient availability favor protozoa-resisting bacteria in aquatic systems. Sci Rep 2018; 8:8415. [PMID: 29849061 PMCID: PMC5976761 DOI: 10.1038/s41598-018-26422-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 05/08/2018] [Indexed: 11/30/2022] Open
Abstract
The long co-existence of bacteria and protozoa has led to the development of bacterial protozoa resistance strategies, which are suggested to serve as drivers for the evolution of pathogenic bacteria. However, the ecological mechanisms underpinning selection for protozoa-resistance in aquatic bacteria are poorly known. To assess the role of nutrient availability and predation-pressure on selection for protozoa-resisting bacteria (PRB), an enrichment-dilution experiment was designed using laboratory microcosms containing natural lake water. PRB was monitored by screening 16S rRNA amplicon sequence data for reads assigned to bacteria that previously has been shown to resist degradation by amoebae. To estimate the effects of the microbial food web dynamics (microscopy of; heterotrophic bacteria, phytoplankton, protozoa and rotifers) and physicochemical variables on the PRB abundance in the study system, a joint species distribution modelling approach was used. The predation-pressure (ratio between predator and bacterial biomass) had a positive effect on the abundance of the PRB genus Mycobacterium, while perturbation (enrichment and dilution) favored the PRB genus Pseudomonas that dominated the bacterial community in the disturbed systems. Our results show that PRB with different ecological strategies can be expected in water of high and intermediate nutrient levels and after major disturbances of an aquatic system.
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17
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Sun S, Noorian P, McDougald D. Dual Role of Mechanisms Involved in Resistance to Predation by Protozoa and Virulence to Humans. Front Microbiol 2018; 9:1017. [PMID: 29867902 PMCID: PMC5967200 DOI: 10.3389/fmicb.2018.01017] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 04/30/2018] [Indexed: 12/12/2022] Open
Abstract
Most opportunistic pathogens transit in the environment between hosts and the environment plays a significant role in the evolution of protective traits. The coincidental evolution hypothesis suggests that virulence factors arose as a response to other selective pressures rather for virulence per se. This idea is strongly supported by the elucidation of bacterial-protozoal interactions. In response to protozoan predation, bacteria have evolved various defensive mechanisms which may also function as virulence factors. In this review, we summarize the dual role of factors involved in both grazing resistance and human pathogenesis, and compare the traits using model intracellular and extracellular pathogens. Intracellular pathogens rely on active invasion, blocking of the phagosome and lysosome fusion and resistance to phagocytic digestion to successfully invade host cells. In contrast, extracellular pathogens utilize toxin secretion and biofilm formation to avoid internalization by phagocytes. The complexity and diversity of bacterial virulence factors whose evolution is driven by protozoan predation, highlights the importance of protozoa in evolution of opportunistic pathogens.
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Affiliation(s)
- Shuyang Sun
- ithree Institute, University of Technology Sydney, Sydney, NSW, Australia
| | - Parisa Noorian
- ithree Institute, University of Technology Sydney, Sydney, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Diane McDougald
- ithree Institute, University of Technology Sydney, Sydney, NSW, Australia.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
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18
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Molecular Mechanisms Governing "Hair-Trigger" Induction of Shiga Toxin-Encoding Prophages. Viruses 2018; 10:v10050228. [PMID: 29710828 PMCID: PMC5977221 DOI: 10.3390/v10050228] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/25/2018] [Accepted: 04/25/2018] [Indexed: 01/12/2023] Open
Abstract
Shiga toxin (Stx)-encoding E. coli (STEC) strains are responsible for sporadic outbreaks of food poisoning dating to 1982, when the first STEC strain, E. coli O157:H7, was isolated. Regardless of STEC serotype, the primary symptoms of STEC infections are caused by Stx that is synthesized from genes resident on lambdoid prophage present in STEC. Despite similar etiology, the severity of STEC-mediated disease varies by outbreak. However, it is unclear what modulates the severity of STEC-mediated disease. Stx production and release is controlled by lytic growth of the Stx-encoding bacteriophage, which in turn, is controlled by the phage repressor. Here, we confirm our earlier suggestion that the higher spontaneous induction frequency of Stx-encoding prophage is a consequence, in part, of lower intracellular repressor levels in STEC strains versus non-STEC strains. We also show that this lowered intracellular repressor concentration is a consequence of the utilization of alternative binding/regulatory strategies by the phage repressor. We suggest that a higher spontaneous induction frequency would lead to increased virulence.
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19
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Aijaz I, Koudelka GB. Cheating, facilitation and cooperation regulate the effectiveness of phage-encoded exotoxins as antipredator molecules. Microbiologyopen 2018; 8:e00636. [PMID: 29675935 PMCID: PMC6391270 DOI: 10.1002/mbo3.636] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/09/2018] [Accepted: 03/09/2018] [Indexed: 01/28/2023] Open
Abstract
Temperate phage encoded Shiga toxin (Stx) kills the bacterivorous predator, Tetrahymena thermophila, providing Stx+Escherichia coli with a survival advantage over Stx− cells. Although bacterial death accompanies Stx release, since bacteria grow clonally the fitness benefits of predator killing accrue to the kin of the sacrificed organism, meaning Stx‐mediated protist killing is a form of self‐destructive cooperation. We show here that the fitness benefits of Stx production are not restricted to the kin of the phage‐encoding bacteria. Instead, nearby “free loading” bacteria, irrespective of their genotype, also reap the benefit of Stx‐mediated predator killing. This finding indicates that the phage‐borne Stx exotoxin behaves as a public good. Stx is encoded by a mobile phage. We find that Stx‐encoding phage can use susceptible bacteria in the population as surrogates to enhance toxin and phage production. Moreover, our findings also demonstrate that engulfment and concentration of Stx‐encoding and susceptible Stx− bacteria in the Tetrahymena phagosome enhances the transfer of Stx‐encoding temperate phage from the host to the susceptible bacteria. This transfer increases the population of cooperating bacteria within the community. Since these bacteria now encode Stx, the predation‐stimulated increase in phage transfer increases the population of toxin encoding bacteria in the environment.
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Affiliation(s)
- Iqbal Aijaz
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Gerald B Koudelka
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
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20
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Shiga Toxin Glycosphingolipid Receptors in Human Caco-2 and HCT-8 Colon Epithelial Cell Lines. Toxins (Basel) 2017; 9:toxins9110338. [PMID: 29068380 PMCID: PMC5705953 DOI: 10.3390/toxins9110338] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 10/11/2017] [Accepted: 10/19/2017] [Indexed: 12/21/2022] Open
Abstract
Shiga toxins (Stxs) released by enterohemorrhagic Escherichia coli (EHEC) into the human colon are the causative agents for fatal outcome of EHEC infections. Colon epithelial Caco-2 and HCT-8 cells are widely used for investigating Stx-mediated intestinal cytotoxicity. Only limited data are available regarding precise structures of their Stx receptor glycosphingolipids (GSLs) globotriaosylceramide (Gb3Cer) and globotetraosylceramide (Gb4Cer), and lipid raft association. In this study we identified Gb3Cer and Gb4Cer lipoforms of serum-free cultivated Caco-2 and HCT-8 cells, chiefly harboring ceramide moieties composed of sphingosine (d18:1) and C16:0, C22:0 or C24:0/C24:1 fatty acid. The most significant difference between the two cell lines was the prevalence of Gb3Cer with C16 fatty acid in HCT-8 and Gb4Cer with C22–C24 fatty acids in Caco-2 cells. Lipid compositional analysis of detergent-resistant membranes (DRMs), which were used as lipid raft-equivalents, indicated slightly higher relative content of Stx receptor Gb3Cer in DRMs of HCT-8 cells when compared to Caco-2 cells. Cytotoxicity assays revealed substantial sensitivity towards Stx2a for both cell lines, evidencing little higher susceptibility of Caco-2 cells versus HCT-8 cells. Collectively, Caco-2 and HCT-8 cells express a plethora of different receptor lipoforms and are susceptible towards Stx2a exhibiting somewhat lower sensitivity when compared to Vero cells.
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21
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Induction of Shiga Toxin-Encoding Prophage by Abiotic Environmental Stress in Food. Appl Environ Microbiol 2017; 83:AEM.01378-17. [PMID: 28778890 DOI: 10.1128/aem.01378-17] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 07/24/2017] [Indexed: 11/20/2022] Open
Abstract
The prophage-encoded Shiga toxin is a major virulence factor in Stx-producing Escherichia coli (STEC). Toxin production and phage production are linked and occur after induction of the RecA-dependent SOS response. However, food-related stress and Stx-prophage induction have not been studied at the single-cell level. This study investigated the effects of abiotic environmental stress on stx expression by single-cell quantification of gene expression in STEC O104:H4 Δstx2::gfp::ampr In addition, the effect of stress on production of phage particles was determined. The lethality of stressors, including heat, HCl, lactic acid, hydrogen peroxide, and high hydrostatic pressure, was selected to reduce cell counts by 1 to 2 log CFU/ml. The integrity of the bacterial membrane after exposure to stress was measured by propidium iodide (PI). The fluorescent signals of green fluorescent protein (GFP) and PI were quantified by flow cytometry. The mechanism of prophage induction by stress was evaluated by relative gene expression of recA and cell morphology. Acid (pH < 3.5) and H2O2 (2.5 mM) induced the expression of stx2 in about 18% and 3% of the population, respectively. The mechanism of prophage induction by acid differs from that of induction by H2O2 H2O2 induction but not acid induction corresponded to production of infectious phage particles, upregulation of recA, and cell filamentation. Pressure (200 MPa) or heat did not induce the Stx2-encoding prophage (Stx2-prophage). Overall, the quantification method developed in this study allowed investigation of prophage induction and physiological properties at the single-cell level. H2O2 and acids mediate different pathways to induce Stx2-prophage.IMPORTANCE Induction of the Stx-prophage in STEC results in production of phage particles and Stx and thus relates to virulence as well as the transduction of virulence genes. This study developed a method for a detection of the induction of Stx-prophages at the single-cell level; membrane permeability and an indication of SOS response to environmental stress were additionally assessed. H2O2 and mitomycin C induced expression of the prophage and activated a SOS response. In contrast, HCl and lactic acid induced the Stx-prophage but not the SOS response. The lifestyle of STEC exposes the organism to intestinal and extraintestinal environments that impose oxidative and acid stress. A more thorough understanding of the influence of food processing-related stressors on Stx-prophage expression thus facilitates control of STEC in food systems by minimizing prophage induction during food production and storage.
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22
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Aijaz I, Koudelka GB. Tetrahymena phagocytic vesicles as ecological micro-niches of phage transfer. FEMS Microbiol Ecol 2017; 93:3061358. [PMID: 28334205 DOI: 10.1093/femsec/fix030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/01/2017] [Indexed: 11/14/2022] Open
Abstract
The microbial communities in natural environments such as soil, pond water, or animal rumens are composed of a diverse mixture of bacteria and protozoa including ciliates or flagellates. In such microbiomes, a major source of bacterial mortality is grazing by phagocytic protists. Many protists are omnivorous heterotrophs, feeding on a range of different bacterial species. Due to this indiscriminate feeding, different bacterial species can assemble together in the same phagocytic vesicles where they can potentially exchange genetic material. Here we show that Tetrahymena thermophila imports and accumulates phage donor and recipient bacterial strains in its phagocytic vesicles and that under laboratory conditions the ingested bacteria remain viable for ≥2 h. Prophages in the ingested bacteria induce immediately after ingestion, and the released phages are concentrated in the phagocytic vesicles of the ciliate. These phages retain their ability to infect phage-susceptible bacterial strains. As a consequence of being confined within the phagosome, the frequency of lysogen formation in these vesicles increases 6-fold as compared with the bulk solution. Collectively, these observations suggest that T. thermophila aids in dissemination of bacteriophages by accumulating susceptible bacteria and phages in their phagocytic vesicles.
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23
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Brock DA, Callison WÉ, Strassmann JE, Queller DC. Sentinel cells, symbiotic bacteria and toxin resistance in the social amoeba Dictyostelium discoideum. Proc Biol Sci 2017; 283:rspb.2015.2727. [PMID: 27097923 DOI: 10.1098/rspb.2015.2727] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/29/2016] [Indexed: 01/16/2023] Open
Abstract
The social amoeba Dictyostelium discoideum is unusual among eukaryotes in having both unicellular and multicellular stages. In the multicellular stage, some cells, called sentinels, ingest toxins, waste and bacteria. The sentinel cells ultimately fall away from the back of the migrating slug, thus removing these substances from the slug. However, some D. discoideum clones (called farmers) carry commensal bacteria through the multicellular stage, while others (called non-farmers) do not. Farmers profit from their beneficial bacteria. To prevent the loss of these bacteria, we hypothesize that sentinel cell numbers may be reduced in farmers, and thus farmers may have a diminished capacity to respond to pathogenic bacteria or toxins. In support, we found that farmers have fewer sentinel cells compared with non-farmers. However, farmers produced no fewer viable spores when challenged with a toxin. These results are consistent with the beneficial bacteria Burkholderia providing protection against toxins. The farmers did not vary in spore production with and without a toxin challenge the way the non-farmers did, which suggests the costs of Burkholderia may be fixed while sentinel cells may be inducible. Therefore, the costs for non-farmers are only paid in the presence of the toxin. When the farmers were cured of their symbiotic bacteria with antibiotics, they behaved just like non-farmers in response to a toxin challenge. Thus, the advantages farmers gain from carrying bacteria include not just food and protection against competitors, but also protection against toxins.
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Affiliation(s)
- Debra A Brock
- Department of Biology, Washington University in Saint Louis, Campus Box 1137, One Brookings Drive, Saint Louis, MO, USA
| | - W Éamon Callison
- Department of Biology, Washington University in Saint Louis, Campus Box 1137, One Brookings Drive, Saint Louis, MO, USA
| | - Joan E Strassmann
- Department of Biology, Washington University in Saint Louis, Campus Box 1137, One Brookings Drive, Saint Louis, MO, USA
| | - David C Queller
- Department of Biology, Washington University in Saint Louis, Campus Box 1137, One Brookings Drive, Saint Louis, MO, USA
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24
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Meinel DM, Kuehl R, Zbinden R, Boskova V, Garzoni C, Fadini D, Dolina M, Blümel B, Weibel T, Tschudin-Sutter S, Widmer AF, Bielicki JA, Dierig A, Heininger U, Konrad R, Berger A, Hinic V, Goldenberger D, Blaich A, Stadler T, Battegay M, Sing A, Egli A. Outbreak investigation for toxigenic Corynebacterium diphtheriae wound infections in refugees from Northeast Africa and Syria in Switzerland and Germany by whole genome sequencing. Clin Microbiol Infect 2016; 22:1003.e1-1003.e8. [PMID: 27585943 DOI: 10.1016/j.cmi.2016.08.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 07/28/2016] [Accepted: 08/19/2016] [Indexed: 01/28/2023]
Abstract
Toxigenic Corynebacterium diphtheriae is an important and potentially fatal threat to patients and public health. During the current dramatic influx of refugees into Europe, our objective was to use whole genome sequencing for the characterization of a suspected outbreak of C. diphtheriae wound infections among refugees. After conventional culture, we identified C. diphtheriae using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and investigated toxigenicity by PCR. Whole genome sequencing was performed on a MiSeq Illumina with >70×coverage, 2×250 bp read length, and mapping against a reference genome. Twenty cases of cutaneous C. diphtheriae in refugees from East African countries and Syria identified between April and August 2015 were included. Patients presented with wound infections shortly after arrival in Switzerland and Germany. Toxin production was detected in 9/20 (45%) isolates. Whole genome sequencing-based typing revealed relatedness between isolates using neighbour-joining algorithms. We detected three separate clusters among epidemiologically related refugees. Although the isolates within a cluster showed strong relatedness, isolates differed by >50 nucleotide polymorphisms. Toxigenic C. diphtheriae associated wound infections are currently observed more frequently in Europe, due to refugees travelling under poor hygienic conditions. Close genetic relatedness of C. diphtheriae isolates from 20 refugees with wound infections indicates likely transmission between patients. However, the diversity within each cluster and phylogenetic time-tree analysis suggest that transmissions happened several months ago, most likely outside Europe. Whole genome sequencing offers the potential to describe outbreaks at very high resolution and is a helpful tool in infection tracking and identification of transmission routes.
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Affiliation(s)
- D M Meinel
- Clinical Microbiology, University Hospital Basel, Basel, Switzerland; Bavarian Health and Food Safety Authority (LGL), Oberschleissheim, Germany; Applied Microbiology Research, Department of Biomedicine, University Basel, Basel, Switzerland
| | - R Kuehl
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - R Zbinden
- Institute for Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - V Boskova
- Computational Evolution, D-BSSE, ETH Zurich, Basel, Switzerland
| | - C Garzoni
- Department of Internal Medicine and Infectious Diseases, Clinica Luganese, Lugano, Switzerland
| | - D Fadini
- Internal Medicine, Ospedale di Mendrisio, Mendrisio, Switzerland
| | - M Dolina
- Clinical Microbiology, EOLAB, Bellinzona, Switzerland
| | - B Blümel
- Institute of Medical Microbiology and Hygiene, University Medical Centre Freiburg, Freiburg, Germany
| | - T Weibel
- Clinical Microbiology, Labor Team W, Saint Gallen, Switzerland
| | - S Tschudin-Sutter
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - A F Widmer
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - J A Bielicki
- Paediatric Infectious Diseases, University of Basel Children's Hospital, Basel, Switzerland
| | - A Dierig
- Paediatric Infectious Diseases, University of Basel Children's Hospital, Basel, Switzerland
| | - U Heininger
- Paediatric Infectious Diseases, University of Basel Children's Hospital, Basel, Switzerland
| | - R Konrad
- Bavarian Health and Food Safety Authority (LGL), Oberschleissheim, Germany; German National Consiliary Laboratory on Diphtheria, Oberschleissheim, Germany
| | - A Berger
- Bavarian Health and Food Safety Authority (LGL), Oberschleissheim, Germany; German National Consiliary Laboratory on Diphtheria, Oberschleissheim, Germany
| | - V Hinic
- Clinical Microbiology, University Hospital Basel, Basel, Switzerland
| | - D Goldenberger
- Clinical Microbiology, University Hospital Basel, Basel, Switzerland
| | - A Blaich
- Clinical Microbiology, University Hospital Basel, Basel, Switzerland
| | - T Stadler
- Computational Evolution, D-BSSE, ETH Zurich, Basel, Switzerland
| | - M Battegay
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - A Sing
- Bavarian Health and Food Safety Authority (LGL), Oberschleissheim, Germany; German National Consiliary Laboratory on Diphtheria, Oberschleissheim, Germany
| | - A Egli
- Clinical Microbiology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University Basel, Basel, Switzerland.
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25
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Ghai R, Mehrshad M, Mizuno CM, Rodriguez-Valera F. Metagenomic recovery of phage genomes of uncultured freshwater actinobacteria. ISME JOURNAL 2016; 11:304-308. [PMID: 27505348 DOI: 10.1038/ismej.2016.110] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/09/2016] [Accepted: 07/04/2016] [Indexed: 01/20/2023]
Abstract
Low-GC Actinobacteria are among the most abundant and widespread microbes in freshwaters and have largely resisted all cultivation efforts. Consequently, their phages have remained totally unknown. In this work, we have used deep metagenomic sequencing to assemble eight complete genomes of the first tailed phages that infect freshwater Actinobacteria. Their genomes encode the actinobacterial-specific transcription factor whiB, frequently found in mycobacteriophages and also in phages infecting marine pelagic Actinobacteria. Its presence suggests a common and widespread strategy of modulation of host transcriptional machinery upon infection via this transcriptional switch. We present evidence that some whiB-carrying phages infect the acI lineage of Actinobacteria. At least one of them encodes the ADP-ribosylating component of the widespread bacterial AB toxins family (for example, clostridial toxin). We posit that the presence of this toxin reflects a 'trojan horse' strategy, providing protection at the population level to the abundant host microbes against eukaryotic predators.
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Affiliation(s)
- Rohit Ghai
- Institute of Hydrobiology, Department of Aquatic Microbial Ecology, Biology Center of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Maliheh Mehrshad
- Departamento de Producción Vegetal y Microbiología, Evolutionary Genomics Group, Universidad Miguel Hernandez, Alicante, Spain.,Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Carolina Megumi Mizuno
- Departamento de Producción Vegetal y Microbiología, Evolutionary Genomics Group, Universidad Miguel Hernandez, Alicante, Spain.,Unit of Molecular Biology of the Gene in Extremophiles, Department of Microbiology, Institut Pasteur, Paris, France
| | - Francisco Rodriguez-Valera
- Departamento de Producción Vegetal y Microbiología, Evolutionary Genomics Group, Universidad Miguel Hernandez, Alicante, Spain
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26
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Arnold JW, Spacht D, Koudelka GB. Determinants that govern the recognition and uptake of
Escherichia coli
O157 : H7 by
Acanthamoeba castellanii. Cell Microbiol 2016; 18:1459-70. [DOI: 10.1111/cmi.12591] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 03/07/2016] [Accepted: 03/08/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Jason W. Arnold
- Department of Biological Sciences University at Buffalo Buffalo NY 14260 USA
| | - Drew Spacht
- Department of Biology Mercyhurst University Erie PA 16546 USA
- Department of Entomology The Ohio State University 318 W. 12th Ave. 300 Aronoff Laboratory Columbus OH 43210 USA
| | - Gerald B. Koudelka
- Department of Biological Sciences University at Buffalo Buffalo NY 14260 USA
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Colon MP, Chakraborty D, Pevzner Y, Koudelka GB. Mechanisms that Determine the Differential Stability of Stx⁺ and Stx(-) Lysogens. Toxins (Basel) 2016; 8:96. [PMID: 27043626 PMCID: PMC4848623 DOI: 10.3390/toxins8040096] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/23/2016] [Accepted: 03/25/2016] [Indexed: 01/29/2023] Open
Abstract
Phages 933W, BAA2326, 434, and λ are evolutionarily-related temperate lambdoid phages that infect Escherichia coli. Although these are highly-similar phages, BAA2326 and 933W naturally encode Shiga toxin 2 (Stx+), but phage 434 and λ do not (Stx−). Previous reports suggest that the 933W Stx+ prophage forms less stable lysogens in E. coli than does the Stx− prophages λ, P22, and 434. The higher spontaneous induction frequency of the Stx+ prophage may be correlated with both virulence and dispersion of the Stx2-encoding phage. Here, we examined the hypothesis that lysogen instability is a common feature of Stx+ prophages. We found in both the absence and presence of prophage inducers (DNA damaging agents, salts), the Stx+ prophages induce at higher frequencies than do Stx− prophages. The observed instability of Stx+ prophages does not appear to be the result of any differences in phage development properties between Stx+ and Stx− phages. Our results indicate that differential stability of Stx+ and Stx− prophages results from both RecA-dependent and RecA-independent effects on the intracellular concentration of the respective cI repressors.
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Affiliation(s)
- Michael P Colon
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA.
| | | | - Yonatan Pevzner
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA.
| | - Gerald B Koudelka
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA.
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De Paepe M, Tournier L, Moncaut E, Son O, Langella P, Petit MA. Carriage of λ Latent Virus Is Costly for Its Bacterial Host due to Frequent Reactivation in Monoxenic Mouse Intestine. PLoS Genet 2016; 12:e1005861. [PMID: 26871586 PMCID: PMC4752277 DOI: 10.1371/journal.pgen.1005861] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 01/22/2016] [Indexed: 01/21/2023] Open
Abstract
Temperate phages, the bacterial viruses able to enter in a dormant prophage state in bacterial genomes, are present in the majority of bacterial strains for which the genome sequence is available. Although these prophages are generally considered to increase their hosts’ fitness by bringing beneficial genes, studies demonstrating such effects in ecologically relevant environments are relatively limited to few bacterial species. Here, we investigated the impact of prophage carriage in the gastrointestinal tract of monoxenic mice. Combined with mathematical modelling, these experimental results provided a quantitative estimation of key parameters governing phage-bacteria interactions within this model ecosystem. We used wild-type and mutant strains of the best known host/phage pair, Escherichia coli and phage λ. Unexpectedly, λ prophage caused a significant fitness cost for its carrier, due to an induction rate 50-fold higher than in vitro, with 1 to 2% of the prophage being induced. However, when prophage carriers were in competition with isogenic phage susceptible bacteria, the prophage indirectly benefited its carrier by killing competitors: infection of susceptible bacteria led to phage lytic development in about 80% of cases. The remaining infected bacteria were lysogenized, resulting overall in the rapid lysogenization of the susceptible lineage. Moreover, our setup enabled to demonstrate that rare events of phage gene capture by homologous recombination occurred in the intestine of monoxenic mice. To our knowledge, this study constitutes the first quantitative characterization of temperate phage-bacteria interactions in a simplified gut environment. The high prophage induction rate detected reveals DNA damage-mediated SOS response in monoxenic mouse intestine. We propose that the mammalian gut, the most densely populated bacterial ecosystem on earth, might foster bacterial evolution through high temperate phage activity. Dormant bacterial viruses, or prophages, are found in the genomes of almost all bacteria, but their impact on bacterial host fitness is largely unknown. Through experiments in mice, supported by a mathematical model, we quantified the activity of Escherichia coli prophage λ in monoxenic mouse gut, as well as its impact on its carrier bacteria. λ carriage negatively impacted its hosts due to frequent reactivation, but indirectly benefited its host by killing susceptible bacterial competitors. The high prophage activity unraveled in this study reflects a constant rate of SOS response, resulting from DNA damage in monoxenic mouse intestine. Our results should motivate researchers to take the presence of prophages into account when studying the action of specific bacteria in the gastrointestinal tract of mammals.
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Affiliation(s)
- Marianne De Paepe
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- * E-mail:
| | | | - Elisabeth Moncaut
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Olivier Son
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Philippe Langella
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Marie-Agnès Petit
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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Schmidt CE, Shringi S, Besser TE. Protozoan Predation of Escherichia coli O157:H7 Is Unaffected by the Carriage of Shiga Toxin-Encoding Bacteriophages. PLoS One 2016; 11:e0147270. [PMID: 26824472 PMCID: PMC4732659 DOI: 10.1371/journal.pone.0147270] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 12/25/2015] [Indexed: 12/28/2022] Open
Abstract
Escherichia coli O157:H7 is a food-borne bacterium that causes hemorrhagic diarrhea and hemolytic uremic syndrome in humans. While cattle are a known source of E. coli O157:H7 exposure resulting in human infection, environmental reservoirs may also be important sources of infection for both cattle and humans. Bacteriophage-encoded Shiga toxins (Stx) carried by E. coli O157:H7 may provide a selective advantage for survival of these bacteria in the environment, possibly through their toxic effects on grazing protozoa. To determine Stx effects on protozoan grazing, we co-cultured Paramecium caudatum, a common ciliate protozoon in cattle water sources, with multiple strains of Shiga-toxigenic E. coli O157:H7 and non-Shiga toxigenic cattle commensal E. coli. Over three days at ambient laboratory temperature, P. caudatum consistently reduced both E. coli O157:H7 and non-Shiga toxigenic E. coli populations by 1-3 log cfu. Furthermore, a wild-type strain of Shiga-toxigenic E. coli O157:H7 (EDL933) and isogenic mutants lacking the A subunit of Stx 2a, the entire Stx 2a-encoding bacteriophage, and/or the entire Stx 1-encoding bacteriophage were grazed with similar efficacy by both P. caudatum and Tetrahymena pyriformis (another ciliate protozoon). Therefore, our data provided no evidence of a protective effect of either Stx or the products of other bacteriophage genes on protozoan predation of E. coli. Further research is necessary to determine if the grazing activity of naturally-occurring protozoa in cattle water troughs can serve to decrease cattle exposure to E. coli O157:H7 and other Shiga-toxigenic E. coli.
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Affiliation(s)
- Carrie E. Schmidt
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
- * E-mail:
| | - Smriti Shringi
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Thomas E. Besser
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
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Oxidative Stress in Shiga Toxin Production by Enterohemorrhagic Escherichia coli. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2015; 2016:3578368. [PMID: 26798420 PMCID: PMC4699097 DOI: 10.1155/2016/3578368] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 09/30/2015] [Indexed: 12/28/2022]
Abstract
Virulence of enterohemorrhagic Escherichia coli (EHEC) strains depends on production of Shiga toxins. These toxins are encoded in genomes of lambdoid bacteriophages (Shiga toxin-converting phages), present in EHEC cells as prophages. The genes coding for Shiga toxins are silent in lysogenic bacteria, and prophage induction is necessary for their efficient expression and toxin production. Under laboratory conditions, treatment with UV light or antibiotics interfering with DNA replication are commonly used to induce lambdoid prophages. Since such conditions are unlikely to occur in human intestine, various research groups searched for other factors or agents that might induce Shiga toxin-converting prophages. Among other conditions, it was reported that treatment with H2O2 caused induction of these prophages, though with efficiency significantly lower relative to UV-irradiation or mitomycin C treatment. A molecular mechanism of this phenomenon has been proposed. It appears that the oxidative stress represents natural conditions provoking induction of Shiga toxin-converting prophages as a consequence of H2O2 excretion by either neutrophils in infected humans or protist predators outside human body. Finally, the recently proposed biological role of Shiga toxin production is described in this paper, and the “bacterial altruism” and “Trojan Horse” hypotheses, which are connected to the oxidative stress, are discussed.
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Grau-Leal F, Quirós P, Martínez-Castillo A, Muniesa M. Free Shiga toxin 1-encoding bacteriophages are less prevalent than Shiga toxin 2 phages in extraintestinal environments. Environ Microbiol 2015; 17:4790-801. [DOI: 10.1111/1462-2920.13053] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 08/31/2015] [Accepted: 09/11/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Ferran Grau-Leal
- Department of Microbiology; University of Barcelona; Diagonal 643, Annex, Floor 0 Barcelona E-08028 Spain
| | - Pablo Quirós
- Department of Microbiology; University of Barcelona; Diagonal 643, Annex, Floor 0 Barcelona E-08028 Spain
| | | | - Maite Muniesa
- Department of Microbiology; University of Barcelona; Diagonal 643, Annex, Floor 0 Barcelona E-08028 Spain
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Vaerewijck MJ, Baré J, Lambrecht E, Sabbe K, Houf K. Interactions of Foodborne Pathogens with Free-living Protozoa: Potential Consequences for Food Safety. Compr Rev Food Sci Food Saf 2014. [DOI: 10.1111/1541-4337.12100] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | - Julie Baré
- Dept. of Veterinary Public Health and Food Safety, Ghent Univ; Belgium
| | - Ellen Lambrecht
- Dept. of Veterinary Public Health and Food Safety, Ghent Univ; Belgium
| | - Koen Sabbe
- Laboratory of Protistology and Aquatic Ecology; Dept. of Biology, Ghent Univ; Belgium
| | - Kurt Houf
- Dept. of Veterinary Public Health and Food Safety, Ghent Univ; Belgium
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Ghequire MGK, De Mot R. Ribosomally encoded antibacterial proteins and peptides from Pseudomonas. FEMS Microbiol Rev 2014; 38:523-68. [PMID: 24923764 DOI: 10.1111/1574-6976.12079] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/05/2014] [Accepted: 05/16/2014] [Indexed: 12/26/2022] Open
Abstract
Members of the Pseudomonas genus produce diverse secondary metabolites affecting other bacteria, fungi or predating nematodes and protozoa but are also equipped with the capacity to secrete different types of ribosomally encoded toxic peptides and proteins, ranging from small microcins to large tailocins. Studies with the human pathogen Pseudomonas aeruginosa have revealed that effector proteins of type VI secretion systems are part of the antibacterial armamentarium deployed by pseudomonads. A novel class of antibacterial proteins with structural similarity to plant lectins was discovered by studying antagonism among plant-associated Pseudomonas strains. A genomic perspective on pseudomonad bacteriocinogeny shows that the modular architecture of S pyocins of P. aeruginosa is retained in a large diversified group of bacteriocins, most of which target DNA or RNA. Similar modularity is present in as yet poorly characterized Rhs (recombination hot spot) proteins and CDI (contact-dependent inhibition) proteins. Well-delimited domains for receptor recognition or cytotoxicity enable the design of chimeric toxins with novel functionalities, which has been applied successfully for S and R pyocins. Little is known regarding how these antibacterials are released and ultimately reach their targets. Other remaining issues concern the identification of environmental triggers activating these systems and assessment of their ecological impact in niches populated by pseudomonads.
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Johnke J, Cohen Y, de Leeuw M, Kushmaro A, Jurkevitch E, Chatzinotas A. Multiple micro-predators controlling bacterial communities in the environment. Curr Opin Biotechnol 2014; 27:185-90. [PMID: 24598212 DOI: 10.1016/j.copbio.2014.02.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 02/03/2014] [Accepted: 02/04/2014] [Indexed: 12/24/2022]
Abstract
Predator-prey interactions are a main issue in ecological theory, including multispecies predator-prey relationships and intraguild predation. This knowledge is mainly based on the study of plants and animals, while its relevance for microorganisms is not well understood. The three key groups of micro-predators include protists, predatory bacteria and bacteriophages. They greatly differ in size, in prey specificity, in hunting strategies and in the resulting population dynamics. Yet, their potential to jointly control bacterial populations and reducing biomass in complex environments such as wastewater treatment plants is vast. Here, we present relevant ecological concepts and recent findings on micropredators, and propose that an integrative approach to predation at the microscale should be developed enabling the exploitation of this potential.
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Affiliation(s)
- Julia Johnke
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
| | - Yossi Cohen
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
| | - Marina de Leeuw
- Department of Biotechnology Engineering and The National Institute for Biotechnology, Ben Gurion University, 84105 Beer Sheva, Israel
| | - Ariel Kushmaro
- Department of Biotechnology Engineering and The National Institute for Biotechnology, Ben Gurion University, 84105 Beer Sheva, Israel
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100 Rehovot, Israel.
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
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