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Ilyas SZ, Tariq H, Basit A, Tahir H, Haider Z, Rehman SU. SGP-C: A Broad Host Range Temperate Bacteriophage; Against Salmonella gallinarum. Front Microbiol 2022; 12:768931. [PMID: 35095790 PMCID: PMC8790156 DOI: 10.3389/fmicb.2021.768931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/03/2021] [Indexed: 11/13/2022] Open
Abstract
Salmonella gallinarum is a poultry restricted-pathogen causing fowl-typhoid disease in adult birds with mortality rates up-to 80% and exhibit resistance against commonly used antibiotics. In this current study, a temperate broad host range bacteriophage SGP-C was isolated against S. gallinarum from poultry digesta. It showed infection ability in all the 15 tested field strains of S. gallinarum. The SGP-C phage produced circular, turbid plaques with alternate rings. Its optimum activity was observed at pH 7.0 and 37-42°C, with a latent period of 45 min and burst size of 187 virions/bacterial cell. The SGP-C lysogens, SGPC-L5 and SGPC-L6 exhibited super-infection immunity against the same phage, an already reported feature of lysogens. A virulence index of 0.5 and 0.001 as MV50 of SGP-C suggests its moderate virulence. The genome of SGP-C found circular double stranded DNA of 42 Kbp with 50.04% GC content, which encodes 63 ORFs. The presence of repressor gene at ORF49, and absence of tRNA sequence in SGP-C genome indicates its lysogenic nature. Furthermore, from NGS analysis of lysogens we propose that SGP-C genome might exist either as an episome, or both as integrated and temporary episome in the host cell and warrants further studies. Phylogenetic analysis revealed its similarity with Salmonella temperate phages belonging to family Siphoviridae. The encoded proteins by SGP-C genome have not showed homology with any known toxin and virulence factor. Although plenty of lytic bacteriophages against this pathogen are already reported, to our knowledge SGP-C is the first lysogenic phage against S. gallinarum reported so far.
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Affiliation(s)
| | | | | | | | | | - Shafiq ur Rehman
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
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Zuppi M, Hendrickson HL, O’Sullivan JM, Vatanen T. Phages in the Gut Ecosystem. Front Cell Infect Microbiol 2022; 11:822562. [PMID: 35059329 PMCID: PMC8764184 DOI: 10.3389/fcimb.2021.822562] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/10/2021] [Indexed: 12/23/2022] Open
Abstract
Phages, short for bacteriophages, are viruses that specifically infect bacteria and are the most abundant biological entities on earth found in every explored environment, from the deep sea to the Sahara Desert. Phages are abundant within the human biome and are gaining increasing recognition as potential modulators of the gut ecosystem. For example, they have been connected to gastrointestinal diseases and the treatment efficacy of Fecal Microbiota Transplant. The ability of phages to modulate the human gut microbiome has been attributed to the predation of bacteria or the promotion of bacterial survival by the transfer of genes that enhance bacterial fitness upon infection. In addition, phages have been shown to interact with the human immune system with variable outcomes. Despite the increasing evidence supporting the importance of phages in the gut ecosystem, the extent of their influence on the shape of the gut ecosystem is yet to be fully understood. Here, we discuss evidence for phage modulation of the gut microbiome, postulating that phages are pivotal contributors to the gut ecosystem dynamics. We therefore propose novel research questions to further elucidate the role(s) that they have within the human ecosystem and its impact on our health and well-being.
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Affiliation(s)
- Michele Zuppi
- The Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Heather L. Hendrickson
- The School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Justin M. O’Sullivan
- The Liggins Institute, University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, United Kingdom
| | - Tommi Vatanen
- The Liggins Institute, University of Auckland, Auckland, New Zealand
- The Broad Institute of MIT and Harvard, Cambridge, MA, United States
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53
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Tkachev PV, Goncharov A, Dmitriev A. Temperate enterococcal bacteriophages: genetic features and practical application. CLINICAL MICROBIOLOGY AND ANTIMICROBIAL CHEMOTHERAPY 2022. [DOI: 10.36488/cmac.2022.3.213-218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Temperate bacteriophages are of interest as carriers and vectors of pathogenicity factors that determine an epidemic potential of opportunistic bacteria as well as biotechnology objects. This review describes studies of temperate bacteriophages infecting bacteria of the genus Enterococcus, including strains associated with the development of nosocomial infections. Genetic features of moderate enterococcal phages as well as their potential for practical application in medicine are considered.
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Affiliation(s)
| | - A.E. Goncharov
- Institute of Experimental Medicine (Saint-Petersburg, Russia)
| | - A.V. Dmitriev
- Institute of Experimental Medicine (Saint-Petersburg, Russia)
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Nair A, Vyawahare R, Khairnar K. Characterization of a novel, biofilm dispersing, lytic bacteriophage against drug-resistant Enterobacter cloacae. J Appl Microbiol 2021; 132:2721-2732. [PMID: 34927785 DOI: 10.1111/jam.15420] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/26/2021] [Accepted: 12/16/2021] [Indexed: 11/28/2022]
Abstract
AIM To characterize a novel bacteriophage, En5822, isolated from the environment against Enterobacter cloacae and exploring its application as an alternate antimicrobial. METHODS AND RESULTS Bacteriophage was isolated from sewage sample by membrane-filtration immobilization technique. It was purified and studied for its various physical properties like microscopic structure, thermal and pH stability, latent period and burst time, antimicrobial and anti-biofilm activity as well as molecular aspects by genome sequencing and analysis. En5822 is a myovirus with relative pH and thermal stability. En5822 shows a notable reduction of host bacterial biofilm as well as planktonic cultures. Whole genome sequence analysis revealed that the En5822 genome does not contain undesirable temperate lifestyle genes, antibiotic resistance genes and toxin-encoding genes. CONCLUSIONS En5822 displays high lytic activity, specificity and biofilm reduction capability. It has a short latent period and high burst size that aid faster activity. Its genomic and physical attributes offer possibilities for its as an alternative antimicrobial for the treatment of drug-resistant E. cloacae infections. SIGNIFICANCE AND IMPACT OF STUDY The study describes a novel, naturally virulent bacteriophage from environment capable of lysing multi-drug resistant E. cloacae effectively. The phage could potentially serve as an alternative strategy for treating antibiotic-resistant infections.
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Affiliation(s)
- Aparna Nair
- CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Renuka Vyawahare
- CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, India
| | - Krishna Khairnar
- CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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55
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Hsu CL, Duan Y, Fouts DE, Schnabl B. Intestinal virome and therapeutic potential of bacteriophages in liver disease. J Hepatol 2021; 75:1465-1475. [PMID: 34437908 PMCID: PMC8929164 DOI: 10.1016/j.jhep.2021.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/20/2021] [Accepted: 08/02/2021] [Indexed: 12/19/2022]
Abstract
Humans harbour a large quantity of microbes in the intestinal tract and have evolved symbiotic relationships with many of them. However, several specific bacterial pathobionts are associated with liver disease pathogenesis. Although bacteriophages (phages) and eukaryotic viruses (collectively known as "the virome") outnumber bacteria and fungi in the intestine, little is known about the intestinal virome in patients with liver disease. As natural predators of bacteria, phages can precisely edit the bacterial microbiota. Hence, there is interest in using them to target bacterial pathobionts in several diseases, including those of the liver. Herein, we will summarise changes in the faecal virome associated with fatty liver diseases and cirrhosis, and describe the therapeutic potential of phages and potential challenges to their clinical application.
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Affiliation(s)
- Cynthia L Hsu
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yi Duan
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA; Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA.
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56
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Makky S, Dawoud A, Safwat A, Abdelsattar AS, Rezk N, El-Shibiny A. The bacteriophage decides own tracks: When they are with or against the bacteria. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100050. [PMID: 34841341 PMCID: PMC8610337 DOI: 10.1016/j.crmicr.2021.100050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/09/2021] [Accepted: 07/20/2021] [Indexed: 11/18/2022] Open
Abstract
Bacteriophages, bacteria-infecting viruses, are considered by many researchers a promising solution for antimicrobial resistance. On the other hand, some phages have shown contribution to bacterial resistance phenomenon by transducing antimicrobial resistance genes to their bacterial hosts. Contradictory consequences of infections are correlated to different phage lifecycles. Out of four known lifecycles, lysogenic and lytic pathways have been riddles since the uncontrolled conversion between them could negatively affect the intended use of phages. However, phages still can be engineered for applications against bacterial and viral infections to ensure high efficiency. This review highlights two main aspects: (1) the different lifecycles as well as the different factors that affect lytic-lysogenic switch are discussed, including the intracellular and molecular factors control this decision. In addition, different models which describe the effect of phages on the ecosystem are compared, besides the approaches to study the switch. (2) An overview on the contribution of the phage in the evolution of the bacteria, instead of eating them, as a consequence of different mode of actions. As well, how phage display has helped in restricting phage cheating and how it could open new gates for immunization and pandemics control will be tacked.
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Affiliation(s)
- Salsabil Makky
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578, Egypt
| | - Alyaa Dawoud
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578, Egypt
- Faculty of Pharmacy and Biotechnology, German University in Cairo, New Cairo, 16482, Egypt
| | - Anan Safwat
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578, Egypt
| | - Abdallah S. Abdelsattar
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578, Egypt
- Center for X-Ray and Determination of Structure of Matter, Zewail City of Science and Technology, October Gardens, 6th of October, Giza, 12578, Egypt
| | - Nouran Rezk
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578, Egypt
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578, Egypt
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57
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Happel AU, Balle C, Maust BS, Konstantinus IN, Gill K, Bekker LG, Froissart R, Passmore JA, Karaoz U, Varsani A, Jaspan H. Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents. Viruses 2021; 13:2341. [PMID: 34960611 PMCID: PMC8708031 DOI: 10.3390/v13122341] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/18/2021] [Accepted: 11/18/2021] [Indexed: 12/11/2022] Open
Abstract
The interaction between gut bacterial and viral microbiota is thought to be important in human health. While fluctuations in female genital tract (FGT) bacterial microbiota similarly determine sexual health, little is known about the presence, persistence, and function of vaginal bacteriophages. We conducted shotgun metagenome sequencing of cervicovaginal samples from South African adolescents collected longitudinally, who received no antibiotics. We annotated viral reads and circular bacteriophages, identified CRISPR loci and putative prophages, and assessed their diversity, persistence, and associations with bacterial microbiota composition. Siphoviridae was the most prevalent bacteriophage family, followed by Myoviridae, Podoviridae, Herelleviridae, and Inoviridae. Full-length siphoviruses targeting bacterial vaginosis (BV)-associated bacteria were identified, suggesting their presence in vivo. CRISPR loci and prophage-like elements were common, and genomic analysis suggested higher diversity among Gardnerella than Lactobacillus prophages. We found that some prophages were highly persistent within participants, and identical prophages were present in cervicovaginal secretions of multiple participants, suggesting that prophages, and thus bacterial strains, are shared between adolescents. The number of CRISPR loci and prophages were associated with vaginal microbiota stability and absence of BV. Our analysis suggests that (pro)phages are common in the FGT and vaginal bacteria and (pro)phages may interact.
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Affiliation(s)
- Anna-Ursula Happel
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (A.-U.H.); (C.B.); (I.N.K.); (J.-A.P.)
| | - Christina Balle
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (A.-U.H.); (C.B.); (I.N.K.); (J.-A.P.)
| | - Brandon S. Maust
- Seattle Children’s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109, USA;
- Department of Pediatrics, University of Washington School of Medicine, 1959 NE Pacific St., Seattle, WA 98195, USA
| | - Iyaloo N. Konstantinus
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (A.-U.H.); (C.B.); (I.N.K.); (J.-A.P.)
- Namibia Institute of Pathology, Hosea Kutako, Windhoek 10005, Namibia
| | - Katherine Gill
- Desmond Tutu HIV Centre, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (K.G.); (L.-G.B.)
- NRF-DST CAPRISA Centre of Excellence in HIV Prevention, 719 Umbilo Road, Congella, Durban 4013, South Africa
| | - Linda-Gail Bekker
- Desmond Tutu HIV Centre, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (K.G.); (L.-G.B.)
- NRF-DST CAPRISA Centre of Excellence in HIV Prevention, 719 Umbilo Road, Congella, Durban 4013, South Africa
| | - Rémy Froissart
- CNRS, IRD, Université Montpellier, UMR 5290, MIVEGEC, 34394 Montpellier, France;
| | - Jo-Ann Passmore
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (A.-U.H.); (C.B.); (I.N.K.); (J.-A.P.)
- Desmond Tutu HIV Centre, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (K.G.); (L.-G.B.)
- NRF-DST CAPRISA Centre of Excellence in HIV Prevention, 719 Umbilo Road, Congella, Durban 4013, South Africa
- National Health Laboratory Service, Anzio Road, Cape Town 7925, South Africa
| | - Ulas Karaoz
- Earth and Environmental Science, Lawrence Berkeley National Laboratories, 1 Cyclotron Rd., Berkeley, CA 94720, USA;
| | - Arvind Varsani
- The Biodesign Center of Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa
| | - Heather Jaspan
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (A.-U.H.); (C.B.); (I.N.K.); (J.-A.P.)
- Seattle Children’s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109, USA;
- Department of Pediatrics, University of Washington School of Medicine, 1959 NE Pacific St., Seattle, WA 98195, USA
- Department of Global Health, University of Washington School of Public Health, 1510 San Juan Road NE, Seattle, WA 98195, USA
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58
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DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes. mBio 2021; 12:e0259521. [PMID: 34724822 PMCID: PMC8567247 DOI: 10.1128/mbio.02595-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Soil viruses are abundant, but the influence of the environment and climate on soil viruses remains poorly understood. Here, we addressed this gap by comparing the diversity, abundance, lifestyle, and metabolic potential of DNA viruses in three grassland soils with historical differences in average annual precipitation, low in eastern Washington (WA), high in Iowa (IA), and intermediate in Kansas (KS). Bioinformatics analyses were applied to identify a total of 2,631 viral contigs, including 14 complete viral genomes from three deep metagenomes (1 terabase [Tb] each) that were sequenced from bulk soil DNA. An additional three replicate metagenomes (∼0.5 Tb each) were obtained from each location for statistical comparisons. Identified viruses were primarily bacteriophages targeting dominant bacterial taxa. Both viral and host diversity were higher in soil with lower precipitation. Viral abundance was also significantly higher in the arid WA location than in IA and KS. More lysogenic markers and fewer clustered regularly interspaced short palindromic repeats (CRISPR) spacer hits were found in WA, reflecting more lysogeny in historically drier soil. More putative auxiliary metabolic genes (AMGs) were also detected in WA than in the historically wetter locations. The AMGs occurring in 18 pathways could potentially contribute to carbon metabolism and energy acquisition in their hosts. Structural equation modeling (SEM) suggested that historical precipitation influenced viral life cycle and selection of AMGs. The observed and predicted relationships between soil viruses and various biotic and abiotic variables have value for predicting viral responses to environmental change.
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Abstract
Lactococcus lactis strains residing in the microbial community of a complex dairy starter culture named “Ur” are hosts to prophages belonging to the family Siphoviridae. L. lactis strains (TIFN1 to TIFN7) showed detectable spontaneous phage production and release (109 to 1010 phage particles/ml) and up to 10-fold increases upon prophage induction, while in both cases we observed no obvious cell lysis typically described for the lytic life cycle of Siphoviridae phages. Intrigued by this phenomenon, we investigated the host-phage interaction using strain TIFN1 (harboring prophage proPhi1) as a representative. We confirmed that during the massive phage release, all bacterial cells remain viable. Further, by monitoring phage replication in vivo, using a green fluorescence protein reporter combined with flow cytometry, we demonstrated that the majority of the bacterial population (over 80%) is actively producing phage particles when induced with mitomycin C. The released tailless phage particles were found to be engulfed in lipid membranes, as evidenced by electron microscopy and lipid staining combined with chemical lipid analysis. Based on the collective observations, we propose a model of phage-host interaction in L. lactis TIFN1 where the phage particles are engulfed in membranes upon release, thereby leaving the producing host intact. Moreover, we discuss possible mechanisms of chronic, or nonlytic, release of LAB Siphoviridae phages and its impact on the bacterial host. IMPORTANCE In complex microbial consortia such as fermentation starters, bacteriophages can alter the dynamics and diversity of microbial communities. Bacteriophages infecting Lactococcus lactis are mostly studied for their detrimental impact on industrial dairy fermentation processes. In this study, we describe a novel form of phage-bacterium interaction in an L. lactis strain isolated from a complex dairy starter culture: when the prophages harbored in the L. lactis genome are activated, the phage particles are engulfed in lipid membranes upon release, leaving the producing host intact. Findings from this study provide additional insights into the diverse manners of phage-bacterium interactions and coevolution, which are essential for understanding the population dynamics in complex microbial communities like fermentation starters.
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60
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Exploring the diversity of bacteriophage specific to Oenococcus oeni and Lactobacillus spp and their role in wine production. Appl Microbiol Biotechnol 2021; 105:8575-8592. [PMID: 34694447 DOI: 10.1007/s00253-021-11509-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 12/19/2022]
Abstract
The widespread existence of bacteriophage has been of great interest to the biological research community and ongoing investigations continue to explore their diversity and role. They have also attracted attention and in-depth research in connection to fermented food processing, in particular from the dairy and wine industries. Bacteriophage, mostly oenophage, may in fact be a 'double edged sword' for winemakers: whilst they have been implicated as a causal agent of difficulties with malolactic fermentation (although not proven), they are also beginning to be considered as alternatives to using sulphur dioxide to prevent wine spoilage. Investigation and characterisation of oenophage of Oenococcus oeni, the main species used in winemaking, are still limited compared to lactococcal bacteriophage of Lactococcus lactis and Lactiplantibacillus plantarum (formally Lactobacillus plantarum), the drivers of most fermented dairy products. Interestingly, these strains are also being used or considered for use in winemaking. In this review, the genetic diversity and life cycle of phage, together with the debate on the consequent impact of phage predation in wine, and potential control strategies are discussed. KEY POINTS: • Bacteriophage detected in wine are diverse. • Many lysogenic bacteriophage are found in wine bacteria. • Phage impact on winemaking can depend on the stage of the winemaking process. • Bacteriophage as potential antimicrobial agents against spoilage organisms.
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Egido JE, Costa AR, Aparicio-Maldonado C, Haas PJ, Brouns SJJ. Mechanisms and clinical importance of bacteriophage resistance. FEMS Microbiol Rev 2021; 46:6374866. [PMID: 34558600 PMCID: PMC8829019 DOI: 10.1093/femsre/fuab048] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 09/15/2021] [Indexed: 12/24/2022] Open
Abstract
We are in the midst of a golden age of uncovering defense systems against bacteriophages. Apart from the fundamental interest in these defense systems, and revolutionary applications that have been derived from them (e.g. CRISPR-Cas9 and restriction endonucleases), it is unknown how defense systems contribute to resistance formation against bacteriophages in clinical settings. Bacteriophages are now being reconsidered as therapeutic agents against bacterial infections due the emergence of multidrug resistance. However, bacteriophage resistance through defense systems and other means could hinder the development of successful phage-based therapies. Here, we review the current state of the field of bacteriophage defense, highlight the relevance of bacteriophage defense for potential clinical use of bacteriophages as therapeutic agents and suggest new directions of research.
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Affiliation(s)
- Julia E Egido
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, Netherlands
| | - Ana Rita Costa
- Department of Bionanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, Netherlands.,Kavli Institute of Nanoscience, Delft, Netherlands.,Fagenbank, Delft, Netherlands
| | - Cristian Aparicio-Maldonado
- Department of Bionanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, Netherlands.,Kavli Institute of Nanoscience, Delft, Netherlands
| | - Pieter-Jan Haas
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, Netherlands.,Kavli Institute of Nanoscience, Delft, Netherlands.,Fagenbank, Delft, Netherlands
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62
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Pascu B, Negrea A, Ciopec M, Duteanu N, Negrea P, Nemeş NS, Seiman C, Marian E, Micle O. A Green, Simple and Facile Way to Synthesize Silver Nanoparticles Using Soluble Starch. pH Studies and Antimicrobial Applications. MATERIALS 2021; 14:ma14164765. [PMID: 34443288 PMCID: PMC8399506 DOI: 10.3390/ma14164765] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/15/2021] [Accepted: 08/17/2021] [Indexed: 11/25/2022]
Abstract
Along with the progress of nanoscience and nanotechnology came the means to synthesize nanometric scale materials. While changing their physical and chemical properties, they implicitly changed their application area. The aim of this paper was the synthesis of colloidal silver nanoparticles (Ag-NPs by ultrasonic disruption), using soluble starch as a reducing agent and further as a stabilizing agent for produced Ag-NPs. In this context, an important parameter for Ag-NPs preparation is the pH, which can determine the particle size and stability. The physical-chemical behavior of the synthesized Ag-NPs (shape, size, dispersion, electric charge) is strongly influenced by the pH value (experiment being conducted for pH values in the range between 8 and 13). The presence of a peak located at 412 nm into the UV-VIS spectra demonstrates the presence of silver nano-spheres into the produced material. In UV/VIS spectra, we observed a specific peak for yellow silver nano-spheres located at 412 nm. Samples characterization was performed by scanning electron microscopy, SEM, energy-dispersive X-ray spectroscopy, EDX, Fourier-transform infrared spectroscopy, and FT-IR. For all Ag-NP samples, we determined the zeta and observed that the Ag-NP particles obtained at higher pH and have better stability. Due to the intrinsic therapeutic properties and broad antimicrobial spectrum, silver nanoparticles have opened new horizons and new approaches for the control of different types of infections and wound healing abilities. In this context, the present study also aims to confirm the antimicrobial effect of prepared Ag-NPs against several bacterial strains (indicator and clinically isolated strains). In this way, it was confirmed that the antimicrobial activity of synthesized Ag-NPs was good against Staphylococcus aureus (ATCC 25923 and S. aureus MSSA) and Escherichia coli (ATTC 25922 and clinically isolated strain). Based on this observation, we conclude that the prepared Ag-NPs can represent an alternative or auxiliary material used for controlling important nosocomial pathogens. The fungal reference strain Candida albicans was more sensitive at Ag-NPs actions (zone of inhibition = 20 mm) compared with the clinically isolated strain (zone of inhibition = 10 mm), which emphasizes the greater resistance of fungal strains at antimicrobial agent’s action.
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Affiliation(s)
- Bogdan Pascu
- Faculty of Industrial Chemistry and Environmental Engineering, Politehnica University of Timisoara, 300006 Timisoara, Romania; (B.P.); (P.N.)
- Renewable Energy Research Institute, Politehnica University of Timisoara, 300501 Timişoara, Romania
| | - Adina Negrea
- Faculty of Industrial Chemistry and Environmental Engineering, Politehnica University of Timisoara, 300006 Timisoara, Romania; (B.P.); (P.N.)
- Correspondence: (A.N.); (M.C.); (N.D.); (N.S.N.)
| | - Mihaela Ciopec
- Faculty of Industrial Chemistry and Environmental Engineering, Politehnica University of Timisoara, 300006 Timisoara, Romania; (B.P.); (P.N.)
- Correspondence: (A.N.); (M.C.); (N.D.); (N.S.N.)
| | - Narcis Duteanu
- Faculty of Industrial Chemistry and Environmental Engineering, Politehnica University of Timisoara, 300006 Timisoara, Romania; (B.P.); (P.N.)
- Correspondence: (A.N.); (M.C.); (N.D.); (N.S.N.)
| | - Petru Negrea
- Faculty of Industrial Chemistry and Environmental Engineering, Politehnica University of Timisoara, 300006 Timisoara, Romania; (B.P.); (P.N.)
| | - Nicoleta Sorina Nemeş
- Renewable Energy Research Institute, Politehnica University of Timisoara, 300501 Timişoara, Romania
- Correspondence: (A.N.); (M.C.); (N.D.); (N.S.N.)
| | - Corina Seiman
- Faculty of Chemistry, Biology, Geography, West University Timisoara, 300115 Timisoara, Romania;
| | - Eleonora Marian
- Faculty of Medicine and Pharmacy, University of Oradea, 410068 Oradea, Romania; (E.M.); (O.M.)
| | - Otilia Micle
- Faculty of Medicine and Pharmacy, University of Oradea, 410068 Oradea, Romania; (E.M.); (O.M.)
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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: 60] [Impact Index Per Article: 20.0] [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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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: 12] [Impact Index Per Article: 4.0] [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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Arsın H, Jasilionis A, Dahle H, Sandaa RA, Stokke R, Nordberg Karlsson E, Steen IH. Exploring Codon Adjustment Strategies towards Escherichia coli-Based Production of Viral Proteins Encoded by HTH1, a Novel Prophage of the Marine Bacterium Hypnocyclicus thermotrophus. Viruses 2021; 13:v13071215. [PMID: 34201869 PMCID: PMC8310279 DOI: 10.3390/v13071215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 01/15/2023] Open
Abstract
Marine viral sequence space is immense and presents a promising resource for the discovery of new enzymes interesting for research and biotechnology. However, bottlenecks in the functional annotation of viral genes and soluble heterologous production of proteins hinder access to downstream characterization, subsequently impeding the discovery process. While commonly utilized for the heterologous expression of prokaryotic genes, codon adjustment approaches have not been fully explored for viral genes. Herein, the sequence-based identification of a putative prophage is reported from within the genome of Hypnocyclicus thermotrophus, a Gram-negative, moderately thermophilic bacterium isolated from the Seven Sisters hydrothermal vent field. A prophage-associated gene cluster, consisting of 46 protein coding genes, was identified and given the proposed name Hypnocyclicus thermotrophus phage H1 (HTH1). HTH1 was taxonomically assigned to the viral family Siphoviridae, by lowest common ancestor analysis of its genome and phylogeny analyses based on proteins predicted as holin and DNA polymerase. The gene neighbourhood around the HTH1 lytic cassette was found most similar to viruses infecting Gram-positive bacteria. In the HTH1 lytic cassette, an N-acetylmuramoyl-L-alanine amidase (Amidase_2) with a peptidoglycan binding motif (LysM) was identified. A total of nine genes coding for enzymes putatively related to lysis, nucleic acid modification and of unknown function were subjected to heterologous expression in Escherichia coli. Codon optimization and codon harmonization approaches were applied in parallel to compare their effects on produced proteins. Comparison of protein yields and thermostability demonstrated that codon optimization yielded higher levels of soluble protein, but codon harmonization led to proteins with higher thermostability, implying a higher folding quality. Altogether, our study suggests that both codon optimization and codon harmonization are valuable approaches for successful heterologous expression of viral genes in E. coli, but codon harmonization may be preferable in obtaining recombinant viral proteins of higher folding quality.
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Affiliation(s)
- Hasan Arsın
- Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway; (R.-A.S.); (R.S.)
- Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway;
- Correspondence: (H.A.); (I.H.S.); Tel.: +47-555-88-375 (I.H.S.)
| | - Andrius Jasilionis
- Division of Biotechnology, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (A.J.); (E.N.K.)
| | - Håkon Dahle
- Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway;
- Computational Biology Unit, University of Bergen, N-5020 Bergen, Norway
| | - Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway; (R.-A.S.); (R.S.)
| | - Runar Stokke
- Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway; (R.-A.S.); (R.S.)
- Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway;
| | - Eva Nordberg Karlsson
- Division of Biotechnology, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (A.J.); (E.N.K.)
| | - Ida Helene Steen
- Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway; (R.-A.S.); (R.S.)
- Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway;
- Correspondence: (H.A.); (I.H.S.); Tel.: +47-555-88-375 (I.H.S.)
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A Metzincin and TIMP-Like Protein Pair of a Phage Origin Sensitize Listeria monocytogenes to Phage Lysins and Other Cell Wall Targeting Agents. Microorganisms 2021; 9:microorganisms9061323. [PMID: 34207021 PMCID: PMC8235301 DOI: 10.3390/microorganisms9061323] [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: 05/06/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 11/17/2022] Open
Abstract
Infection of mammalian cells by Listeria monocytogenes (Lm) was shown to be facilitated by its phage elements. In a search for additional phage remnants that play a role in Lm’s lifecycle, we identified a conserved locus containing two XRE regulators and a pair of genes encoding a secreted metzincin protease and a lipoprotein structurally similar to a TIMP-family metzincin inhibitor. We found that the XRE regulators act as a classic CI/Cro regulatory switch that regulates the expression of the metzincin and TIMP-like genes under intracellular growth conditions. We established that when these genes are expressed, their products alter Lm morphology and increase its sensitivity to phage mediated lysis, thereby enhancing virion release. Expression of these proteins also sensitized the bacteria to cell wall targeting compounds, implying that they modulate the cell wall structure. Our data indicate that these effects are mediated by the cleavage of the TIMP-like protein by the metzincin, and its subsequent release to the extracellular milieu. While the importance of this locus to Lm pathogenicity remains unclear, the observation that this phage-associated protein pair act upon the bacterial cell wall may hold promise in the field of antibiotic potentiation to combat antibiotic resistant bacterial pathogens.
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Friends or Foes-Microbial Interactions in Nature. BIOLOGY 2021; 10:biology10060496. [PMID: 34199553 PMCID: PMC8229319 DOI: 10.3390/biology10060496] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/27/2021] [Accepted: 05/31/2021] [Indexed: 12/16/2022]
Abstract
Simple Summary Microorganisms like bacteria, archaea, fungi, microalgae, and viruses mostly form complex interactive networks within the ecosystem rather than existing as single planktonic cells. Interactions among microorganisms occur between the same species, with different species, or even among entirely different genera, families, or even domains. These interactions occur after environmental sensing, followed by converting those signals to molecular and genetic information, including many mechanisms and classes of molecules. Comprehensive studies on microbial interactions disclose key strategies of microbes to colonize and establish in a variety of different environments. Knowledge of the mechanisms involved in the microbial interactions is essential to understand the ecological impact of microbes and the development of dysbioses. It might be the key to exploit strategies and specific agents against different facing challenges, such as chronic and infectious diseases, hunger crisis, pollution, and sustainability. Abstract Microorganisms are present in nearly every niche on Earth and mainly do not exist solely but form communities of single or mixed species. Within such microbial populations and between the microbes and a eukaryotic host, various microbial interactions take place in an ever-changing environment. Those microbial interactions are crucial for a successful establishment and maintenance of a microbial population. The basic unit of interaction is the gene expression of each organism in this community in response to biotic or abiotic stimuli. Differential gene expression is responsible for producing exchangeable molecules involved in the interactions, ultimately leading to community behavior. Cooperative and competitive interactions within bacterial communities and between the associated bacteria and the host are the focus of this review, emphasizing microbial cell–cell communication (quorum sensing). Further, metagenomics is discussed as a helpful tool to analyze the complex genomic information of microbial communities and the functional role of different microbes within a community and to identify novel biomolecules for biotechnological applications.
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Gogokhia L, Round JL. Immune-bacteriophage interactions in inflammatory bowel diseases. Curr Opin Virol 2021; 49:30-35. [PMID: 34029992 DOI: 10.1016/j.coviro.2021.04.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/25/2021] [Accepted: 04/26/2021] [Indexed: 01/03/2023]
Abstract
Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), are influenced by the bacterial and fungal organisms found within the intestine. However, the intestine is also home to a vast number of viral particles, with most of them being viruses that infect prokaryotes, called bacteriophages. While use of bacteriophages to specifically target pathogenic bacterial species involved in IBD is currently under investigation, recent studies have also highlighted that these viral particles can impact the mammalian immune system. IBD is a chronic multi-factorial inflammatory condition with unknown etiology. This review will highlight the current investigations that have revealed that bacteriophage-mammalian immune cell interactions can influence disease processes beyond their known role for infecting bacteria, which might identify novel ways to treat or diagnose IBD.
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Affiliation(s)
- Lasha Gogokhia
- Department of Pathology, University of Utah School of Medicine, Division of Microbiology and Immunology, UT 84112, United States; Department of Internal Medicine, St. Mary's Hospital, Waterbury, CT 06706, United States
| | - June L Round
- Department of Pathology, University of Utah School of Medicine, Division of Microbiology and Immunology, UT 84112, United States.
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Characterization and in vitro activity of a lytic phage RDN37 isolated from community sewage water active against MDR Uropathogenic E. coli. Indian J Med Microbiol 2021; 39:343-348. [PMID: 33994226 DOI: 10.1016/j.ijmmb.2021.04.011] [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] [Received: 12/07/2020] [Revised: 04/26/2021] [Accepted: 04/30/2021] [Indexed: 01/04/2023]
Abstract
PURPOSE Due to the emergence of multidrug-resistant Uropathogenic E. coli (MDR-UPEC) strains, alternatives to antibiotics like phage therapy have been sought. The present study was planned to characterize and test the activity of a phage (RDN37) which was isolated from community sewage water of Chandigarh and was found to be active against MDR-UPEC. MATERIALS AND METHODS We studied the morphology of the phage by transmission electron microscopy and determined one-step growth curve analysis and stability of the phage at various temperature and pH ranges. PCR amplification and Sanger sequencing were performed to confirm the phage family. Genome sequences from 12 related phages (BLASTn identity >95%) were obtained from the NCBI database in GenBank format. A phylogenetic analysis was conducted using the neighbour-joining method in ClustalX2 and MEGAX. Host range and lytic activity were tested by spot assay and time-kill experiment, respectively. RESULTS Phage RDN37 had a large burst size and belonged to the Myoviridae family as per transmission electron microscopy and Sanger sequencing results. It was stable over wide range of temperature (-20°,4°, 25°, 37 °C) and pH (6,7,8). The phylogenetic analysis of amplified PCR product (major coat protein gp23) grouped the phage RDN37 with Escherichia phage vB_EcoM_IME537 (MT179807) isolated from community sewage water in China. RDN37 phage was active against MDR-UPEC strains resistant to third generation cephalosporins, aminoglycosides, carbapenems, fluoroquinolones and cotrimoxazole. The multiplicity of infection (MOI) of 0.01 was found to be optimum to reduce the bacterial cell density in the time-kill assay. CONCLUSIONS RDN37 is a stable lytic phage with large burst size, specific to E. coli, has a therapeutic potential to treat UTI caused by highly drug resistant UPEC. A cocktail of multiple phages will be required to overcome its narrow host range.
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Abstract
Bacteriophages are the most diverse and abundant biological entities on the Earth and require host bacteria to replicate. Because of this obligate relationship, in addition to the challenging conditions of surrounding environments, phages must integrate information about extrinsic and intrinsic factors when infecting their host. This integration helps to determine whether the infection becomes lytic or lysogenic, which likely influences phage spreading and long-term survival. Although a variety of environmental and physiological clues are known to modulate lysis-lysogeny decisions, the social interplay among phages and host populations has been overlooked until recently. A growing body of evidence indicates that cell-cell communication in bacteria and, more recently, peptide-based communication among phage-phage populations, affect phage-host interactions by controlling phage lysis-lysogeny decisions and phage counter-defensive strategies in bacteria. Here, we explore and discuss the role of signal molecules as well as quorum sensing and quenching factors that mediate phage-host interactions. Our aim is to provide an overview of population-dependent mechanisms that influence phage replication, and how social communication may affect the dynamics and evolution of microbial communities, including their implications in phage therapy.
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Orellana R, Arancibia A, Badilla L, Acosta J, Arancibia G, Escar R, Ferrada G, Seeger M. Ecophysiological Features Shape the Distribution of Prophages and CRISPR in Sulfate Reducing Prokaryotes. Microorganisms 2021; 9:microorganisms9050931. [PMID: 33925267 PMCID: PMC8146710 DOI: 10.3390/microorganisms9050931] [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: 03/13/2021] [Revised: 04/18/2021] [Accepted: 04/23/2021] [Indexed: 12/28/2022] Open
Abstract
Sulfate reducing prokaryotes (SRP) are a phylogenetically and physiologically diverse group of microorganisms that use sulfate as an electron acceptor. SRP have long been recognized as key players of the carbon and sulfur cycles, and more recently, they have been identified to play a relevant role as part of syntrophic and symbiotic relations and the human microbiome. Despite their environmental relevance, there is a poor understanding about the prevalence of prophages and CRISPR arrays and how their distribution and dynamic affect the ecological role of SRP. We addressed this question by analyzing the results of a comprehensive survey of prophages and CRISPR in a total of 91 genomes of SRP with several genotypic, phenotypic, and physiological traits, including genome size, cell volume, minimum doubling time, cell wall, and habitat, among others. Our analysis discovered 81 prophages in 51 strains, representing the 56% of the total evaluated strains. Prophages are non-uniformly distributed across the SRP phylogeny, where prophage-rich lineages belonged to Desulfovibrionaceae and Peptococcaceae. Furthermore, our study found 160 CRISPR arrays in 71 SRP, which is more abundant and widely spread than previously expected. Although there is no correlation between presence and abundance of prophages and CRISPR arrays at the strain level, our analysis showed that there is a directly proportional relation between cellular volumes and number of prophages per cell. This result suggests that there is an additional selective pressure for strains with smaller cells to get rid of foreign DNA, such as prophages, but not CRISPR, due to less availability of cellular resources. Analysis of the prophage genes encoding viral structural proteins reported that 44% of SRP prophages are classified as Myoviridae, and comparative analysis showed high level of homology, but not synteny, among prophages belonging to the Family Desulfovibrionaceae. We further recovered viral-like particles and structures that resemble outer membrane vesicles from D. vulgaris str. Hildenborough. The results of this study improved the current understanding of dynamic interactions between prophages and CRISPR with their hosts in both cultured and hitherto-uncultured SRP strains, and how their distribution affects the microbial community dynamics in several sulfidogenic natural and engineered environments.
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Affiliation(s)
- Roberto Orellana
- Laboratorio de Biología Celular y Ecofisiología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Leopoldo Carvallo 270, Valparaíso 2360001, Chile; (A.A.); (L.B.)
- Correspondence:
| | - Alejandra Arancibia
- Laboratorio de Biología Celular y Ecofisiología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Leopoldo Carvallo 270, Valparaíso 2360001, Chile; (A.A.); (L.B.)
| | - Leonardo Badilla
- Laboratorio de Biología Celular y Ecofisiología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Leopoldo Carvallo 270, Valparaíso 2360001, Chile; (A.A.); (L.B.)
| | - Jonathan Acosta
- Departamento de Estadística, Pontificia Universidad Católica de Chile, Avda. Vicuña Mackenna 4860, Santiago 7820436, Chile;
| | - Gabriela Arancibia
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.A.); (R.E.); (G.F.); (M.S.)
| | - Rodrigo Escar
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.A.); (R.E.); (G.F.); (M.S.)
| | - Gustavo Ferrada
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.A.); (R.E.); (G.F.); (M.S.)
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.A.); (R.E.); (G.F.); (M.S.)
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Fulci V, Stronati L, Cucchiara S, Laudadio I, Carissimi C. Emerging Roles of Gut Virome in Pediatric Diseases. Int J Mol Sci 2021; 22:4127. [PMID: 33923593 PMCID: PMC8073368 DOI: 10.3390/ijms22084127] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 12/15/2022] Open
Abstract
In the last decade, the widespread application of shotgun metagenomics provided extensive characterization of the bacterial "dark matter" of the gut microbiome, propelling the development of dedicated, standardized bioinformatic pipelines and the systematic collection of metagenomic data into comprehensive databases. The advent of next-generation sequencing also unravels a previously underestimated viral population (virome) present in the human gut. Despite extensive efforts to characterize the human gut virome, to date, little is known about the childhood gut virome. However, alterations of the gut virome in children have been linked to pathological conditions such as inflammatory bowel disease, type 1 diabetes, malnutrition, diarrhea and celiac disease.
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Affiliation(s)
- Valerio Fulci
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.F.); (L.S.)
| | - Laura Stronati
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.F.); (L.S.)
| | - Salvatore Cucchiara
- Department of Women’s and Children’s Health, Sapienza University of Rome, 00161 Rome, Italy;
| | - Ilaria Laudadio
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.F.); (L.S.)
| | - Claudia Carissimi
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.F.); (L.S.)
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Temperate and chronic virus competition leads to low lysogen frequency. J Theor Biol 2021; 523:110710. [PMID: 33839160 DOI: 10.1016/j.jtbi.2021.110710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 04/04/2021] [Accepted: 04/05/2021] [Indexed: 11/23/2022]
Abstract
The canonical bacteriophage is obligately lytic: the virus infects a bacterium and hijacks cell functions to produce large numbers of new viruses which burst from the cell. These viruses are well-studied, but there exist a wide range of coexisting virus lifestyles that are less understood. Temperate viruses exhibit both a lytic cycle and a latent (lysogenic) cycle, in which viral genomes are integrated into the bacterial host. Meanwhile, chronic (persistent) viruses use cell functions to produce more viruses without killing the cell; chronic viruses may also exhibit a latent stage in addition to the productive stage. Here, we study the ecology of these competing viral strategies. We demonstrate the conditions under which each strategy is dominant, which aids in control of human bacterial infections using viruses. We find that low lysogen frequencies provide competitive advantages for both virus types; however, chronic viruses maximize steady state density by eliminating lysogeny entirely, while temperate viruses exhibit a non-zero 'sweet spot' lysogen frequency. Viral steady state density maximization leads to coexistence of temperate and chronic viruses, explaining the presence of multiple viral strategies in natural environments.
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75
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Zünd M, Ruscheweyh HJ, Field CM, Meyer N, Cuenca M, Hoces D, Hardt WD, Sunagawa S. High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains. MICROBIOME 2021; 9:77. [PMID: 33781335 PMCID: PMC8008629 DOI: 10.1186/s40168-021-01033-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/09/2021] [Indexed: 05/17/2023]
Abstract
BACKGROUND Temperate phages influence the density, diversity and function of bacterial populations. Historically, they have been described as carriers of toxins. More recently, they have also been recognised as direct modulators of the gut microbiome, and indirectly of host health and disease. Despite recent advances in studying prophages using non-targeted sequencing approaches, methodological challenges in identifying inducible prophages in bacterial genomes and quantifying their activity have limited our understanding of prophage-host interactions. RESULTS We present methods for using high-throughput sequencing data to locate inducible prophages, including those previously undiscovered, to quantify prophage activity and to investigate their replication. We first used the well-established Salmonella enterica serovar Typhimurium/p22 system to validate our methods for (i) quantifying phage-to-host ratios and (ii) accurately locating inducible prophages in the reference genome based on phage-to-host ratio differences and read alignment alterations between induced and non-induced prophages. Investigating prophages in bacterial strains from a murine gut model microbiota known as Oligo-MM12 or sDMDMm2, we located five novel inducible prophages in three strains, quantified their activity and showed signatures of lateral transduction potential for two of them. Furthermore, we show that the methods were also applicable to metagenomes of induced faecal samples from Oligo-MM12 mice, including for strains with a relative abundance below 1%, illustrating its potential for the discovery of inducible prophages also in more complex metagenomes. Finally, we show that predictions of prophage locations in reference genomes of the strains we studied were variable and inconsistent for four bioinformatic tools we tested, which highlights the importance of their experimental validation. CONCLUSIONS This study demonstrates that the integration of experimental induction and bioinformatic analysis presented here is a powerful approach to accurately locate inducible prophages using high-throughput sequencing data and to quantify their activity. The ability to generate such quantitative information will be critical in helping us to gain better insights into the factors that determine phage activity and how prophage-bacteria interactions influence our microbiome and impact human health. Video abstract.
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Affiliation(s)
- Mirjam Zünd
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Christopher M. Field
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Natalie Meyer
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Miguelangel Cuenca
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Daniel Hoces
- Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Wolf-Dietrich Hardt
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
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76
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Alessandri G, van Sinderen D, Ventura M. The genus bifidobacterium: From genomics to functionality of an important component of the mammalian gut microbiota running title: Bifidobacterial adaptation to and interaction with the host. Comput Struct Biotechnol J 2021; 19:1472-1487. [PMID: 33777340 PMCID: PMC7979991 DOI: 10.1016/j.csbj.2021.03.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/03/2021] [Accepted: 03/03/2021] [Indexed: 02/07/2023] Open
Abstract
Members of the genus Bifidobacterium are dominant and symbiotic inhabitants of the mammalian gastrointestinal tract. Being vertically transmitted, bifidobacterial host colonization commences immediately after birth and leads to a phase of host infancy during which bifidobacteria are highly prevalent and abundant to then transit to a reduced, yet stable abundance phase during host adulthood. However, in order to reach and stably colonize their elective niche, i.e. the large intestine, bifidobacteria have to cope with a multitude of oxidative, osmotic and bile salt/acid stress challenges that occur along the gastrointestinal tract (GIT). Concurrently, bifidobacteria not only have to compete with the myriad of other gut commensals for nutrient acquisition, but they also require protection against bacterial viruses. In this context, Next-Generation Sequencing (NGS) techniques, allowing large-scale comparative and functional genome analyses have helped to identify the genetic strategies that bifidobacteria have developed in order to colonize, survive and adopt to the highly competitive mammalian gastrointestinal environment. The current review is aimed at providing a comprehensive overview concerning the molecular strategies on which bifidobacteria rely to stably and successfully colonize the mammalian gut.
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Affiliation(s)
- Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Ireland and School of Microbiology, University College Cork, Western Road, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
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77
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Kittler S, Steffan S, Peh E, Plötz M. Phage Biocontrol of Campylobacter: A One Health Approach. Curr Top Microbiol Immunol 2021; 431:127-168. [PMID: 33620651 DOI: 10.1007/978-3-030-65481-8_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Human infections by Campylobacter species are among the most reported bacterial gastrointestinal diseases in the European Union and worldwide with severe outcomes in rare cases. Considering the transmission routes and farm animal reservoirs of these zoonotic pathogens, a comprehensive One Health approach will be necessary to reduce human infection rates. Bacteriophages are viruses that specifically infect certain bacterial genera, species, strains or isolates. Multiple studies have demonstrated the general capacity of phage treatments to reduce Campylobacter loads in the chicken intestine. However, phage treatments are not yet approved for extensive use in the agro-food industry in Europe. Technical inconvenience is mainly related to the efficacy of phages, depending on the optimal choice of phages and their combination, as well as application route, concentration and timing. Additionally, regulatory uncertainties have been a major concern for investment in commercial phage-based products. This review addresses the question as to how phages can be put into practice and can help to solve the issue of human campylobacteriosis in a sustainable One Health approach. By compiling the reported findings from the literature in a standardized manner, we enabled inter-experimental comparisons to increase our understanding of phage infection in Campylobacter spp. and practical on-farm studies. Further, we address some of the hurdles that still must be overcome before this new methodology can be adapted on an industrial scale. We envisage that phage treatment can become an integrated and standardized part of a multi-hurdle anti-bacterial strategy in food production. The last part of this chapter deals with some of the issues raised by legal authorities, bringing together current knowledge on Campylobacter-specific phages and the biosafety requirements for approval of phage treatment in the food industry.
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Affiliation(s)
- Sophie Kittler
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, 30173, Hannover, Germany.
| | - Severin Steffan
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, 30173, Hannover, Germany
| | - Elisa Peh
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, 30173, Hannover, Germany
| | - Madeleine Plötz
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, 30173, Hannover, Germany
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78
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Pseudomonas aeruginosa Resistance to Bacteriophages and Its Prevention by Strategic Therapeutic Cocktail Formulation. Antibiotics (Basel) 2021; 10:antibiotics10020145. [PMID: 33540528 PMCID: PMC7912912 DOI: 10.3390/antibiotics10020145] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/23/2021] [Accepted: 01/27/2021] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial resistance poses a significant threat to modern healthcare as it limits treatment options for bacterial infections, particularly impacting those with chronic conditions such as cystic fibrosis (CF). Viscous mucus accumulation in the lungs of individuals genetically predisposed to CF leads to recurrent bacterial infections, necessitating prolonged antimicrobial chemotherapy. Pseudomonas aeruginosa infections are the predominant driver of CF lung disease, and airway isolates are frequently resistant to multiple antimicrobials. Bacteriophages, or phages, are viruses that specifically infect bacteria and are a promising alternative to antimicrobials for CF P. aeruginosa infections. However, the narrow host range of P. aeruginosa-targeting phages and the rapid evolution of phage resistance could limit the clinical efficacy of phage therapy. A promising approach to overcome these issues is the strategic development of mixtures of phages (cocktails). The aim is to combine phages with broad host ranges and target multiple distinct bacterial receptors to prevent the evolution of phage resistance. However, further research is required to identify and characterize phage resistance mechanisms in CF-derived P. aeruginosa, which differ from their non-CF counterparts. In this review, we consider the mechanisms of P. aeruginosa phage resistance and how these could be overcome by an effective future phage therapy formulation.
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79
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Yan A, Butcher J, Mack D, Stintzi A. Virome Sequencing of the Human Intestinal Mucosal-Luminal Interface. Front Cell Infect Microbiol 2020; 10:582187. [PMID: 33194818 PMCID: PMC7642909 DOI: 10.3389/fcimb.2020.582187] [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: 07/10/2020] [Accepted: 09/14/2020] [Indexed: 01/12/2023] Open
Abstract
While the human gut virome has been increasingly explored in recent years, nearly all studies have been limited to fecal sampling. The mucosal-luminal interface has been established as a viable sample type for profiling the microbial biogeography of the gastrointestinal tract. We have developed a protocol to extract nucleic acids from viruses at the mucosal-luminal interface of the proximal and distal colon. Colonic viromes from pediatric patients with Crohn's disease demonstrated high interpatient diversity and low but significant intrapatient variation between sites. Whole metagenomics was also performed to explore virome-bacteriome interactions and to compare the viral communities observed in virome and whole metagenomic sequencing. A site-specific study of the human gut virome is a necessary step to advance our understanding of virome-bacteriome-host interactions in human diseases.
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Affiliation(s)
- Austin Yan
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - James Butcher
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - David Mack
- Department of Pediatrics, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Inflammatory Bowel Disease Centre and CHEO Research Institute, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Alain Stintzi
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
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80
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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: 40] [Impact Index Per Article: 10.0] [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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81
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Happel AU, Varsani A, Balle C, Passmore JA, Jaspan H. The Vaginal Virome-Balancing Female Genital Tract Bacteriome, Mucosal Immunity, and Sexual and Reproductive Health Outcomes? Viruses 2020; 12:E832. [PMID: 32751611 PMCID: PMC7472209 DOI: 10.3390/v12080832] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 12/12/2022] Open
Abstract
Besides bacteria, fungi, protists and archaea, the vaginal ecosystem also contains a range of prokaryote- and eukaryote-infecting viruses, which are collectively referred to as the "virome". Despite its well-described role in the gut and other environmental niches, the vaginal virome remains understudied. With a focus on sexual and reproductive health, we summarize the currently known components of the vaginal virome, its relationship with other constituents of the vaginal microbiota and its association with adverse health outcomes. While a range of eukaryote-infecting viruses has been described to be present in the female genital tract (FGT), few prokaryote-infecting viruses have been described. Literature suggests that various vaginal viruses interact with vaginal bacterial microbiota and host immunity and that any imbalance thereof may contribute to the risk of adverse reproductive health outcomes, including infertility and adverse birth outcomes. Current limitations of vaginal virome research include experimental and analytical constraints. Considering the vaginal virome may represent the missing link in our understanding of the relationship between FGT bacteria, mucosal immunity, and adverse sexual and reproductive health outcomes, future studies evaluating the vaginal microbiome and its population dynamics holistically will be important for understanding the role of the vaginal virome in balancing health and disease.
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Affiliation(s)
- Anna-Ursula Happel
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa; (C.B.); (J.-A.P.); (H.J.)
| | - Arvind Varsani
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287-5001, USA;
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
| | - Christina Balle
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa; (C.B.); (J.-A.P.); (H.J.)
| | - Jo-Ann Passmore
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa; (C.B.); (J.-A.P.); (H.J.)
- NRF-DST CAPRISA Centre of Excellence in HIV Prevention, 719 Umbilo Road, Congella, Durban 4013, South Africa
- National Health Laboratory Service, Anzio Road, Observatory, Cape Town 7925, South Africa
| | - Heather Jaspan
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa; (C.B.); (J.-A.P.); (H.J.)
- Department of Pediatrics and Global Health, University of Washington, 1510 San Juan Road NE, Seattle, WA 98195, USA
- Seattle Children’s Research Institute, 307 Westlake Ave N, Seattle, WA 98109, USA
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82
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White RA, Visscher PT, Burns BP. Between a Rock and a Soft Place: The Role of Viruses in Lithification of Modern Microbial Mats. Trends Microbiol 2020; 29:204-213. [PMID: 32654857 DOI: 10.1016/j.tim.2020.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/07/2020] [Accepted: 06/16/2020] [Indexed: 12/22/2022]
Abstract
Stromatolites are geobiological systems formed by complex microbial communities, and fossilized stromatolites provide a record of some of the oldest life on Earth. Microbial mats are precursors of extant stromatolites; however, the mechanisms of transition from mat to stromatolite are controversial and are still not well understood. To fully recognize the profound impact that these ecosystems have had on the evolution of the biosphere requires an understanding of modern lithification mechanisms and how they relate to the geological record. We propose here viral mechanisms in carbonate precipitation, leading to stromatolite formation, whereby viruses directly or indirectly impact microbial metabolisms that govern the transition from microbial mat to stromatolite. Finding a tangible link between host-virus interactions and changes in biogeochemical processes will provide tools to interpret mineral biosignatures through geologic time, including those on Earth and beyond.
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Affiliation(s)
- Richard Allen White
- Plant Pathology, Washington State University, Pullman, WA, USA; Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia; RAW Molecular Systems (RMS) LLC, Spokane, WA, USA
| | - Pieter T Visscher
- Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia; Departments of Marine Sciences and Geosciences, University of Connecticut, CT, USA; Biogeosciences, the Université de Bourgogne Franche-Comté, Dijon, France
| | - Brendan P Burns
- Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia; School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia.
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83
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Brix A, Cafora M, Aureli M, Pistocchi A. Animal Models to Translate Phage Therapy to Human Medicine. Int J Mol Sci 2020; 21:ijms21103715. [PMID: 32466194 PMCID: PMC7279175 DOI: 10.3390/ijms21103715] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 12/13/2022] Open
Abstract
Phagotherapy, the use of bacteriophages to fight bacterial infections as an alternative to antibiotic treatments, has become of increasing interest in the last years. This is mainly due to the diffusion of multi-drug resistant (MDR) bacterial infections that constitute a serious issue for public health. Phage therapy is gaining favor due to its success in agriculture and veterinary treatments and its extensive utilization for human therapeutic protocols in the Eastern world. In the last decades, some clinical trials and compassionate treatments have also been performed in the Western world, indicating that phage therapy is getting closer to its introduction in standard therapy protocols. However, several questions concerning the use of phages in human therapeutic treatments are still present and need to be addressed. In this review, we illustrate the state of art of phage therapy and examine the role of animal models to translate these treatments to humans.
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Affiliation(s)
- Alessia Brix
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (A.B.); (M.C.); (M.A.)
| | - Marco Cafora
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (A.B.); (M.C.); (M.A.)
- Dipartimento di Scienze Cliniche e Comunità, Università degli Studi di Milano, Via San Barnaba 8, 20122 Milano, Italy
| | - Massimo Aureli
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (A.B.); (M.C.); (M.A.)
| | - Anna Pistocchi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (A.B.); (M.C.); (M.A.)
- Correspondence:
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84
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Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics. SOIL SYSTEMS 2020. [DOI: 10.3390/soilsystems4020023] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The study of soil viruses, though not new, has languished relative to the study of marine viruses. This is particularly due to challenges associated with separating virions from harboring soils. Generally, three approaches to analyzing soil viruses have been employed: (1) Isolation, to characterize virus genotypes and phenotypes, the primary method used prior to the start of the 21st century. (2) Metagenomics, which has revealed a vast diversity of viruses while also allowing insights into viral community ecology, although with limitations due to DNA from cellular organisms obscuring viral DNA. (3) Viromics (targeted metagenomics of virus-like-particles), which has provided a more focused development of ‘virus-sequence-to-ecology’ pipelines, a result of separation of presumptive virions from cellular organisms prior to DNA extraction. This separation permits greater sequencing emphasis on virus DNA and thereby more targeted molecular and ecological characterization of viruses. Employing viromics to characterize soil systems presents new challenges, however. Ones that only recently are being addressed. Here we provide a guide to implementing these three approaches to studying environmental viruses, highlighting benefits, difficulties, and potential contamination, all toward fostering greater focus on viruses in the study of soil ecology.
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85
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Gilbert RA, Townsend EM, Crew KS, Hitch TCA, Friedersdorff JCA, Creevey CJ, Pope PB, Ouwerkerk D, Jameson E. Rumen Virus Populations: Technological Advances Enhancing Current Understanding. Front Microbiol 2020; 11:450. [PMID: 32273870 PMCID: PMC7113391 DOI: 10.3389/fmicb.2020.00450] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/02/2020] [Indexed: 01/07/2023] Open
Abstract
The rumen contains a multi-kingdom, commensal microbiome, including protozoa, bacteria, archaea, fungi and viruses, which enables ruminant herbivores to ferment and utilize plant feedstuffs that would be otherwise indigestible. Within the rumen, virus populations are diverse and highly abundant, often out-numbering the microbial populations that they both predate on and co-exist with. To date the research effort devoted to understanding rumen-associated viral populations has been considerably less than that given to the other microbial populations, yet their contribution to maintaining microbial population balance, intra-ruminal microbial lysis, fiber breakdown, nutrient cycling and genetic transfer may be highly significant. This review follows the technological advances which have contributed to our current understanding of rumen viruses and drawing on knowledge from other environmental and animal-associated microbiomes, describes the known and potential roles and impacts viruses have on rumen function and speculates on the future directions of rumen viral research.
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Affiliation(s)
- Rosalind A. Gilbert
- Department of Agriculture and Fisheries, Brisbane, QLD, Australia
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Eleanor M. Townsend
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Kathleen S. Crew
- Department of Agriculture and Fisheries, Brisbane, QLD, Australia
| | - Thomas C. A. Hitch
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Jessica C. A. Friedersdorff
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Christopher J. Creevey
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Phillip B. Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Diane Ouwerkerk
- Department of Agriculture and Fisheries, Brisbane, QLD, Australia
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Eleanor Jameson
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, United Kingdom
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86
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Storms ZJ, Teel MR, Mercurio K, Sauvageau D. The Virulence Index: A Metric for Quantitative Analysis of Phage Virulence. PHAGE (NEW ROCHELLE, N.Y.) 2020; 1:27-36. [PMID: 36147620 PMCID: PMC9041455 DOI: 10.1089/phage.2019.0001] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Background: One of the main challenges in developing phage therapy and manufacturing phage products is the reliable evaluation of their efficacy, performance, and quality. Since phage virulence is intrinsically difficult to fully capture, researchers have turned to rapid but partially inadequate methods for its evaluation. Materials and Methods: This study demonstrates a standardized quantitative method to assess phage virulence based on three parameters: the virulence index (VP )-quantifying the virulence of a phage against a host, the local virulence (vi )-assessing killing potential at given multiplicities of infection (MOIs), and MV50 -the MOI at which the phage achieves 50% of its maximum theoretical virulence. This was shown through comparative analysis of the virulence of phages T4, T5, and T7. Results: Under the conditions tested, phage T7 displayed the highest virulence, followed by phage T4 and, finally, by phage T5. The impact of parameters such as temperature and medium composition on virulence was shown for each phage. The use of the method to evaluate the virulence of combinations of phages-for example, for cocktail formulation-is also shown with phages T5 and T7. Conclusions: The method presented provides a platform for high-throughput quantitative assessment of phage virulence and quality control of phage products. It can also be applied to phage screening, evaluation of phage strains, phage mutants, infection conditions and/or the susceptibility of host strains, and the formulation of phage cocktails.
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Affiliation(s)
- Zachary J. Storms
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada
| | - Matthew R. Teel
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada
| | - Kevin Mercurio
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada
| | - Dominic Sauvageau
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada.,Address correspondence to: Dominic Sauvageau, PhD, Department of Chemical and Materials Engineering, University of Alberta, 9211-116 Street NW, Edmonton, AB T6G 1H9, Canada
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87
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Titze I, Lehnherr T, Lehnherr H, Krömker V. Efficacy of Bacteriophages Against Staphylococcus aureus Isolates from Bovine Mastitis. Pharmaceuticals (Basel) 2020; 13:ph13030035. [PMID: 32110980 PMCID: PMC7151712 DOI: 10.3390/ph13030035] [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: 11/24/2019] [Revised: 02/05/2020] [Accepted: 02/24/2020] [Indexed: 01/16/2023] Open
Abstract
The lytic efficacy of bacteriophages against Staphylococcus aureus isolates from bovine milk was investigated in vitro, regarding possible applications in the therapy of udder inflammation caused by bacterial infections (mastitis). The host range of sequenced, lytic bacteriophages was determined against a collection of 92 Staphylococcus (S.) aureus isolates. The isolates originated from quarter foremilk samples of clinical and subclinical mastitis cases. A spot test and a subsequent plaque assay were used to determine the phage host range. According to their host range, propagation and storage properties, three phages, STA1.ST29, EB1.ST11, and EB1.ST27, were selected for preparing a bacteriophage mixture (1:1:1), which was examined for its lytic activity against S. aureus in pasteurized and raw milk. It was found that almost two thirds of the isolates could be lysed by at least one of the tested phages. The bacteriophage mixture was able to reduce the S. aureus germ density in pasteurized milk and its reduction ability was maintained in raw milk, with only a moderate decrease compared to the results in pasteurized milk. The significant reduction ability of the phage mixture in raw milk promotes further in vivo investigation.
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Affiliation(s)
- Isabel Titze
- Department of Bioprocess Engineering and Microbiology, University of Applied Sciences and Arts Hannover, D-30453 Hannover, Germany;
| | - Tatiana Lehnherr
- Phage Technology Center GmbH, D-59199 Bönen, Germany; (T.L.); (H.L.)
| | - Hansjörg Lehnherr
- Phage Technology Center GmbH, D-59199 Bönen, Germany; (T.L.); (H.L.)
| | - Volker Krömker
- Department of Bioprocess Engineering and Microbiology, University of Applied Sciences and Arts Hannover, D-30453 Hannover, Germany;
- Section for Production, Nutrition and Health, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870 Frederiksberg C, Denmark
- Correspondence:
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88
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Anomaly J. The Future of Phage: Ethical Challenges of Using Phage Therapy to Treat Bacterial Infections. Public Health Ethics 2020; 13:82-88. [PMID: 32760449 PMCID: PMC7392637 DOI: 10.1093/phe/phaa003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
For over a century, scientists have run experiments using phage viruses to treat bacterial infections. Until recently, the results were inconclusive because the mechanisms viruses use to attack bacteria were poorly understood. With the development of molecular biology, scientists now have a better sense of how phage work, and how they can be used to target infections. As resistance to traditional antibiotics continues to spread around the world, there is a moral imperative to facilitate research into phage therapy as an alternative treatment. This essay reviews ethical questions raised by phage therapy, and discusses regulatory challenges associated with phage research, and phage treatments.
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89
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Application of a Broad Range Lytic Phage LPST94 for Biological Control of Salmonella in Foods. Microorganisms 2020; 8:microorganisms8020247. [PMID: 32069865 PMCID: PMC7074677 DOI: 10.3390/microorganisms8020247] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/08/2020] [Accepted: 02/11/2020] [Indexed: 02/07/2023] Open
Abstract
Salmonella, one of the most common food-borne pathogens, is a significant public health and economic burden worldwide. Lytic phages are viable alternatives to conventional technologies for pathogen biocontrol in food products. In this study, 40 Salmonella phages were isolated from environmentally sourced water samples. We characterized the lytic range against Salmonella and among all isolates, phage LPST94 showed the broadest lytic spectrum and the highest lytic activity. Electron microscopy and genome sequencing indicated that LPST94 belongs to the Ackermannviridae family. Further studies showed this phage is robust, tolerating a wide range of pH (4–12) and temperature (30–60 °C) over 60 min. The efficacy of phage LPST94 as a biological control agent was evaluated in various food products (milk, apple juice, chicken breast, and lettuce) inoculated with non-typhoidal Salmonella species at different temperatures. Interestingly, the anti-Salmonella efficacy of phage LPST94 was greater at 4 °C than 25 °C, although the efficacy varied between different food models. Adding phage LPST94 to Salmonella inoculated milk decreased the Salmonella count by 3 log10 CFU/mL at 4 °C and 0.84 to 2.56 log10 CFU/mL at 25 °C using an MOI of 1000 and 10000, respectively. In apple juice, chicken breast, and lettuce, the Salmonella count was decreased by 3 log10 CFU/mL at both 4 °C and 25 °C after applying phage LPST94 at an MOI of 1000 and 10,000, within a timescale of 48 h. The findings demonstrated that phage LPST94 is a promising candidate for biological control agents against pathogenic Salmonella and has the potential to be applied across different food matrices.
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Abstract
The discovery of bacteria in the female urinary bladder has fundamentally changed current dogma regarding the urinary tract and related urinary disorders. Previous research characterized many of the bacterial components of the female urinary tract, but the viral fraction of this community is largely unknown. Viruses within the human microbiota far outnumber bacterial cells, with the most abundant viruses being those that infect bacteria (bacteriophages). Similar to observations within the microbiota of the gut and oral cavity, preliminary surveys of the urinary tract and bladder microbiota indicate a rich diversity of uncharacterized bacteriophage (phage) species. Phages are vital members of the microbiota, having critical roles in shaping bacterial metabolism and community structure. Although phages have been discovered in the urinary tract, such as phages that infect Escherichia coli, sampling them is challenging owing to low biomass, possible contamination when using non-invasive methods and the invasiveness of methods that reduce the potential for contamination. Phages could influence bladder health, but an understanding of the association between phage communities, bacterial populations and bladder health is in its infancy. However, evidence suggests that phages can defend the host against pathogenic bacteria and, therefore, modulation of the microbiome using phages has therapeutic potential for lower urinary tract symptoms. Furthermore, as natural predators of bacteria, phages have garnered renewed interest for their use as antimicrobial agents, for instance, in the treatment of urinary tract infections.
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91
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Sabino J, Hirten RP, Colombel JF. Review article: bacteriophages in gastroenterology-from biology to clinical applications. Aliment Pharmacol Ther 2020; 51:53-63. [PMID: 31696976 DOI: 10.1111/apt.15557] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 04/25/2019] [Accepted: 10/03/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND The gut microbiota plays an important role in the pathogenesis of several gastrointestinal diseases. Its composition and function are shaped by host-microbiota and intra-microbiota interactions. Bacteriophages (phages) are viruses that target bacteria and have the potential to modulate bacterial communities. AIMS To summarise phage biology and the clinical applications of phages in gastroenterology METHODS: PubMed was searched to identify relevant studies. RESULTS Phages induce bacterial cell lysis, integration of viral DNA into the bacteria and/or coexistence in a stable equilibrium. Bacteria and phages have co-evolved and their dynamic interactions are yet to be fully understood. The increasing need to modulate microbial communities (e.g., gut microbiota, multidrug-resistant bacteria) has been a strong stimulus for research in phages as an antibacterial therapy. In gastroenterology, phage therapy has been mainly studied in infectious diseases such as cholera. However, it is currently being explored in several other circumstances such as treating Clostridioides difficile colitis, targeting adherent-invasive Escherichia coli in Crohn's disease or eradicating Fusobacterium nucleatum in colorectal cancer. Overall, phage therapy has a favourable and acceptable safety profile. Presently, trials with phage therapy are ongoing in Crohn's disease. CONCLUSIONS Phage therapy is a promising therapeutic tool against pathogenic bacteria in the fields of infectious diseases and gastroenterology. Randomised, placebo-controlled trials with phage therapy for gastroenterological diseases are ongoing.
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Affiliation(s)
- João Sabino
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Gastroenterology, University Hospitals of Leuven, Leuven, Belgium
| | - Robert P Hirten
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Frederic Colombel
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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92
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Nasr P. Genetics, epidemiology, and clinical manifestations of multidrug-resistant Acinetobacter baumannii. J Hosp Infect 2020; 104:4-11. [DOI: 10.1016/j.jhin.2019.09.021] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 11/24/2022]
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93
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Kwiatek M, Parasion S, Nakonieczna A. Therapeutic bacteriophages as a rescue treatment for drug-resistant infections - an in vivo studies overview. J Appl Microbiol 2019; 128:985-1002. [PMID: 31778593 DOI: 10.1111/jam.14535] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 11/15/2019] [Accepted: 11/26/2019] [Indexed: 01/21/2023]
Abstract
Bacteriophages, highly prevalent in all environments, have found their use in medicine as an alternative or complement to antibiotics. The therapeutic use of bacteriophages was particularly popular in the 1920s and 1930s, until the discovery and introduction of antibiotics. Due to the dynamic growth of antibiotic resistance among bacterial strains, numerous international institutions (such as the FDA) have declared the search for novel treatment modalities to be of the highest priority. To date, bacteriophage therapy has not been registered for general use in Western countries. The regulation of biological medicinal products (within medicinal product regulation) does not contain a specific documentation frame for bacteriophages (only for vaccines, blood derived products, etc.) which, as active substances, need to meet specific requirements. Recently, the FDA allowed bacteriophage therapy to be used in the United States, via the Emergency Investigational New Drug scheme; clinical trials to compare the safety and efficacy of bacteriophage therapy are also permitted. To date, several therapeutic products of this type have made it to phase I or II; some clinical programmes have also been completed. This article cites numerous animal model studies and registered clinical trials, showing the safety and effectiveness of bacteriophage therapy, including infections caused by bacterial strains resistant to antibiotic treatment.
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Affiliation(s)
- M Kwiatek
- The Biological Threats Identification and Countermeasure Centre of the Military Institute of Hygiene and Epidemiology, Puławy, Poland
| | | | - A Nakonieczna
- The Biological Threats Identification and Countermeasure Centre of the Military Institute of Hygiene and Epidemiology, Puławy, Poland
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94
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Dąbrowska K, Abedon ST. Pharmacologically Aware Phage Therapy: Pharmacodynamic and Pharmacokinetic Obstacles to Phage Antibacterial Action in Animal and Human Bodies. Microbiol Mol Biol Rev 2019; 83:e00012-19. [PMID: 31666296 PMCID: PMC6822990 DOI: 10.1128/mmbr.00012-19] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The use of viruses infecting bacteria (bacteriophages or phages) to treat bacterial infections has been ongoing clinically for approximately 100 years. Despite that long history, the growing international crisis of resistance to standard antibiotics, abundant anecdotal evidence of efficacy, and one successful modern clinical trial of efficacy, this phage therapy is not yet a mainstream approach in medicine. One explanation for why phage therapy has not been subject to more widespread implementation is that phage therapy research, both preclinical and clinical, can be insufficiently pharmacologically aware. Consequently, here we consider the pharmacological obstacles to phage therapy effectiveness, with phages in phage therapy explicitly being considered to serve as drug equivalents. The study of pharmacology has traditionally been differentiated into pharmacokinetic and pharmacodynamic aspects. We therefore separately consider the difficulties that phages as virions can have in traveling through body compartments toward reaching their target bacteria (pharmacokinetics) and the difficulties that phages can have in exerting antibacterial activity once they have reached those bacteria (pharmacodynamics). The latter difficulties, at least in part, are functions of phage host range and bacterial resistance to phages. Given the apparently low toxicity of phages and the minimal side effects of phage therapy as practiced, phage therapy should be successful so long as phages can reach the targeted bacteria in sufficiently high numbers, adsorb, and then kill those bacteria. Greater awareness of what obstacles to this success generally or specifically can exist, as documented in this review, should aid in the further development of phage therapy toward wider use.
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Affiliation(s)
- Krystyna Dąbrowska
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Stephen T Abedon
- Department of Microbiology, The Ohio State University, Mansfield, Ohio, USA
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96
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Garmaeva S, Sinha T, Kurilshikov A, Fu J, Wijmenga C, Zhernakova A. Studying the gut virome in the metagenomic era: challenges and perspectives. BMC Biol 2019; 17:84. [PMID: 31660953 PMCID: PMC6819614 DOI: 10.1186/s12915-019-0704-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 09/22/2019] [Indexed: 12/12/2022] Open
Abstract
The human gut harbors a complex ecosystem of microorganisms, including bacteria and viruses. With the rise of next-generation sequencing technologies, we have seen a quantum leap in the study of human-gut-inhabiting bacteria, yet the viruses that infect these bacteria, known as bacteriophages, remain underexplored. In this review, we focus on what is known about the role of bacteriophages in human health and the technical challenges involved in studying the gut virome, of which they are a major component. Lastly, we discuss what can be learned from studies of bacteriophages in other ecosystems.
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Affiliation(s)
- Sanzhima Garmaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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Abedon ST. Look Who's Talking: T-Even Phage Lysis Inhibition, the Granddaddy of Virus-Virus Intercellular Communication Research. Viruses 2019; 11:v11100951. [PMID: 31623057 PMCID: PMC6832632 DOI: 10.3390/v11100951] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/15/2019] [Accepted: 09/30/2019] [Indexed: 12/13/2022] Open
Abstract
That communication can occur between virus-infected cells has been appreciated for nearly as long as has virus molecular biology. The original virus communication process specifically was that seen with T-even bacteriophages-phages T2, T4, and T6-resulting in what was labeled as a lysis inhibition. Another proposed virus communication phenomenon, also seen with T-even phages, can be described as a phage-adsorption-induced synchronized lysis-inhibition collapse. Both are mediated by virions that were released from earlier-lysing, phage-infected bacteria. Each may represent ecological responses, in terms of phage lysis timing, to high local densities of phage-infected bacteria, but for lysis inhibition also to locally reduced densities of phage-uninfected bacteria. With lysis inhibition, the outcome is a temporary avoidance of lysis, i.e., a lysis delay, resulting in increased numbers of virions (greater burst size). Synchronized lysis-inhibition collapse, by contrast, is an accelerated lysis which is imposed upon phage-infected bacteria by virions that have been lytically released from other phage-infected bacteria. Here I consider some history of lysis inhibition, its laboratory manifestation, its molecular basis, how it may benefit expressing phages, and its potential ecological role. I discuss as well other, more recently recognized examples of virus-virus intercellular communication.
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Affiliation(s)
- Stephen T Abedon
- Department of Microbiology, The Ohio State University, Mansfield, OH 44906, USA.
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98
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Divya Ganeshan S, Hosseinidoust Z. Phage Therapy with a Focus on the Human Microbiota. Antibiotics (Basel) 2019; 8:E131. [PMID: 31461990 PMCID: PMC6783874 DOI: 10.3390/antibiotics8030131] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/14/2019] [Accepted: 08/23/2019] [Indexed: 01/12/2023] Open
Abstract
Bacteriophages are viruses that infect bacteria. After their discovery in the early 1900s, bacteriophages were a primary cure against infectious disease for almost 25 years, before being completely overshadowed by antibiotics. With the rise of antibiotic resistance, bacteriophages are being explored again for their antibacterial activity. One of the critical apprehensions regarding bacteriophage therapy, however, is the possibility of genome evolution, development of phage resistance, and subsequent perturbations to our microbiota. Through this review, we set out to explore the principles supporting the use of bacteriophages as a therapeutic agent, discuss the human gut microbiome in relation to the utilization of phage therapy, and the co-evolutionary arms race between host bacteria and phage in the context of the human microbiota.
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Affiliation(s)
| | - Zeinab Hosseinidoust
- School of Biomedical Engineering, McMaster University, Hamilton, ON L8S 4K1, Canada.
- Department of Chemical Engineering, McMaster University, Hamilton, ON L8S 4L7, Canada.
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON L8S 4K1, Canada.
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada.
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Fernández L, Gutiérrez D, García P, Rodríguez A. The Perfect Bacteriophage for Therapeutic Applications-A Quick Guide. Antibiotics (Basel) 2019; 8:E126. [PMID: 31443585 PMCID: PMC6783975 DOI: 10.3390/antibiotics8030126] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 11/16/2022] Open
Abstract
The alarming spread of multiresistant infections has kick-started the quest for alternative antimicrobials. In a way, given the steady increase in untreatable infectious diseases, success in this endeavor has become a matter of life and death. Perhaps we should stop searching for an antibacterial panacea and explore a multifaceted strategy in which a wide range of compounds are available on demand depending on the specific situation. In the context of this novel tailor-made approach to combating bacterial pathogens, the once forgotten phage therapy is undergoing a revival. Indeed, the compassionate use of bacteriophages against seemingly incurable infections has been attracting a lot of media attention lately. However, in order to take full advantage of this strategy, bacteria's natural predators must be taken from their environment and then carefully selected to suit our needs. In this review, we have explored the vast literature regarding phage isolation and characterization for therapeutic purposes, paying special attention to the most recent studies, in search of findings that hint at the most efficient strategies to identify suitable candidates. From this information, we will list and discuss the traits that, at the moment, are considered particularly valuable in phages destined for antimicrobial therapy applications. Due to the growing importance given to biofilms in the context of bacterial infections, we will dedicate a specific section to those characteristics that indicate the suitability of a bacteriophage as an antibiofilm agent. Overall, the objective is not just to have a large collection of phages, but to have the best possible candidates to guarantee elimination of the target pathogens.
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Affiliation(s)
- Lucía Fernández
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), (DairySafe Group), Paseo Río Linares s/n -Villaviciosa, 33300 Asturias, Spain.
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain.
| | - Diana Gutiérrez
- Laboratory of Applied Biotechnology, Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Pilar García
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), (DairySafe Group), Paseo Río Linares s/n -Villaviciosa, 33300 Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Ana Rodríguez
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), (DairySafe Group), Paseo Río Linares s/n -Villaviciosa, 33300 Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
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100
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Ye M, Sun M, Huang D, Zhang Z, Zhang H, Zhang S, Hu F, Jiang X, Jiao W. A review of bacteriophage therapy for pathogenic bacteria inactivation in the soil environment. ENVIRONMENT INTERNATIONAL 2019; 129:488-496. [PMID: 31158595 DOI: 10.1016/j.envint.2019.05.062] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/22/2019] [Accepted: 05/23/2019] [Indexed: 06/09/2023]
Abstract
The emerging contamination of pathogenic bacteria in the soil has caused a serious threat to public health and environmental security. Therefore, effective methods to inactivate pathogenic bacteria and decrease the environmental risks are urgently required. As a century-old technique, bacteriophage (phage) therapy has a high efficiency in targeting and inactivating pathogenic bacteria in different environmental systems. This review provides an update on the status of bacteriophage therapy for the inactivation of pathogenic bacteria in the soil environment. Specifically, the applications of phage therapy in soil-plant and soil-groundwater systems are summarized. In addition, the impact of phage therapy on soil functioning is described, including soil function gene transmission, soil microbial community stability, and soil nutrient cycling. Soil factors, such as soil temperature, pH, clay mineral, water content, and nutrient components, influence the survival and activity of phages in the soil. Finally, the future research prospects of phage therapy in soil environments are described.
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Affiliation(s)
- Mao Ye
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Mingming Sun
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Dan Huang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zhongyun Zhang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Hui Zhang
- Jiangsu Key Laboratory of Food Quality and Safety-State Key Laboratory Cultivation Base of MOST, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Shengtian Zhang
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection of China, Nanjing 210042, China
| | - Feng Hu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Jiang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Wentao Jiao
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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