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Rabiey M, Grace ER, Pawlos P, Bihi M, Ahmed H, Hampson GE, Al Riyami A, Alharbi L, Sanchez‐Lucas R, Korotania N, Ciusa ML, Mosley O, Hulin MT, Baxter L, Dhaouadi S, Vinchira‐Villarraga D, Jackson RW. Coevolutionary analysis of Pseudomonas syringae-phage interactions to help with rational design of phage treatments. Microb Biotechnol 2024; 17:e14489. [PMID: 38864499 PMCID: PMC11167607 DOI: 10.1111/1751-7915.14489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 05/09/2024] [Indexed: 06/13/2024] Open
Abstract
Treating plant bacterial diseases is notoriously difficult because of the lack of available antimicrobials. Pseudomonas syringae pathovar syringae (Pss) is a major pathogen of cherry (Prunus avium) causing bacterial canker of the stem, leaf and fruit, impacting productivity and leading to a loss of trees. In an attempt to find a treatment for this disease, naturally occurring bacteriophage (phage) that specifically target Pss is being investigated as a biocontrol strategy. However, before using them as a biocontrol treatment, it is important to both understand their efficacy in reducing the bacterial population and determine if the bacterial pathogens can evolve resistance to evade phage infection. To investigate this, killing curve assays of five MR phages targeting Pss showed that phage resistance rapidly emerges in vitro, even when using a cocktail of the five phages together. To gain insight to the changes occurring, Pss colonies were collected three times during a 66-h killing curve assay and separately, Pss and phage were also coevolved over 10 generations, enabling the measurement of genomic and fitness changes in bacterial populations. Pss evolved resistance to phages through modifications in lipopolysaccharide (LPS) synthesis pathways. Bacterial fitness (growth) and virulence were affected in only a few mutants. Deletion of LPS-associated genes suggested that LPS was the main target receptor for all five MR phages. Later generations of coevolved phages from the coevolution experiment were more potent at reducing the bacterial density and when used with wild-type phages could reduce the emergence of phage-resistant mutants. This study shows that understanding the genetic mechanisms of bacterial pathogen resistance to phages is important for helping to design a more effective approach to kill the bacteria while minimizing the opportunity for phage resistance to manifest.
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Affiliation(s)
- Mojgan Rabiey
- School of Life Sciences, Gibbet Hill CampusUniversity of WarwickCoventryUK
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Emily R. Grace
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Paulina Pawlos
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Muscab Bihi
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Haleem Ahmed
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Georgina E. Hampson
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Amna Al Riyami
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Leena Alharbi
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Rosa Sanchez‐Lucas
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Naina Korotania
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Maria Laura Ciusa
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Olivia Mosley
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Michelle T. Hulin
- Department of Plant Soil & Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Laura Baxter
- Bioinformatics Research Technology PlatformUniversity of WarwickCoventryUK
| | - Sabrine Dhaouadi
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Diana Vinchira‐Villarraga
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Robert W. Jackson
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
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Hou F, Yi F, Song L, Zhan S, Zhang R, Han X, Sun X, Liu Z. Bacterial community dynamics and metabolic functions prediction in white button mushroom (Agaricus bisporus) during storage. Food Res Int 2023; 171:113077. [PMID: 37330835 DOI: 10.1016/j.foodres.2023.113077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/19/2023]
Abstract
White button mushroom (Agaricus bisporus) is rich in nutritional value, but it is easily infected by microorganisms during storage, which leads to spoilage and shortens the storage time. In this paper, A. bisporus at different storage times was sequenced by Illumina Novaseq 6000 platform. QIIME2 and PICRUSt2 were used to analyze the changes of bacterial community diversity and predict metabolic functions during storage of A. bisporus. Then, the pathogenic bacteria were isolated and identified from the spoilt samples of A. bisporus with black spot. The results showed that the bacterial species richness of A. bisporus surface gradually decreased. 2,291 ASVs were finally obtained through DADA2 denoising, belonging to 27 phyla, 60 classes, 154 orders, 255 families and 484 genera. The abundance of Pseudomonas on the surface of fresh A. bisporus sample was 22.8%, which increased to 68.7% after 6 days of storage. The abundance significantly increased and became a dominant spoilage bacterium. In addition, A total of 46 secondary metabolic pathways belonging to 6 categories of primary biological metabolic pathways were predicted during storage of A. bisporus, and metabolism (71.8%) was the main functional pathway. Co-occurrence network analysis revealed that the dominant bacterium Pseudomonas was positively correlated with 13 functional pathways (level 3). A total of 5 strains were isolated and purified from diseased A. bisporus surface. The test of pathogenicity showed that Pseudomonas tolaasii caused serious spoilage of A. bisporus. The study provided a theoretical basis for the development of antibacterial materials to reduce related diseases and prolong the storage time of A. bisporus.
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Affiliation(s)
- Fanyun Hou
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255049 Shandong, PR China
| | - Fangxuan Yi
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255049 Shandong, PR China
| | - Lisha Song
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255049 Shandong, PR China
| | - Shouqing Zhan
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255049 Shandong, PR China
| | - Rongfei Zhang
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255049 Shandong, PR China
| | - Xiangbo Han
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255049 Shandong, PR China
| | - Xia Sun
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255049 Shandong, PR China
| | - Zhanli Liu
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255049 Shandong, PR China.
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Knezevic P, Petrovic Fabijan A, Gavric D, Pejic J, Doffkay Z, Rakhely G. Phages from Genus Bruynoghevirus and Phage Therapy: Pseudomonas Phage Delta Case. Viruses 2021; 13:1965. [PMID: 34696396 PMCID: PMC8540360 DOI: 10.3390/v13101965] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022] Open
Abstract
The applicability and safety of bacteriophage Delta as a potential anti-Pseudomonas aeruginosa agent belonging to genus Bruynoghevirus (family Podoviridae) was characterised. Phage Delta belongs to the species Pseudomonas virus PaP3, which has been described as a temperate, with cos sites at the end of the genome. The phage Delta possesses a genome of 45,970 bp that encodes tRNA for proline (Pro), aspartic acid (Asp) and asparagine (Asn) and does not encode any known protein involved in lysogeny formation or persistence. Analysis showed that phage Delta has 182 bp direct terminal repeats at the end of genome and lysogeny was confirmed, neither upon infection at low nor at high multiplicity of infection (MOI). The turbid plaques that appear on certain host lawns can result from bacteriophage insensitive mutants that occur with higher frequency (10-4). In silico analysis showed that the genome of Delta phage does not encode any known bacterial toxin or virulence factor, determinants of antibiotic resistance and known human allergens. Based on the broad host range and high lytic activity against planktonic and biofilm cells, phage Delta represents a promising candidate for phage therapy.
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Affiliation(s)
- Petar Knezevic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 3, 21 000 Novi Sad, Serbia; (A.P.F.); (D.G.); (J.P.)
| | - Aleksandra Petrovic Fabijan
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 3, 21 000 Novi Sad, Serbia; (A.P.F.); (D.G.); (J.P.)
| | - Damir Gavric
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 3, 21 000 Novi Sad, Serbia; (A.P.F.); (D.G.); (J.P.)
| | - Jovana Pejic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 3, 21 000 Novi Sad, Serbia; (A.P.F.); (D.G.); (J.P.)
| | - Zsolt Doffkay
- Department of Biotechnology, University of Szeged, Temesvari krt. 62, H-6726 Szeged, Hungary; (Z.D.); (G.R.)
| | - Gábor Rakhely
- Department of Biotechnology, University of Szeged, Temesvari krt. 62, H-6726 Szeged, Hungary; (Z.D.); (G.R.)
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