1
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Goff JL, Lui LM, Nielsen TN, Poole FL, Smith HJ, Walker KF, Hazen TC, Fields MW, Arkin AP, Adams MWW. Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes. ISME COMMUNICATIONS 2024; 4:ycae064. [PMID: 38800128 PMCID: PMC11128244 DOI: 10.1093/ismeco/ycae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/11/2024] [Indexed: 05/29/2024]
Abstract
Mobile genetic elements (MGEs) like plasmids, viruses, and transposable elements can provide fitness benefits to their hosts for survival in the presence of environmental stressors. Heavy metal resistance genes (HMRGs) are frequently observed on MGEs, suggesting that MGEs may be an important driver of adaptive evolution in environments contaminated with heavy metals. Here, we report the meta-mobilome of the heavy metal-contaminated regions of the Oak Ridge Reservation subsurface. This meta-mobilome was compared with one derived from samples collected from unimpacted regions of the Oak Ridge Reservation subsurface. We assembled 1615 unique circularized DNA elements that we propose to be MGEs. The circular elements from the highly contaminated subsurface were enriched in HMRG clusters relative to those from the nearby unimpacted regions. Additionally, we found that these HMRGs were associated with Gamma and Betaproteobacteria hosts in the contaminated subsurface and potentially facilitate the persistence and dominance of these taxa in this region. Finally, the HMRGs were associated with conjugative elements, suggesting their potential for future lateral transfer. We demonstrate how our understanding of MGE ecology, evolution, and function can be enhanced through the genomic context provided by completed MGE assemblies.
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Affiliation(s)
- Jennifer L Goff
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY 13210, United States
| | - Lauren M Lui
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Torben N Nielsen
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States
| | - Heidi J Smith
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, United States
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, United States
| | - Kathleen F Walker
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37916, United States
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37916, United States
- Genome Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Matthew W Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, United States
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, United States
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Bioengineering, University of California, Berkeley, CA 94720, United States
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States
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2
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Nikolic N, Anagnostidis V, Tiwari A, Chait R, Gielen F. Droplet-based methodology for investigating bacterial population dynamics in response to phage exposure. Front Microbiol 2023; 14:1260196. [PMID: 38075890 PMCID: PMC10703435 DOI: 10.3389/fmicb.2023.1260196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/23/2023] [Indexed: 02/12/2024] Open
Abstract
An alarming rise in antimicrobial resistance worldwide has spurred efforts into the search for alternatives to antibiotic treatments. The use of bacteriophages, bacterial viruses harmless to humans, represents a promising approach with potential to treat bacterial infections (phage therapy). Recent advances in microscopy-based single-cell techniques have allowed researchers to develop new quantitative methodologies for assessing the interactions between bacteria and phages, especially the ability of phages to eradicate bacterial pathogen populations and to modulate growth of both commensal and pathogen populations. Here we combine droplet microfluidics with fluorescence time-lapse microscopy to characterize the growth and lysis dynamics of the bacterium Escherichia coli confined in droplets when challenged with phage. We investigated phages that promote lysis of infected E. coli cells, specifically, a phage species with DNA genome, T7 (Escherichia virus T7) and two phage species with RNA genomes, MS2 (Emesvirus zinderi) and Qβ (Qubevirus durum). Our microfluidic trapping device generated and immobilized picoliter-sized droplets, enabling stable imaging of bacterial growth and lysis in a temperature-controlled setup. Temporal information on bacterial population size was recorded for up to 25 h, allowing us to determine growth rates of bacterial populations and helping us uncover the extent and speed of phage infection. In the long-term, the development of novel microfluidic single-cell and population-level approaches will expedite research towards fundamental understanding of the genetic and molecular basis of rapid phage-induced lysis and eco-evolutionary aspects of bacteria-phage dynamics, and ultimately help identify key factors influencing the success of phage therapy.
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Affiliation(s)
- Nela Nikolic
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- Department of Physics and Astronomy, Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
- Translational Research Exchange @ Exeter, University of Exeter, Exeter, United Kingdom
| | - Vasileios Anagnostidis
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- Department of Physics and Astronomy, Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
| | - Anuj Tiwari
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Remy Chait
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Fabrice Gielen
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- Department of Physics and Astronomy, Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
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3
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Wang C, Zhao J, Lin Y, Yuan L, El-Telbany M, Maung AT, Abdelaziz MNS, Masuda Y, Honjoh KI, Miyamoto T. Isolation, characterization of Enterococcus phages and their application in control of E. faecalis in milk. J Appl Microbiol 2023; 134:lxad250. [PMID: 37944001 DOI: 10.1093/jambio/lxad250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/02/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023]
Abstract
AIMS Isolation and characterization of Enterococcus phages and application of phage cocktail to control E. faecalis in milk. METHODS AND RESULTS For phage isolations, double layer agar method was used. Host range of the phages were determined by the spot test. Twelve phages with varying host ranges were isolated. Phages PEF1, PEF7b, and PEF9 with different host ranges and lytic activities were selected for phage cocktails. Compared to two-phages cocktails tested, the cocktail containing all the three phages displayed stronger antibacterial and biofilm removal activities. The cocktail treatment reduced viable E. faecalis in biofilm by 6 log within 6 h at both 30°C and 4°C. In milk, the cocktail gradually reduced the viable count of E. faecalis and the count reached below the lower limit of detection at 48 h at 4°C. CONCLUSION The strong bactericidal and biofilm removal activities of the phage cocktail suggest the potential of this cocktail as a natural biocontrol agent for combating E. faecalis in milk.
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Affiliation(s)
- Chen Wang
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Junxin Zhao
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Yunzhi Lin
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Lu Yuan
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Mohamed El-Telbany
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Aye Thida Maung
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Marwa Nabil Sayed Abdelaziz
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Yoshimitsu Masuda
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Ken-Ichi Honjoh
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Takahisa Miyamoto
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
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4
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Chung KM, Liau XL, Tang SS. Bacteriophages and Their Host Range in Multidrug-Resistant Bacterial Disease Treatment. Pharmaceuticals (Basel) 2023; 16:1467. [PMID: 37895938 PMCID: PMC10610060 DOI: 10.3390/ph16101467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/18/2023] [Accepted: 06/26/2023] [Indexed: 10/29/2023] Open
Abstract
The rapid emergence of multidrug-resistant (MDR) bacteria in recent times has prompted the search for new and more potent antibiotics. Bacteriophages (commonly known as phages) are viruses that target and infect their bacterial hosts. As such, they are also a potential alternative to antibiotics. These phages can be broadly categorized into monovalent (with a narrow host range spectrum and specific to a single bacterial genus) and polyvalent (with a broad host range and specific to more than two genera). However, there is still much ambiguity in the use of these terms, with researchers often describing their phages differently. There is considerable research on the use of both narrow- and broad-host range phages in the treatment of infections and diseases caused by MDR bacteria, including tuberculosis, cystic fibrosis, and carbapenem-resistant Enterobacterales (CRE) infectious diseases. From this, it is clear that the host range of these phages plays a vital role in determining the effectiveness of any phage therapy, and this factor is usually analyzed based on the advantages and limitations of different host ranges. There have also been efforts to expand phage host ranges via phage cocktail development, phage engineering and combination therapies, in line with current technological advancements. This literature review aims to provide a more in-depth understanding of the role of phage host ranges in the effectiveness of treating MDR-bacterial diseases, by exploring the following: phage biology, the importance of phages in MDR bacteria diseases treatment, the importance of phage host range and its advantages and limitations, current findings and recent developments, and finally, possible future directions for wide host range phages.
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Affiliation(s)
- Ka Mun Chung
- Division of Microbiology and Molecular Genetics, Institute of Biological Sciences, Faculty of Sciences, University Malaya, Kuala Lumpur 50603, Malaysia
| | - Xiew Leng Liau
- Division of Microbiology and Molecular Genetics, Institute of Biological Sciences, Faculty of Sciences, University Malaya, Kuala Lumpur 50603, Malaysia
| | - Swee Seong Tang
- Division of Microbiology and Molecular Genetics, Institute of Biological Sciences, Faculty of Sciences, University Malaya, Kuala Lumpur 50603, Malaysia
- Centre for Research in Biotechnology for Agriculture, University Malaya, Kuala Lumpur 50603, Malaysia
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5
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Zhang YZ, Liu Y, Bai Z, Fujimoto K, Uematsu S, Imoto S. Zero-shot-capable identification of phage-host relationships with whole-genome sequence representation by contrastive learning. Brief Bioinform 2023; 24:bbad239. [PMID: 37466138 PMCID: PMC10516345 DOI: 10.1093/bib/bbad239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/17/2023] [Accepted: 06/08/2023] [Indexed: 07/20/2023] Open
Abstract
Accurately identifying phage-host relationships from their genome sequences is still challenging, especially for those phages and hosts with less homologous sequences. In this work, focusing on identifying the phage-host relationships at the species and genus level, we propose a contrastive learning based approach to learn whole-genome sequence embeddings that can take account of phage-host interactions (PHIs). Contrastive learning is used to make phages infecting the same hosts close to each other in the new representation space. Specifically, we rephrase whole-genome sequences with frequency chaos game representation (FCGR) and learn latent embeddings that 'encapsulate' phages and host relationships through contrastive learning. The contrastive learning method works well on the imbalanced dataset. Based on the learned embeddings, a proposed pipeline named CL4PHI can predict known hosts and unseen hosts in training. We compare our method with two recently proposed state-of-the-art learning-based methods on their benchmark datasets. The experiment results demonstrate that the proposed method using contrastive learning improves the prediction accuracy on known hosts and demonstrates a zero-shot prediction capability on unseen hosts. In terms of potential applications, the rapid pace of genome sequencing across different species has resulted in a vast amount of whole-genome sequencing data that require efficient computational methods for identifying phage-host interactions. The proposed approach is expected to address this need by efficiently processing whole-genome sequences of phages and prokaryotic hosts and capturing features related to phage-host relationships for genome sequence representation. This approach can be used to accelerate the discovery of phage-host interactions and aid in the development of phage-based therapies for infectious diseases.
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Affiliation(s)
- Yao-zhong Zhang
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Shirokanedai 4-6-1, Minato-ku, 108-8639 Tokyo, Japan
| | - Yunjie Liu
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Shirokanedai 4-6-1, Minato-ku, 108-8639 Tokyo, Japan
| | - Zeheng Bai
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Shirokanedai 4-6-1, Minato-ku, 108-8639 Tokyo, Japan
| | - Kosuke Fujimoto
- Department of Immunology and Genomics, Graduate School of Medicine, Osaka Metropolitan University, Asahi-machi 1-4-3, Abeno-ku, 545-8585 Osaka, Japan
- Division of Metagenome Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Shirokanedai 4-6-1, Minato-ku, 108-8639 Tokyo, Japan
| | - Satoshi Uematsu
- Department of Immunology and Genomics, Graduate School of Medicine, Osaka Metropolitan University, Asahi-machi 1-4-3, Abeno-ku, 545-8585 Osaka, Japan
- Division of Metagenome Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Shirokanedai 4-6-1, Minato-ku, 108-8639 Tokyo, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Shirokanedai 4-6-1, Minato-ku, 108-8639 Tokyo, Japan
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6
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Hussain NAS, Stafford JL. Abiotic and biotic constituents of oil sands process-affected waters. J Environ Sci (China) 2023; 127:169-186. [PMID: 36522051 DOI: 10.1016/j.jes.2022.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/03/2022] [Accepted: 06/04/2022] [Indexed: 06/17/2023]
Abstract
The oil sands in Northern Alberta are the largest oil sands in the world, providing an important economic resource for the Canadian energy industry. The extraction of petroleum in the oil sands begins with the addition of hot water to the bituminous sediment, generating oil sands process-affected water (OSPW), which is acutely toxic to organisms. Trillions of litres of OSPW are stored on oil sands mining leased sites in man-made reservoirs called tailings ponds. As the volume of OSPW increases, concerns arise regarding the reclamation and eventual release of this water back into the environment. OSPW is composed of a complex and heterogeneous mix of components that vary based on factors such as company extraction techniques, age of the water, location, and bitumen ore quality. Therefore, the effective remediation of OSPW requires the consideration of abiotic and biotic constituents within it to understand short and long term effects of treatments used. This review summarizes selected chemicals and organisms in these waters and their interactions to provide a holistic perspective on the physiochemical and microbial dynamics underpinning OSPW .
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Affiliation(s)
- Nora A S Hussain
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2N8, Canada
| | - James L Stafford
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2N8, Canada.
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7
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Friedrich I, Neubauer H, Kuritsyn A, Bodenberger B, Tskhay F, Hartmann S, Poehlein A, Bömeke M, Hoppert M, Schneider D, Hertel R, Daniel R. Brevundimonas and Serratia as host systems for assessing associated environmental viromes and phage diversity by complementary approaches. Front Microbiol 2023; 14:1095850. [PMID: 37025643 PMCID: PMC10070969 DOI: 10.3389/fmicb.2023.1095850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/23/2023] [Indexed: 04/08/2023] Open
Abstract
Focusing on visible plaques for phage isolation leaves the question if we miss the diversity of non-plaque forming phages. We addressed this question through direct plaque-based isolation by employing the new hosts Brevundimonas pondensis LVF1 and Serratia marcescens LVF3 dsDNA, ssDNA, dsRNA, and ssRNA host-associated metavirome analysis. Of the 25 distinctive dsDNA phage isolates, 14 were associated with Brevundimonas and 11 with Serratia. TEM analysis revealed that 6 were myoviruses, 18 siphoviruses and 1 podovirus, while phages infecting Brevundimonas belonged all to siphoviruses. The associated viromes suggested a higher phage diversity in summer than in winter, and dsDNA phages were the dominant group. Isolation of vB_SmaP-Kaonashi was possible after investigating the viromes associated with Serratia, demonstrating the great potential of accompanying host-associated metavirome analysis. The ssDNA virome analysis showed that the B. pondensis LVF1 host is associated with Microviridae and Inoviridae phages, although none of them were isolated. The results demonstrated that the classical isolation technique is not exhausted, leading to the isolation of new dsDNA phages. It can be further improved by combination with metavirome techniques, which revealed further diversity.
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Affiliation(s)
- Ines Friedrich
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Hannes Neubauer
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Alisa Kuritsyn
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Bernhard Bodenberger
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Faina Tskhay
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Sara Hartmann
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Mechthild Bömeke
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Michael Hoppert
- General Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Dominik Schneider
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Robert Hertel
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
- FG Synthetic Microbiology, Institute of Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
- *Correspondence: Rolf Daniel,
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8
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Holtappels D, Fortuna KJ, Vallino M, Lavigne R, Wagemans J. Isolation, characterization and genome analysis of an orphan phage FoX4 of the new Foxquatrovirus genus. BMC Microbiol 2022; 22:304. [PMID: 36513996 PMCID: PMC9746216 DOI: 10.1186/s12866-022-02719-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/30/2022] [Indexed: 12/15/2022] Open
Abstract
The growing interest in the therapeutic application of bacteriophages leads to a drastic increase in the number of sequenced genomes. Luckily, recent insights in phage taxonomy facilitate the classification of phages in a comprehensive and data-driven manner as recently proposed by the International Committee on Taxonomy of Viruses. In this research, we present the taxonomical classification of a novel, narrow host range Xanthomonas phage FoX4, isolated from a Brussels sprouts field in Belgium infested with Xanthomonas campestris pv. campestris. The phage has a limited ability to lyse a bacterial culture, yet adsorbs efficiently to its host. Based on its genome sequence and low similarity to previously described phages, the phage comprises the novel phage genus Foxquatrovirus.
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Affiliation(s)
- D. Holtappels
- grid.5596.f0000 0001 0668 7884Department of Biosystems, KU Leuven, Leuven, Belgium
| | - K. J. Fortuna
- grid.5596.f0000 0001 0668 7884Department of Biosystems, KU Leuven, Leuven, Belgium
| | - M. Vallino
- grid.5326.20000 0001 1940 4177Institute of Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| | - R. Lavigne
- grid.5596.f0000 0001 0668 7884Department of Biosystems, KU Leuven, Leuven, Belgium
| | - J. Wagemans
- grid.5596.f0000 0001 0668 7884Department of Biosystems, KU Leuven, Leuven, Belgium
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9
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D’Iorio M, Dewar K. Replication-associated inversions are the dominant form of bacterial chromosome structural variation. Life Sci Alliance 2022; 6:6/1/e202201434. [PMID: 36261227 PMCID: PMC9584773 DOI: 10.26508/lsa.202201434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/24/2022] Open
Abstract
The structural arrangements of bacterial chromosomes vary widely between closely related species and can result in significant phenotypic outcomes. The appearance of large-scale chromosomal inversions that are symmetric relative to markers for the origin of replication (OriC) has been previously observed; however, the overall prevalence of replication-associated structural rearrangements (RASRs) in bacteria and their causal mechanisms are currently unknown. Here, we systematically identify the locations of RASRs in species with multiple complete-sequenced genomes and investigate potential mediating biological mechanisms. We found that 247 of 313 species contained sequences with at least one large (>50 Kb) inversion in their sequence comparisons, and the aggregated inversion distances away from symmetry were normally distributed with a mean of zero. Many inversions that were offset from dnaA were found to be centered on a different marker for the OriC Instances of flanking repeats provide evidence that breaks formed during the replication process could be repaired to opposing positions. We also found a strong relationship between the later stages of replication and the range in distance variation from symmetry.
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Affiliation(s)
- Matthew D’Iorio
- Quantitative Life Sciences, McGill University, Montreal, Canada,Correspondence:
| | - Ken Dewar
- Department of Human Genetics, McGill University, Montreal, Canada,Centre for Microbiome Research, McGill University, Montreal, Canada
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10
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Korniienko N, Kharina A, Zrelovs N, Jindřichová B, Moravec T, Budzanivska I, Burketová L, Kalachova T. Isolation and Characterization of Two Lytic Phages Efficient Against Phytopathogenic Bacteria From Pseudomonas and Xanthomonas Genera. Front Microbiol 2022; 13:853593. [PMID: 35547140 PMCID: PMC9083414 DOI: 10.3389/fmicb.2022.853593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/24/2022] [Indexed: 01/06/2023] Open
Abstract
Pseudomonas syringae is a bacterial pathogen that causes yield losses in various economically important plant species. At the same time, P. syringae pv. tomato (Pst) is one of the best-studied bacterial phytopathogens and a popular model organism. In this study, we report on the isolation of two phages from the market-bought pepper fruit showing symptoms of bacterial speck. These Pseudomonas phages were named Eir4 and Eisa9 and characterized using traditional microbiological methods and whole-genome sequencing followed by various bioinformatics approaches. Both of the isolated phages were capable only of the lytic life cycle and were efficient against several pathovars from Pseudomonas and Xanthomonas genera. With the combination of transmission electron microscopy (TEM) virion morphology inspection and comparative genomics analyses, both of the phages were classified as members of the Autographiviridae family with different degrees of novelty within the known phage diversity. Eir4, but not Eisa9, phage application significantly decreased the propagation of Pst in the leaf tissues of Arabidopsis thaliana plants. The biological properties of Eir4 phage allow us to propose it as a potential biocontrol agent for use in the prevention of Pst-associated bacterioses and also as a model organism for the future research of mechanisms of phage-host interactions in different plant systems.
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Affiliation(s)
- Nataliia Korniienko
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
- Educational and Scientific Center (ESC) “Institute of Biology and Medicine”, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Alla Kharina
- Educational and Scientific Center (ESC) “Institute of Biology and Medicine”, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Nikita Zrelovs
- Latvian Biomedical Research and Study Centre, Rīga, Latvia
| | - Barbora Jindřichová
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Tomaš Moravec
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Iryna Budzanivska
- Educational and Scientific Center (ESC) “Institute of Biology and Medicine”, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Lenka Burketová
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Tetiana Kalachova
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
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Wójcicki M, Średnicka P, Błażejak S, Gientka I, Kowalczyk M, Emanowicz P, Świder O, Sokołowska B, Juszczuk-Kubiak E. Characterization and Genome Study of Novel Lytic Bacteriophages against Prevailing Saprophytic Bacterial Microflora of Minimally Processed Plant-Based Food Products. Int J Mol Sci 2021; 22:12460. [PMID: 34830335 PMCID: PMC8624825 DOI: 10.3390/ijms222212460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 12/13/2022] Open
Abstract
The food industry is still searching for novel solutions to effectively ensure the microbiological safety of food, especially fresh and minimally processed food products. Nowadays, the use of bacteriophages as potential biological control agents in microbiological food safety and preservation is a promising strategy. The aim of the study was the isolation and comprehensive characterization of novel bacteriophages with lytic activity against saprophytic bacterial microflora of minimally processed plant-based food products, such as mixed leaf salads. From 43 phages isolated from municipal sewage, four phages, namely Enterobacter phage KKP 3263, Citrobacter phage KKP 3664, Enterobacter phage KKP 3262, and Serratia phage KKP 3264 have lytic activity against Enterobacter ludwigii KKP 3083, Citrobacter freundii KKP 3655, Enterobacter cloacae KKP 3082, and Serratia fonticola KKP 3084 bacterial strains, respectively. Transmission electron microscopy (TEM) and whole-genome sequencing (WGS) identified Enterobacter phage KKP 3263 as an Autographiviridae, and Citrobacter phage KKP 3664, Enterobacter phage KKP 3262, and Serratia phage KKP 3264 as members of the Myoviridae family. Genome sequencing revealed that these phages have linear double-stranded DNA (dsDNA) with sizes of 39,418 bp (KKP 3263), 61,608 bp (KKP 3664), 84,075 bp (KKP 3262), and 148,182 bp (KKP 3264). No antibiotic resistance genes, virulence factors, integrase, recombinase, or repressors, which are the main markers of lysogenic viruses, were annotated in phage genomes. Serratia phage KKP 3264 showed the greatest growth inhibition of Serratia fonticola KKP 3084 strain. The use of MOI 1.0 caused an almost 5-fold decrease in the value of the specific growth rate coefficient. The phages retained their lytic activity in a wide range of temperatures (from -20 °C to 50 °C) and active acidity values (pH from 4 to 11). All phages retained at least 70% of lytic activity at 60 °C. At 80 °C, no lytic activity against tested bacterial strains was observed. Serratia phage KKP 3264 was the most resistant to chemical factors, by maintaining high lytic activity across a broader range of pH from 3 to 11. The results indicated that these phages could be a potential biological control agent against saprophytic bacterial microflora of minimally processed plant-based food products.
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Affiliation(s)
- Michał Wójcicki
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
| | - Paulina Średnicka
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
| | - Stanisław Błażejak
- Department of Biotechnology and Food Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences (WULS-SGGW), Nowoursynowska 166 Street, 02-776 Warsaw, Poland; (S.B.); (I.G.)
| | - Iwona Gientka
- Department of Biotechnology and Food Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences (WULS-SGGW), Nowoursynowska 166 Street, 02-776 Warsaw, Poland; (S.B.); (I.G.)
| | - Monika Kowalczyk
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
| | - Paulina Emanowicz
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
| | - Olga Świder
- Department of Food Safety and Chemical Analysis, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland;
| | - Barbara Sokołowska
- Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland;
| | - Edyta Juszczuk-Kubiak
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
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Miroshnikov KA, Evseev PV, Lukianova AA, Ignatov AN. Tailed Lytic Bacteriophages of Soft Rot Pectobacteriaceae. Microorganisms 2021; 9:1819. [PMID: 34576713 PMCID: PMC8472413 DOI: 10.3390/microorganisms9091819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023] Open
Abstract
The study of the ecological and evolutionary traits of Soft Rot Pectobacteriaceae (SRP) comprising genera Pectobacterium and Dickeya often involves bacterial viruses (bacteriophages). Bacteriophages are considered to be a prospective tool for the ecologically safe and highly specific protection of plants and harvests from bacterial diseases. Information concerning bacteriophages has been growing rapidly in recent years, and this has included new genomics-based principles of taxonomic distribution. In this review, we summarise the data on phages infecting Pectobacterium and Dickeya that are available in publications and genomic databases. The analysis highlights not only major genomic properties that assign phages to taxonomic families and genera, but also the features that make them potentially suitable for phage control applications. Specifically, there is a discussion of the molecular mechanisms of receptor recognition by the phages and problems concerning the evolution of phage-resistant mutants.
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Affiliation(s)
- Konstantin A Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
| | - Peter V Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
| | - Anna A Lukianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, bldg. 12, 119234 Moscow, Russia
| | - Alexander N Ignatov
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
- Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str., 6, 117198 Moscow, Russia
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