1
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Bullen NP, Johnson CN, Andersen SE, Arya G, Marotta SR, Lee YJ, Weigele PR, Whitney JC, Duerkop BA. An enterococcal phage protein inhibits type IV restriction enzymes involved in antiphage defense. Nat Commun 2024; 15:6955. [PMID: 39138193 PMCID: PMC11322646 DOI: 10.1038/s41467-024-51346-1] [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: 12/05/2023] [Accepted: 08/05/2024] [Indexed: 08/15/2024] Open
Abstract
The prevalence of multidrug resistant (MDR) bacterial infections continues to rise as the development of antibiotics needed to combat these infections remains stagnant. MDR enterococci are a major contributor to this crisis. A potential therapeutic approach for combating MDR enterococci is bacteriophage (phage) therapy, which uses lytic viruses to infect and kill pathogenic bacteria. While phages that lyse some strains of MDR enterococci have been identified, other strains display high levels of resistance and the mechanisms underlying this resistance are poorly defined. Here, we use a CRISPR interference (CRISPRi) screen to identify a genetic locus found on a mobilizable plasmid from Enterococcus faecalis involved in phage resistance. This locus encodes a putative serine recombinase followed by a Type IV restriction enzyme (TIV-RE) that we show restricts the replication of phage phi47 in vancomycin-resistant E. faecalis. We further find that phi47 evolves to overcome restriction by acquiring a missense mutation in a TIV-RE inhibitor protein. We show that this inhibitor, termed type IV restriction inhibiting factor A (tifA), binds and inactivates diverse TIV-REs. Overall, our findings advance our understanding of phage defense in drug-resistant E. faecalis and provide mechanistic insight into how phages evolve to overcome antiphage defense systems.
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Affiliation(s)
- Nathan P Bullen
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4L8, Canada
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Cydney N Johnson
- Department of Immunology and Microbiology, University of Colorado School-Anschutz Medical Campus, School of Medicine, Aurora, CO, 80045, USA
| | - Shelby E Andersen
- Department of Immunology and Microbiology, University of Colorado School-Anschutz Medical Campus, School of Medicine, Aurora, CO, 80045, USA
| | - Garima Arya
- Department of Immunology and Microbiology, University of Colorado School-Anschutz Medical Campus, School of Medicine, Aurora, CO, 80045, USA
| | - Sonia R Marotta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4L8, Canada
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Yan-Jiun Lee
- Research Department, New England Biolabs, Ipswich, MA, 01938, USA
| | - Peter R Weigele
- Research Department, New England Biolabs, Ipswich, MA, 01938, USA
| | - John C Whitney
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4L8, Canada.
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
| | - Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado School-Anschutz Medical Campus, School of Medicine, Aurora, CO, 80045, USA.
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2
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Beggs GA, Bassler BL. Phage small proteins play large roles in phage-bacterial interactions. Curr Opin Microbiol 2024; 80:102519. [PMID: 39047312 PMCID: PMC11323111 DOI: 10.1016/j.mib.2024.102519] [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: 06/17/2024] [Revised: 07/05/2024] [Accepted: 07/07/2024] [Indexed: 07/27/2024]
Abstract
Phages have wide influence on bacterial physiology, and likewise, bacterial processes impinge on phage biology. Key to these interactions are phage small proteins (<100 aa). Long underappreciated, recent work has revealed millions of phage small proteins, and increasingly, mechanisms by which they function to dictate phage and/or bacterial behavior and evolution. Here, we describe select phage small proteins that mediate phage-bacterial interactions by modulating phage lifestyle decision-making components or by altering host gene expression.
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Affiliation(s)
- Grace A Beggs
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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3
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Vacek L, Polaštík Kleknerová D, Lipový B, Holoubek J, Matysková D, Černá E, Brtníková J, Jeklová E, Kobzová Š, Janda L, Lišková L, Diabelko D, Botka T, Pantůček R, Růžička F, Vojtová L. Phage therapy combined with Gum Karaya injectable hydrogels for treatment of methicillin-resistant Staphylococcus aureus deep wound infection in a porcine model. Int J Pharm 2024; 660:124348. [PMID: 38885776 DOI: 10.1016/j.ijpharm.2024.124348] [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: 02/20/2024] [Revised: 05/24/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024]
Abstract
Skin and soft tissue infections (SSTIs) represent a significant healthcare challenge, particularly in the context of increasing antibiotic resistance. This study investigates the efficacy of a novel therapeutic approach combining bacteriophage (phage) therapy with a gum Karaya (GK)-based hydrogel delivery system in a porcine model of deep staphylococcal SSTIs. The study exploits the lytic activity and safety of the Staphylococcus phage 812K1/420 of the Kayvirus genus, which is active against methicillin-resistant Staphylococcus aureus (MRSA). The GK injectable hydrogels and hydrogel films, developed by our research group, serve as effective, non-toxic, and easy-to-apply delivery systems, supporting moist wound healing and re-epithelialization. In the porcine model, the combined treatment showed asynergistic effect, leading to a significant reduction in bacterial load (2.5 log CFU/gram of tissue) within one week. Local signs of inflammation were significantly reduced by day 8, with clear evidence of re-epithelialization and wound contraction. Importantly, no adverse effects of the GK-based delivery system were observed throughout the study. The results highlight the potential of this innovative therapeutic approach to effectively treat deep staphylococcal SSTIs, providing a promising avenue for further research and clinical application in the field of infections caused by antibiotic-resistant bacteria.
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Affiliation(s)
- L Vacek
- Department of Microbiology, St. Anne's University Hospital and Faculty of Medicine, Masaryk University, Pekařská 53, 602 00 Brno, Czech Republic
| | - D Polaštík Kleknerová
- Department of Microbiology, St. Anne's University Hospital and Faculty of Medicine, Masaryk University, Pekařská 53, 602 00 Brno, Czech Republic
| | - B Lipový
- Department of Burns and Plastic Surgery, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; Advanced Biomaterials Group, Central European Institute of Technology, Brno University of Technology, Purkyňova 656/123, 612 00 Brno, Czech Republic
| | - J Holoubek
- Department of Burns and Plastic Surgery, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - D Matysková
- Department of Burns and Plastic Surgery, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - E Černá
- Advanced Biomaterials Group, Central European Institute of Technology, Brno University of Technology, Purkyňova 656/123, 612 00 Brno, Czech Republic
| | - J Brtníková
- Advanced Biomaterials Group, Central European Institute of Technology, Brno University of Technology, Purkyňova 656/123, 612 00 Brno, Czech Republic
| | - E Jeklová
- Clinical Immunology and Immunology of Infectious Diseases, Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic
| | - Š Kobzová
- Clinical Immunology and Immunology of Infectious Diseases, Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic
| | - L Janda
- Clinical Immunology and Immunology of Infectious Diseases, Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic
| | - L Lišková
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - D Diabelko
- Department of Microbiology, St. Anne's University Hospital and Faculty of Medicine, Masaryk University, Pekařská 53, 602 00 Brno, Czech Republic
| | - T Botka
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - R Pantůček
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - F Růžička
- Department of Microbiology, St. Anne's University Hospital and Faculty of Medicine, Masaryk University, Pekařská 53, 602 00 Brno, Czech Republic.
| | - L Vojtová
- Advanced Biomaterials Group, Central European Institute of Technology, Brno University of Technology, Purkyňova 656/123, 612 00 Brno, Czech Republic
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4
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Wang Y, Tong G, Jiang X, Tu C, Cai H, Fang W, Tan H, Weng Q, Wei X, Lin M. Biologic and genomic characterization of a novel virulent Aeromonas hydrophila phage phiA051, with high homology to prophages. Front Vet Sci 2024; 11:1415685. [PMID: 39091387 PMCID: PMC11292799 DOI: 10.3389/fvets.2024.1415685] [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: 04/11/2024] [Accepted: 07/05/2024] [Indexed: 08/04/2024] Open
Abstract
Introduction Aeromonas hydrophila is particularly harmful to freshwater aquaculture, and the search for phage is an effective biological control method, but reports of possible temperate phages and their mutants are rare in this field. In this study, a virulent phage highly homologous to prophage in the genomes of A. hydrophila was collected and preliminary biological characterization was carried out to understand its nature. Materials and methods Water samples taken from eel ponds in Fujian, China were combined with the strain. Spot test method and double-layer agar plate assay was used for confirmation and purification. Phage virions were observed using transmission electron microscope. A total of 68 strains of Aeromonas spp. were used to determine the host range. MOI groups of 1,000, 100, 10, 1, 0.1, 0.01, 0.001, 0.0001, 0.00001 were prepared to detect the optimal MOI. The conditions of thermal stability assay were set as 30, 40, 50, 60, 70 and 80°C for 1 h, respectively, and conditions of acid and alkali stability assay were set as 2.0, 4.0, 6.0, 8.0, 10.0 and 12.0 of pH. MOI of 0.01 and 0.1, respectively, are set to determine the inhibitory capacity of phage. Results A novel virulent A. hydrophila phage designated phiA051 has been isolated from aquaculture water. Electron microscopic observation showed that the phage phiA051 was composed of an icosahedral capsid. The phage phiA051 possesses an optimal multiplicity of infection (MOI) of 0.01, and its burst size was 108 PFU/cell. The phage maintained a high viability at temperatures of 30-50°C or pH 6.0-10.0 for 1 h. Phage phiA051 has certain potentials in rapidly inhibiting the spread of pathogen early in the outbreak, and it has a linear dsDNA with GC content of 60.55% and a total length of 32,212 bp, including 46 ORFs. Discussion The phage phiA051 behaved as a virulent phage. However, the BLASTN result showed that 23 of the top 25 hits were genomes of Aeromonas strains. It was suggested that phiA051 was probably derived from some prophage in the chromosome of Aeromonas. Further investigation of the mechanism how phage phiA051 transforms from a temperate phage to a virulent phage will provide a unique perspective and idea to explore the potential of prophages.
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Affiliation(s)
- Yuzhi Wang
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen, China
| | - Guixiang Tong
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Xinglong Jiang
- Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Xiamen, China
| | - Chuandeng Tu
- Xiamen Key Laboratory of Intelligent Fishery, Xiamen Ocean Vocational College, Xiamen, China
| | - Hongjiao Cai
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen, China
| | - Wenhong Fang
- East China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Shanghai, China
| | - Honglian Tan
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Qibiao Weng
- Key Laboratory of Eel Aquaculture and Processing of Fujian Province, Fuzhou, China
| | - Xinxian Wei
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Mao Lin
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen, China
- Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Xiamen, China
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5
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Bullen NP, Johnson CN, Andersen SE, Arya G, Marotta SR, Lee YJ, Weigele PR, Whitney JC, Duerkop BA. An enterococcal phage protein broadly inhibits type IV restriction enzymes involved in antiphage defense. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.16.567456. [PMID: 38014348 PMCID: PMC10680825 DOI: 10.1101/2023.11.16.567456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The prevalence of multidrug resistant (MDR) bacterial infections continues to rise as the development of antibiotics needed to combat these infections remains stagnant. MDR enterococci are a major contributor to this crisis. A potential therapeutic approach for combating MDR enterococci is bacteriophage (phage) therapy, which uses lytic viruses to infect and kill pathogenic bacteria. While phages that lyse some strains of MDR enterococci have been identified, other strains display high levels of resistance and the mechanisms underlying this resistance are poorly defined. Here, we use a CRISPR interference (CRISPRi) screen to identify a genetic locus found on a mobilizable plasmid from Enterococcus faecalis involved in phage resistance. This locus encodes a putative serine recombinase followed by a Type IV restriction enzyme (TIV-RE) that we show restricts the replication of phage phi47 in E. faecalis. We further find that phi47 evolves to overcome restriction by acquiring a missense mutation in a TIV-RE inhibitor protein. We show that this inhibitor, termed type IV restriction inhibiting factor A (tifA), binds and inactivates diverse TIV-REs. Overall, our findings advance our understanding of phage defense in drug-resistant E. faecalis and provide mechanistic insight into how phages evolve to overcome antiphage defense systems.
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Affiliation(s)
- Nathan P. Bullen
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada, L8S 4L8
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Cydney N. Johnson
- Department of Immunology and Microbiology, University of Colorado School – Anschutz Medical Campus, School of Medicine, Aurora, CO, USA, 80045
| | - Shelby E. Andersen
- Department of Immunology and Microbiology, University of Colorado School – Anschutz Medical Campus, School of Medicine, Aurora, CO, USA, 80045
| | - Garima Arya
- Department of Immunology and Microbiology, University of Colorado School – Anschutz Medical Campus, School of Medicine, Aurora, CO, USA, 80045
| | - Sonia R. Marotta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada, L8S 4L8
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Yan-Jiun Lee
- Research Department, New England Biolabs, Ipswich, MA, USA, 01938
| | - Peter R. Weigele
- Research Department, New England Biolabs, Ipswich, MA, USA, 01938
| | - John C. Whitney
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada, L8S 4L8
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado School – Anschutz Medical Campus, School of Medicine, Aurora, CO, USA, 80045
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6
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Nguyen TVP, Wu Y, Yao T, Trinh JT, Zeng L, Chemla YR, Golding I. Coinfecting phages impede each other's entry into the cell. Curr Biol 2024; 34:2841-2853.e18. [PMID: 38878771 PMCID: PMC11233250 DOI: 10.1016/j.cub.2024.05.032] [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: 08/11/2023] [Revised: 02/15/2024] [Accepted: 05/16/2024] [Indexed: 06/25/2024]
Abstract
The developmental choice made by temperate phages, between cell death (lysis) and viral dormancy (lysogeny), is influenced by the relative abundance of viruses and hosts in the environment. The paradigm for this abundance-driven decision is phage lambda of E. coli, whose propensity to lysogenize increases with the number of viruses coinfecting the same bacterium. It is believed that lambda uses this number to infer whether phages or bacteria outnumber each other. However, this interpretation is premised on an accurate mapping between the extracellular phage-to-bacteria ratio and the intracellular multiplicity of infection (MOI). Here, we show this premise to be faulty. By simultaneously labeling phage capsids and genomes, we find that, while the number of phages landing on each cell reliably samples the population ratio, the number of phages entering the cell does not. Single-cell infections, performed in a microfluidic device and interpreted using a stochastic model, reveal that the probability and rate of phage entry decrease with the number of adsorbed phages. This decrease reflects an MOI-dependent perturbation to host physiology caused by phage attachment, as evidenced by compromised membrane integrity and loss of membrane potential. The dependence of entry dynamics on the surrounding medium results in a strong impact on the infection outcome, while the protracted entry of coinfecting phages increases the heterogeneity in infection outcome at a given MOI. Our findings in lambda, and similar results we obtained for phages T5 and P1, demonstrate the previously unappreciated role played by entry dynamics in determining the outcome of bacteriophage infection.
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Affiliation(s)
- Thu Vu Phuc Nguyen
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yuchen Wu
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Tianyou Yao
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Jimmy T Trinh
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Yann R Chemla
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Ido Golding
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA.
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7
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Zhang L, Wang H, Zeng J, Cao X, Gao Z, Liu Z, Li F, Wang J, Zhang Y, Yang M, Feng Y. Cas1 mediates the interference stage in a phage-encoded CRISPR-Cas system. Nat Chem Biol 2024:10.1038/s41589-024-01659-5. [PMID: 38977786 DOI: 10.1038/s41589-024-01659-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 05/31/2024] [Indexed: 07/10/2024]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems are prokaryotic adaptive immune systems against invading phages and other mobile genetic elements. Notably, some phages, including the Vibrio cholerae-infecting ICP1 (International Center for Diarrheal Disease Research, Bangladesh cholera phage 1), harbor CRISPR-Cas systems to counteract host defenses. Nevertheless, ICP1 Cas8f lacks the helical bundle domain essential for recruitment of helicase-nuclease Cas2/3 during target DNA cleavage and how this system accomplishes the interference stage remains unknown. Here, we found that Cas1, a highly conserved component known to exclusively work in the adaptation stage, also mediates the interference stage through connecting Cas2/3 to the DNA-bound CRISPR-associated complex for antiviral defense (Cascade; CRISPR system yersinia, Csy) of the ICP1 CRISPR-Cas system. A series of structures of Csy, Csy-dsDNA (double-stranded DNA), Cas1-Cas2/3 and Csy-dsDNA-Cas1-Cas2/3 complexes reveal the whole process of Cas1-mediated target DNA cleavage by the ICP1 CRISPR-Cas system. Together, these data support an unprecedented model in which Cas1 mediates the interference stage in a phage-encoded CRISPR-Cas system and the study also sheds light on a unique model of primed adaptation.
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Affiliation(s)
- Laixing Zhang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Hao Wang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jianwei Zeng
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xueli Cao
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Zhengyu Gao
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Zihe Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Feixue Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jiawei Wang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yi Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
| | - Maojun Yang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
- SUSTech Cryo-EM Facility Center, Southern University of Science and Technology, Shenzhen, China.
| | - Yue Feng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
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8
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Dong Y, Chen WH, Zhao XM. VirRep: a hybrid language representation learning framework for identifying viruses from human gut metagenomes. Genome Biol 2024; 25:177. [PMID: 38965579 PMCID: PMC11229495 DOI: 10.1186/s13059-024-03320-9] [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: 12/18/2023] [Accepted: 06/24/2024] [Indexed: 07/06/2024] Open
Abstract
Identifying viruses from metagenomes is a common step to explore the virus composition in the human gut. Here, we introduce VirRep, a hybrid language representation learning framework, for identifying viruses from human gut metagenomes. VirRep combines a context-aware encoder and an evolution-aware encoder to improve sequence representation by incorporating k-mer patterns and sequence homologies. Benchmarking on both simulated and real datasets with varying viral proportions demonstrates that VirRep outperforms state-of-the-art methods. When applied to fecal metagenomes from a colorectal cancer cohort, VirRep identifies 39 high-quality viral species associated with the disease, many of which cannot be detected by existing methods.
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Affiliation(s)
- Yanqi Dong
- Department of Neurology, Zhongshan Hospital and Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
- Institution of Medical Artificial Intelligence, Binzhou Medical University, Yantai, 264003, China.
| | - Xing-Ming Zhao
- Department of Neurology, Zhongshan Hospital and Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China.
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, China.
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China.
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9
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Santoriello FJ, Bassler BL. The LuxO-OpaR quorum-sensing cascade differentially controls Vibriophage VP882 lysis-lysogeny decision making in liquid and on surfaces. PLoS Genet 2024; 20:e1011243. [PMID: 39078816 PMCID: PMC11315295 DOI: 10.1371/journal.pgen.1011243] [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: 04/01/2024] [Revised: 08/09/2024] [Accepted: 07/12/2024] [Indexed: 08/10/2024] Open
Abstract
Quorum sensing (QS) is a process of cell-to-cell communication that bacteria use to synchronize collective behaviors. QS relies on the production, release, and group-wide detection of extracellular signaling molecules called autoinducers. Vibrios use two QS systems: the LuxO-OpaR circuit and the VqmA-VqmR circuit. Both QS circuits control group behaviors including biofilm formation and surface motility. The Vibrio parahaemolyticus temperate phage φVP882 encodes a VqmA homolog (called VqmAφ). When VqmAφ is produced by φVP882 lysogens, it binds to the host-produced autoinducer called DPO and launches the φVP882 lytic cascade. This activity times induction of lysis with high host cell density and presumably promotes maximal phage transmission to new cells. Here, we explore whether, in addition to induction from lysogeny, QS controls the initial establishment of lysogeny by φVP882 in naïve host cells. Using mutagenesis, phage infection assays, and phenotypic analyses, we show that φVP882 connects its initial lysis-lysogeny decision to both host cell density and whether the host resides in liquid or on a surface. Host cells in the low-cell-density QS state primarily undergo lysogenic conversion. The QS regulator LuxO~P promotes φVP882 lysogenic conversion of low-cell-density planktonic host cells. By contrast, the ScrABC surface-sensing system regulates lysogenic conversion of low-cell-density surface-associated host cells. ScrABC controls the abundance of the second messenger molecule cyclic diguanylate, which in turn, modulates motility. The scrABC operon is only expressed when its QS repressor, OpaR, is absent. Thus, at low cell density, QS-dependent derepression of scrABC drives lysogenic conversion in surface-associated host cells. These results demonstrate that φVP882 integrates cues from multiple sensory pathways into its lifestyle decision making upon infection of a new host cell.
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Affiliation(s)
- Francis J. Santoriello
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Bonnie L. Bassler
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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10
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Wu Q, An N, Fang Z, Li S, Xiang L, Liu Q, Tan L, Weng Q. Characteristics and whole-genome analysis of a novel Pseudomonas syringae pv. tomato bacteriophage D6 isolated from a karst cave. Virus Genes 2024; 60:295-308. [PMID: 38594490 PMCID: PMC11139720 DOI: 10.1007/s11262-024-02064-9] [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: 03/17/2023] [Accepted: 03/01/2024] [Indexed: 04/11/2024]
Abstract
Pseudomonas syringae is a gram-negative plant pathogen that infects plants such as tomato and poses a threat to global crop production. In this study, a novel lytic phage infecting P. syringae pv. tomato DC3000, named phage D6, was isolated and characterized from sediments in a karst cave. The latent period of phage D6 was found to be 60 min, with a burst size of 16 plaque-forming units per cell. Phage D6 was stable at temperatures between 4 and 40 °C but lost infectivity when heated to 70 °C. Its infectivity was unaffected at pH 6-10 but became inactivated at pH ≤ 5 or ≥ 12. The genome of phage D6 is a linear double-stranded DNA of 307,402 bp with a G + C content of 48.43%. There is a codon preference between phage D6 and its host, and the translation of phage D6 gene may not be entirely dependent on the tRNA library provided by the host. A total of 410 open reading frames (ORFs) and 14 tRNAs were predicted in its genome, with 92 ORFs encoding proteins with predicted functions. Phage D6 showed low genomic similarity to known phage genomes in the GenBank and Viral sequence databases. Genomic and phylogenetic analyses revealed that phage D6 is a novel phage. The tomato plants were first injected with phage D6, and subsequently with Pst DC3000, using the foliar spraying and root drenching inoculum approach. Results obtained after 14 days indicated that phage D6 inoculation decreased P. syringae-induced symptoms in tomato leaves and inhibited the pathogen's growth in the leaves. The amount of Pst DC3000 was reduced by 150- and 263-fold, respectively. In conclusion, the lytic phage D6 identified in this study belongs to a novel phage within the Caudoviricetes class and has potential for use in biological control of plant diseases.
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Affiliation(s)
- Qingshan Wu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Ni An
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Zheng Fang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Shixia Li
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Lan Xiang
- Qiannan Normal College for Nationalities, Duyun, 558000, People's Republic of China
| | - Qiuping Liu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Leitao Tan
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China.
- Qiannan Normal College for Nationalities, Duyun, 558000, People's Republic of China.
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11
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Li X, Chen T, Ren Q, Lu J, Cao S, Liu C, Li Y. Phages in sludge from the A/O wastewater treatment process play an important role in the transmission of ARGs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:172111. [PMID: 38565354 DOI: 10.1016/j.scitotenv.2024.172111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/24/2024] [Accepted: 03/28/2024] [Indexed: 04/04/2024]
Abstract
Phages can influence the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) through transduction, but their profiles and effects on the transmission of ARGs are unclear, especially in complex swine sludge. In this study, we investigated the characterization of phage and ARG profiles in sludge generated from anoxic/oxic (A/O) wastewater treatment processes on swine farms using metagenomes and viromes. The results demonstrated that 205-221 subtypes of ARGs could be identified in swine sludge, among which sul1, tet(M), and floR were the dominant ARGs, indicating that sludge is an important reservoir of ARGs, especially in sludge (S) tanks. The greater abundance of mobile genetic elements (MGEs) in the S tank could significantly contribute to the greater abundance of ARGs there compared to the anoxic (A) and oxic (O) tanks (P < 0.05). However, when we compared the abundances of ARGs and MGEs in the A and O tanks, we observed opposite significant differences (P < 0.05), suggesting that MGEs are not the only factor influencing the abundance of ARGs. The high proportion of lysogenic phages in sludge from the S tank can also have a major impact on the ARG profile. Siphoviridae, Myoviridae, and Podoviridae were the dominant phage families in sludge, and a network diagram of bacteria-ARG-phages revealed that dominant phages and bacteria acted simultaneously as potential hosts for ARGs, which may have led to phage-mediated HGT of ARGs. Therefore, the risk of phage-mediated HGT of ARGs cannot be overlooked.
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Affiliation(s)
- Xiaoting Li
- Phage Research Center, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Tao Chen
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Qinghai Ren
- Phage Research Center, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Jianbiao Lu
- Phage Research Center, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Shengliang Cao
- Phage Research Center, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Cheng Liu
- Phage Research Center, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Yubao Li
- Phage Research Center, Liaocheng University, Liaocheng, Shandong 252000, China.
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12
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Sprenger M, Siemers M, Krautwurst S, Papenfort K. Small RNAs direct attack and defense mechanisms in a quorum sensing phage and its host. Cell Host Microbe 2024; 32:727-738.e6. [PMID: 38579715 DOI: 10.1016/j.chom.2024.03.010] [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: 11/21/2023] [Revised: 02/02/2024] [Accepted: 03/13/2024] [Indexed: 04/07/2024]
Abstract
Many, if not all, bacteria use quorum sensing (QS) to control collective behaviors, and more recently, QS has also been discovered in bacteriophages (phages). Phages can produce communication molecules of their own, or "listen in" on the host's communication processes, to switch between lytic and lysogenic modes of infection. Here, we study the interaction of Vibrio cholerae with the lysogenic phage VP882, which is activated by the QS molecule DPO. We discover that induction of VP882 results in the binding of phage transcripts to the major RNA chaperone Hfq, which in turn outcompetes and downregulates host-encoded small RNAs (sRNAs). VP882 itself also encodes Hfq-binding sRNAs, and we demonstrate that one of these sRNAs, named VpdS, promotes phage replication by regulating host and phage mRNA levels. We further show that host-encoded sRNAs can antagonize phage replication by downregulating phage mRNA expression and thus might be part of the host's phage defense arsenal.
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Affiliation(s)
- Marcel Sprenger
- Friedrich Schiller University, Institute of Microbiology, 07745 Jena, Germany
| | - Malte Siemers
- Friedrich Schiller University, Institute of Microbiology, 07745 Jena, Germany; Microverse Cluster, Friedrich Schiller University Jena, 07743 Jena, Germany
| | | | - Kai Papenfort
- Friedrich Schiller University, Institute of Microbiology, 07745 Jena, Germany; Microverse Cluster, Friedrich Schiller University Jena, 07743 Jena, Germany.
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13
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Zhen J, Liu R, Man C, Xu S, Zhang W, Zou L, Liu W, Ni HB, Zou M, He T, Wang R, Zhang XX, Zhang C. Bacteriophage LHE83 targeting OmpA as a receptor exhibited synergism with spectinomycin against Escherichia coli. Poult Sci 2024; 103:103643. [PMID: 38537406 PMCID: PMC10987938 DOI: 10.1016/j.psj.2024.103643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 04/07/2024] Open
Abstract
Understanding the characteristics of bacteriophages is crucial for the optimization of phage therapy. In this study, the biological and genomic characteristics of coliphage LHE83 were determined and its synergistic effects with different types of antibiotics against E. coli E82 were investigated. Phage LHE83 displayed a contractile tail morphology and had a titer of 3.02 × 109 pfu/mL at an optimal MOI of 0.01. Meanwhile, phage LHE83 exhibited good physical and chemical factors tolerance. The 1-step growth analysis revealed a latent period of approx. 10 min with a burst size of 87 pfu/infected cell. Phage LHE83 belongs to the genus Dhakavirus. Its genome consists of 170,464 bp with a 40% GC content, and a total of 268 Open Reading Frames (ORF) were predicted with no detected virulent or resistant genes. ORF 213 was predicted to encode the receptor binding protein (RBP) and confirmed by the antibody-blocking assay. Furthermore, a phage-resistant strain E. coli E82R was generated by co-culturing phage LHE83 with E. coli E82. Genomic analysis revealed that OmpA served as the receptor for phage LHE83, which was further confirmed by phage adsorption assay using E. coli BL21ΔOmpA, E. coli BL21ΔOmpA: OmpA and E. coli BL21:OmpA strains. Additionally, a synergistic effect was observed between phage LHE83 and spectinomycin against the drug-resistant strain E. coli E82. These results provide a theoretical basis for understanding the interactions between phages, antibiotics, and host bacteria, which can assist in the clinical application of phages and antibiotics against drug-resistant bacteria.
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Affiliation(s)
- Jianyu Zhen
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Rui Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Cheng Man
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Shijie Xu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Wenxiu Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Ling Zou
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Wenhua Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Hong-Bo Ni
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Ming Zou
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Tao He
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Ran Wang
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiao-Xuan Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Can Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China.
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14
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Martínez M, Rizzuto I, Molina R. Knowing Our Enemy in the Antimicrobial Resistance Era: Dissecting the Molecular Basis of Bacterial Defense Systems. Int J Mol Sci 2024; 25:4929. [PMID: 38732145 PMCID: PMC11084316 DOI: 10.3390/ijms25094929] [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: 03/20/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
Bacteria and their phage adversaries are engaged in an ongoing arms race, resulting in the development of a broad antiphage arsenal and corresponding viral countermeasures. In recent years, the identification and utilization of CRISPR-Cas systems have driven a renewed interest in discovering and characterizing antiphage mechanisms, revealing a richer diversity than initially anticipated. Currently, these defense systems can be categorized based on the bacteria's strategy associated with the infection cycle stage. Thus, bacterial defense systems can degrade the invading genetic material, trigger an abortive infection, or inhibit genome replication. Understanding the molecular mechanisms of processes related to bacterial immunity has significant implications for phage-based therapies and the development of new biotechnological tools. This review aims to comprehensively cover these processes, with a focus on the most recent discoveries.
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Affiliation(s)
| | | | - Rafael Molina
- Department of Crystallography and Structural Biology, Instituto de Química-Física Blas Cabrera, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
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15
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Chen T, Mo C, Yuan Y, Li S, Wu Y, Liao X, Yang Y. Short-, long-read metagenome and virome reveal the profile of phage-mediated ARGs in anoxic-oxic processes for swine wastewater treatment. JOURNAL OF HAZARDOUS MATERIALS 2024; 468:133789. [PMID: 38394893 DOI: 10.1016/j.jhazmat.2024.133789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 02/06/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024]
Abstract
Phages are among the most widely spread viruses, but their profiles and the antibiotic resistance genes (ARGs) they carry in swine wastewater remain underexplored. The present study investigated the distribution characteristics of phages and their ARG risk in anoxic/oxic (A/O) wastewater treatment processes of swine farms using short- and long-read metagenome and virome. The results demonstrated that the virome could extract more phage sequences than the total metagenome; thus, it was more suited for studying phages in wastewater settings. Intriguingly, phages had significantly lower abundance of ARG than ARGs harbored by total microorganisms (P < 0.01). Eleven ARGs co-occurred with phages and bacteria (R > 0.6 and P < 0.05), with Siphoviridae being the phage co-occurring with the most ARGs (5). Horizontal gene transfer (HGT) events were observed between Proteobacteria and the major phyla except for Bacteroidota. Furthermore, there were prophage sequences and ARGs on the same contig in bacterial MAGs. These data strongly demonstrate that phages promote horizontal transfer of ARG between bacterial hosts in A/O processes for swine wastewater treatment. Therefore, the risk of phage-mediated horizontal transfer of ARGs cannot be overlooked despite the low abundance of phage ARGs (pARG).
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Affiliation(s)
- Tao Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Chunhao Mo
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Yilin Yuan
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Shengjie Li
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Yinbao Wu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Xindi Liao
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Yiwen Yang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China.
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16
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Wang X, Tang Y, Yue X, Wang S, Yang K, Xu Y, Shen Q, Friman VP, Wei Z. The role of rhizosphere phages in soil health. FEMS Microbiol Ecol 2024; 100:fiae052. [PMID: 38678007 PMCID: PMC11065364 DOI: 10.1093/femsec/fiae052] [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: 12/31/2023] [Revised: 03/22/2024] [Accepted: 04/25/2024] [Indexed: 04/29/2024] Open
Abstract
While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups-bacterial viruses, i.e. phages-has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation, and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness, and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.
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Affiliation(s)
- Xiaofang Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Yike Tang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiufeng Yue
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuo Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Keming Yang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Yangchun Xu
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Qirong Shen
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Ville-Petri Friman
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Department of Microbiology, University of Helsinki, 00014 Helsinki, Finland
| | - Zhong Wei
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
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17
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Zhao J, Han M, Ma A, Jiang F, Chen R, Dong Y, Wang X, Ruan S, Chen Y. A machine vision-assisted Argonaute-mediated fluorescence biosensor for the detection of viable Salmonella in food without convoluted DNA extraction and amplification procedures. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133648. [PMID: 38306835 DOI: 10.1016/j.jhazmat.2024.133648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/17/2024] [Accepted: 01/26/2024] [Indexed: 02/04/2024]
Abstract
The precise identification viable pathogens hold paramount significance in the prevention of foodborne diseases outbreaks. In this study, we integrated machine vision and learning with single microsphere to develop a phage and Clostridium butyricum Argonaute (CbAgo)-mediated fluorescence biosensor for detecting viable Salmonella typhimurium (S. typhimurium) without convoluted DNA extraction and amplification procedures. Phage and lysis buffer was utilized to capture and lyse viable S. typhimurium, respectively. Subsequently, CbAgo can cleave the bacterial DNA to obtain target DNA that guides a newly targeted cleavage of fluorescent probes. After that, the resulting fluorescent signal accumulates on the streptavidin-modified single microsphere. The overall detection process is then analyzed and interpreted by machine vision and learning algorithms, achieving highly sensitive detection of S. typhimurium with a limit of detection at 40.5 CFU/mL and a linear range of 50-107 CFU/mL. Furthermore, the proposed biosensor demonstrates standard recovery rates and coefficients of variation at 93.22% - 106.02% and 1.47% - 12.75%, respectively. This biosensor exhibits exceptional sensitivity and selectivity, presenting a promising method for the rapid and effective detection of foodborne pathogens. ENVIRONMENTAL IMPLICATION: Bacterial pathogens exist widely in the environment and seriously threaten the safety of human life. In this study, we developed a phage and Clostridium butyricum Argonaute-mediated fluorescence biosensor for the detection of viable Salmonella typhimurium in environmental water and food samples. Compared with other Salmonella detection methods, this method does not need complex DNA extraction and amplification steps, which reduces the use of chemical reagents and experimental consumables in classic DNA extraction kit methods.
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Affiliation(s)
- Junpeng Zhao
- College of Food Science and Technology, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China
| | - Minjie Han
- College of Food Science and Technology, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China
| | - Aimin Ma
- College of Food Science and Technology, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China
| | - Feng Jiang
- Key Laboratory of Detection Technology of Focus Chemical Hazards in Animal-derived Food for State Market Regulation, Wuhan 430075, Hubei, China
| | - Rui Chen
- College of Food Science and Technology, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China
| | - Yongzhen Dong
- State Key Laboratory of Marine Food Processing and Safety Control, Dalian Polytechnic University, Dalian 116034, Liaoning, China
| | - Xufeng Wang
- College of Food Science and Technology, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China
| | - Shilong Ruan
- Daye Public Inspection and Test Center, Daye 435100, Hubei, China
| | - Yiping Chen
- State Key Laboratory of Marine Food Processing and Safety Control, Dalian Polytechnic University, Dalian 116034, Liaoning, China.
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18
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Wang M, Zhang J, Wei J, Jiang L, Jiang L, Sun Y, Zeng Z, Wang Z. Phage-inspired strategies to combat antibacterial resistance. Crit Rev Microbiol 2024; 50:196-211. [PMID: 38400715 DOI: 10.1080/1040841x.2023.2181056] [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: 12/09/2022] [Accepted: 02/07/2023] [Indexed: 02/25/2023]
Abstract
Antimicrobial resistance (AMR) in clinically priority pathogensis now a major threat to public health worldwide. Phages are bacterial parasites that efficiently infect or kill specific strains and represent the most abundant biological entities on earth, showing great attraction as potential antibacterial therapeutics in combating AMR. This review provides a summary of phage-inspired strategies to combat AMR. We firstly cover the phage diversity, and then explain the biological principles of phage therapy that support the use of phages in the post-antimicrobial era. Furthermore, we state the versatility methods of phage therapy both from direct access as well as collateral access. Among the direct access approaches, we discuss the use of phage cocktail therapy, phage-encoded endolysins and the bioengineering for function improvement of used phages or endolysins. On the other hand, we introduce the collateral access, including the phages antimicrobial immunity combined therapy and phage-based novel antibacterial mimic molecules. Nowadays, more and more talented and enthusiastic scientist, doctors, pharmacists, media, authorities, and industry are promoting the progress of phage therapy, and proposed more phages-inspired strategy to make them more tractable to combat AMR and benefit more people, more animal and diverse environment in "one health" framework.
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Affiliation(s)
- Mianzhi Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Junxuan Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jingyi Wei
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Lei Jiang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Li Jiang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yongxue Sun
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhenling Zeng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou, China
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19
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Putzeys L, Wicke L, Boon M, van Noort V, Vogel J, Lavigne R. Refining the transcriptional landscapes for distinct clades of virulent phages infecting Pseudomonas aeruginosa. MICROLIFE 2024; 5:uqae002. [PMID: 38444699 PMCID: PMC10914365 DOI: 10.1093/femsml/uqae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/24/2024] [Accepted: 02/27/2024] [Indexed: 03/07/2024]
Abstract
The introduction of high-throughput sequencing has resulted in a surge of available bacteriophage genomes, unveiling their tremendous genomic diversity. However, our current understanding of the complex transcriptional mechanisms that dictate their gene expression during infection is limited to a handful of model phages. Here, we applied ONT-cappable-seq to reveal the transcriptional architecture of six different clades of virulent phages infecting Pseudomonas aeruginosa. This long-read microbial transcriptomics approach is tailored to globally map transcription start and termination sites, transcription units, and putative RNA-based regulators on dense phage genomes. Specifically, the full-length transcriptomes of LUZ19, LUZ24, 14-1, YuA, PAK_P3, and giant phage phiKZ during early, middle, and late infection were collectively charted. Beyond pinpointing traditional promoter and terminator elements and transcription units, these transcriptional profiles provide insights in transcriptional attenuation and splicing events and allow straightforward validation of Group I intron activity. In addition, ONT-cappable-seq data can guide genome-wide discovery of novel regulatory element candidates, including noncoding RNAs and riboswitches. This work substantially expands the number of annotated phage-encoded transcriptional elements identified to date, shedding light on the intricate and diverse gene expression regulation mechanisms in Pseudomonas phages, which can ultimately be sourced as tools for biotechnological applications in phage and bacterial engineering.
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Affiliation(s)
- Leena Putzeys
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
| | - Laura Wicke
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
| | - Vera van Noort
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Jörg Vogel
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
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20
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Huang H, Jiang J, Wang X, Jiang K, Cao H. Exposure to prescribed medication in early life and impacts on gut microbiota and disease development. EClinicalMedicine 2024; 68:102428. [PMID: 38312240 PMCID: PMC10835216 DOI: 10.1016/j.eclinm.2024.102428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/31/2023] [Accepted: 01/05/2024] [Indexed: 02/06/2024] Open
Abstract
The gut microbiota during early life plays a crucial role in infant development. This microbial-host interaction is also essential for metabolism, immunity, and overall human health in later life. Early-life pharmaceutical exposure, mainly referring to exposure during pregnancy, childbirth, and infancy, may change the structure and function of gut microbiota and affect later human health. In this Review, we describe how healthy gut microbiota is established in early life. We summarise the commonly prescribed medications during early life, including antibiotics, acid suppressant medications and other medications such as antidepressants, analgesics and steroid hormones, and discuss how these medication-induced changes in gut microbiota are involved in the pathological process of diseases, including infections, inflammatory bowel disease, metabolic diseases, allergic diseases and neurodevelopmental disorders. Finally, we review some critical methods such as dietary therapy, probiotics, prebiotics, faecal microbiota transplantation, genetically engineered phages, and vagus nerve stimulation in early life, aiming to provide a new strategy for the prevention of adverse health outcomes caused by prescribed medications exposure in early life.
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Affiliation(s)
- Huan Huang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
- Department of Gastroenterology, the Affiliated Jinyang Hospital of Guizhou Medical University, the Second People's Hospital of Guiyang, Guiyang, China
| | - Jiayin Jiang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xinyu Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Kui Jiang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Hailong Cao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
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21
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Ruan S, Tu CH, Bourne CR. Friend or Foe: Protein Inhibitors of DNA Gyrase. BIOLOGY 2024; 13:84. [PMID: 38392303 PMCID: PMC10886550 DOI: 10.3390/biology13020084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/20/2024] [Accepted: 01/26/2024] [Indexed: 02/24/2024]
Abstract
DNA gyrase is essential for the successful replication of circular chromosomes, such as those found in most bacterial species, by relieving topological stressors associated with unwinding the double-stranded genetic material. This critical central role makes gyrase a valued target for antibacterial approaches, as exemplified by the highly successful fluoroquinolone class of antibiotics. It is reasonable that the activity of gyrase could be intrinsically regulated within cells, thereby helping to coordinate DNA replication with doubling times. Numerous proteins have been identified to exert inhibitory effects on DNA gyrase, although at lower doses, it can appear readily reversible and therefore may have regulatory value. Some of these, such as the small protein toxins found in plasmid-borne addiction modules, can promote cell death by inducing damage to DNA, resulting in an analogous outcome as quinolone antibiotics. Others, however, appear to transiently impact gyrase in a readily reversible and non-damaging mechanism, such as the plasmid-derived Qnr family of DNA-mimetic proteins. The current review examines the origins and known activities of protein inhibitors of gyrase and highlights opportunities to further exert control over bacterial growth by targeting this validated antibacterial target with novel molecular mechanisms. Furthermore, we are gaining new insights into fundamental regulatory strategies of gyrase that may prove important for understanding diverse growth strategies among different bacteria.
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Affiliation(s)
- Shengfeng Ruan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Chih-Han Tu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Christina R Bourne
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
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22
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Lou YC, Chen L, Borges AL, West-Roberts J, Firek BA, Morowitz MJ, Banfield JF. Infant gut DNA bacteriophage strain persistence during the first 3 years of life. Cell Host Microbe 2024; 32:35-47.e6. [PMID: 38096814 PMCID: PMC11156429 DOI: 10.1016/j.chom.2023.11.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/27/2023] [Accepted: 11/16/2023] [Indexed: 01/13/2024]
Abstract
Bacteriophages are key components of gut microbiomes, yet the phage colonization process in the infant gut remains uncertain. Here, we establish a large phage sequence database and use strain-resolved analyses to investigate DNA phage succession in infants throughout the first 3 years of life. Analysis of 819 fecal metagenomes collected from 28 full-term and 24 preterm infants and their mothers revealed that early-life phageome richness increases over time and reaches adult-like complexity by age 3. Approximately 9% of early phage colonizers, which are mostly maternally transmitted and infect Bacteroides, persist for 3 years and are more prevalent in full-term than in preterm infants. Although rare, phages with stop codon reassignment are more likely to persist than non-recoded phages and generally display an increase in in-frame reassigned stop codons over 3 years. Overall, maternal seeding, stop codon reassignment, host CRISPR-Cas locus prevalence, and diverse phage populations contribute to stable viral colonization.
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Affiliation(s)
- Yue Clare Lou
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - LinXing Chen
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94709, USA
| | - Adair L Borges
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jacob West-Roberts
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Brian A Firek
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Michael J Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA.
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23
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Rossi FPN, Flores VS, Uceda-Campos G, Amgarten DE, Setubal JC, da Silva AM. Comparative Analyses of Bacteriophage Genomes. Methods Mol Biol 2024; 2802:427-453. [PMID: 38819567 DOI: 10.1007/978-1-0716-3838-5_14] [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] [Indexed: 06/01/2024]
Abstract
Bacterial viruses (bacteriophages or phages) are the most abundant and diverse biological entities on Earth. There is a renewed worldwide interest in phage-centered research motivated by their enormous potential as antimicrobials to cope with multidrug-resistant pathogens. An ever-growing number of complete phage genomes are becoming available, derived either from newly isolated phages (cultivated phages) or recovered from metagenomic sequencing data (uncultivated phages). Robust comparative analysis is crucial for a comprehensive understanding of genotypic variations of phages and their related evolutionary processes, and to investigate the interaction mechanisms between phages and their hosts. In this chapter, we present a protocol for phage comparative genomics employing tools selected out of the many currently available, focusing on complete genomes of phages classified in the class Caudoviricetes. This protocol provides accurate identification of similarities, differences, and patterns among new and previously known complete phage genomes as well as phage clustering and taxonomic classification.
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Affiliation(s)
| | - Vinicius Sousa Flores
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil
| | - Guillermo Uceda-Campos
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil
| | | | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil
| | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil.
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24
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Fujiki J, Schnabl B. Phage therapy: Targeting intestinal bacterial microbiota for the treatment of liver diseases. JHEP Rep 2023; 5:100909. [PMID: 37965159 PMCID: PMC10641246 DOI: 10.1016/j.jhepr.2023.100909] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 11/16/2023] Open
Abstract
Phage therapy has been overshadowed by antibiotics for decades. However, it is being revisited as a powerful approach against antimicrobial-resistant bacteria. As bacterial microbiota have been mechanistically linked to gastrointestinal and liver diseases, precise editing of the gut microbiota via the selective bactericidal action of phages has prompted renewed interest in phage therapy. In this review, we summarise the basic virological properties of phages and the latest findings on the composition of the intestinal phageome and the changes associated with liver diseases. We also review preclinical and clinical studies assessing phage therapy for the treatment of gastrointestinal and liver diseases, as well as future prospects and challenges.
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Affiliation(s)
- Jumpei Fujiki
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan
| | - 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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25
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Smug BJ, Szczepaniak K, Rocha EPC, Dunin-Horkawicz S, Mostowy RJ. Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with bacterial hosts. Nat Commun 2023; 14:7460. [PMID: 38016962 PMCID: PMC10684548 DOI: 10.1038/s41467-023-43236-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 11/03/2023] [Indexed: 11/30/2023] Open
Abstract
Biological modularity enhances evolutionary adaptability. This principle is vividly exemplified by bacterial viruses (phages), which display extensive genomic modularity. Phage genomes are composed of independent functional modules that evolve separately and recombine in various configurations. While genomic modularity in phages has been extensively studied, less attention has been paid to protein modularity-proteins consisting of distinct building blocks that can evolve and recombine, enhancing functional and genetic diversity. Here, we use a set of 133,574 representative phage proteins and highly sensitive homology detection to capture instances of domain mosaicism, defined as fragment sharing between two otherwise unrelated proteins, and to understand its relationship with functional diversity in phage genomes. We discover that unrelated proteins from diverse functional classes frequently share homologous domains. This phenomenon is particularly pronounced within receptor-binding proteins, endolysins, and DNA polymerases. We also identify multiple instances of recent diversification via domain shuffling in receptor-binding proteins, neck passage structures, endolysins and some members of the core replication machinery, often transcending distant taxonomic and ecological boundaries. Our findings suggest that ongoing diversification via domain shuffling is reflective of a co-evolutionary arms race, driven by the need to overcome various bacterial resistance mechanisms against phages.
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Affiliation(s)
- Bogna J Smug
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Stanislaw Dunin-Horkawicz
- Institute of Evolutionary Biology, Faculty of Biology & Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Rafał J Mostowy
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
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26
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Oh H, Koo J, An SY, Hong SH, Suh JY, Bae E. Structural and functional investigation of GajB protein in Gabija anti-phage defense. Nucleic Acids Res 2023; 51:11941-11951. [PMID: 37897358 PMCID: PMC10681800 DOI: 10.1093/nar/gkad951] [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: 06/01/2023] [Revised: 09/13/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
Bacteriophages (phages) are viruses that infect bacteria and archaea. To fend off invading phages, the hosts have evolved a variety of anti-phage defense mechanisms. Gabija is one of the most abundant prokaryotic antiviral systems and consists of two proteins, GajA and GajB. GajA has been characterized experimentally as a sequence-specific DNA endonuclease. Although GajB was previously predicted to be a UvrD-like helicase, its function is unclear. Here, we report the results of structural and functional analyses of GajB. The crystal structure of GajB revealed a UvrD-like domain architecture, including two RecA-like core and two accessory subdomains. However, local structural elements that are important for the helicase function of UvrD are not conserved in GajB. In functional assays, GajB did not unwind or bind various types of DNA substrates. We demonstrated that GajB interacts with GajA to form a heterooctameric Gabija complex, but GajB did not exhibit helicase activity when bound to GajA. These results advance our understanding of the molecular mechanism underlying Gabija anti-phage defense and highlight the role of GajB as a component of a multi-subunit antiviral complex in bacteria.
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Affiliation(s)
- Hyejin Oh
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Jasung Koo
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - So Young An
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Sung-Hyun Hong
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Jeong-Yong Suh
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Euiyoung Bae
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
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27
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Chen R, Zhao J, Han M, Dong Y, Jiang F, Chen Y. DNA Extraction- and Amplification-Free Nucleic Acid Biosensor for the Detection of Foodborne Pathogens Based on CRISPR/Cas12a and Argonaute Protein-Mediated Cascade Signal Amplification. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18037-18045. [PMID: 37947312 DOI: 10.1021/acs.jafc.3c06530] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
A novel method for detecting low levels of viable foodborne pathogens, specifically Salmonella typhimurium (S. typhimurium), has been developed. Traditional nucleic acid assay, such as polymerase chain reaction (PCR), often requires complex DNA extraction and amplification, making it challenging to differentiate between viable and nonviable pathogens. This assay employed a phage as the recognition element to precisely identify and lyse viable S. typhimurium that can undergo DNA extraction. It combined the efficient trans-cleavage activities of CRISPR/Cas12a with the specific cleavage advantages of Argonaute proteins, enabling ultrasensitive detection. This double-enzyme-mediated nucleic acid test can accurately distinguish viable and nonviable S. typhimurium with a detection limit of 23 CFU/mL without DNA amplification. The method was successfully applied to common food samples, producing results consistent with quantitative PCR tests. This work provides a promising platform for easily detecting viable foodborne pathogens with high sensitivity without the need for DNA extraction and amplification.
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Affiliation(s)
- Rui Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Junpeng Zhao
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Minjie Han
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yongzhen Dong
- State Key Laboratory of Marine Food Processing and Safety Control, Dalian Polytechnic University, Dalian, Liaoning 116034, China
| | - Feng Jiang
- Key Laboratory of Detection Technology of Focus Chemical Hazards in Animal-derived Food for State Market Regulation, Wuhan 430075, China
| | - Yiping Chen
- State Key Laboratory of Marine Food Processing and Safety Control, Dalian Polytechnic University, Dalian, Liaoning 116034, China
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28
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Fujiki J, Nakamura K, Nakamura T, Iwano H. Fitness Trade-Offs between Phage and Antibiotic Sensitivity in Phage-Resistant Variants: Molecular Action and Insights into Clinical Applications for Phage Therapy. Int J Mol Sci 2023; 24:15628. [PMID: 37958612 PMCID: PMC10650657 DOI: 10.3390/ijms242115628] [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: 10/06/2023] [Revised: 10/23/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
In recent decades, phage therapy has been overshadowed by the widespread use of antibiotics in Western countries. However, it has been revitalized as a powerful approach due to the increasing prevalence of antimicrobial-resistant bacteria. Although bacterial resistance to phages has been reported in clinical cases, recent studies on the fitness trade-offs between phage and antibiotic resistance have revealed new avenues in the field of phage therapy. This strategy aims to restore the antibiotic susceptibility of antimicrobial-resistant bacteria, even if phage-resistant variants develop. Here, we summarize the basic virological properties of phages and their applications within the context of antimicrobial resistance. In addition, we review the occurrence of phage resistance in clinical cases, and examine fitness trade-offs between phage and antibiotic sensitivity, exploring the potential of an evolutionary fitness cost as a countermeasure against phage resistance in therapy. Finally, we discuss future strategies and directions for phage-based therapy from the aspect of fitness trade-offs. This approach is expected to provide robust options when combined with antibiotics in this era of phage 're'-discovery.
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Affiliation(s)
- Jumpei Fujiki
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Keisuke Nakamura
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan
| | - Tomohiro Nakamura
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan
- Phage Therapy Institute, Waseda University, Tokyo 169-8050, Japan
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
- Department of Veterinary Medicine, Azabu University, Sagamihara 252-5201, Japan
| | - Hidetomo Iwano
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan
- Phage Therapy Institute, Waseda University, Tokyo 169-8050, Japan
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29
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Heiman CM, Vacheron J, Keel C. Evolutionary and ecological role of extracellular contractile injection systems: from threat to weapon. Front Microbiol 2023; 14:1264877. [PMID: 37886057 PMCID: PMC10598620 DOI: 10.3389/fmicb.2023.1264877] [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: 07/21/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
Contractile injection systems (CISs) are phage tail-related structures that are encoded in many bacterial genomes. These devices encompass the cell-based type VI secretion systems (T6SSs) as well as extracellular CISs (eCISs). The eCISs comprise the R-tailocins produced by various bacterial species as well as related phage tail-like structures such as the antifeeding prophages (Afps) of Serratia entomophila, the Photorhabdus virulence cassettes (PVCs), and the metamorphosis-associated contractile structures (MACs) of Pseudoalteromonas luteoviolacea. These contractile structures are released into the extracellular environment upon suicidal lysis of the producer cell and play important roles in bacterial ecology and evolution. In this review, we specifically portray the eCISs with a focus on the R-tailocins, sketch the history of their discovery and provide insights into their evolution within the bacterial host, their structures and how they are assembled and released. We then highlight ecological and evolutionary roles of eCISs and conceptualize how they can influence and shape bacterial communities. Finally, we point to their potential for biotechnological applications in medicine and agriculture.
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Affiliation(s)
- Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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30
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Georjon H, Bernheim A. The highly diverse antiphage defence systems of bacteria. Nat Rev Microbiol 2023; 21:686-700. [PMID: 37460672 DOI: 10.1038/s41579-023-00934-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 09/14/2023]
Abstract
Bacteria and their viruses have coevolved for billions of years. This ancient and still ongoing arms race has led bacteria to develop a vast antiphage arsenal. The development of high-throughput screening methods expanded our knowledge of defence systems from a handful to more than a hundred systems, unveiling many different molecular mechanisms. These findings reveal that bacterial immunity is much more complex than previously thought. In this Review, we explore recently discovered bacterial antiphage defence systems, with a particular focus on their molecular diversity, and discuss the ecological and evolutionary drivers and implications of the existing diversity of antiphage defence mechanisms.
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Affiliation(s)
- Héloïse Georjon
- Molecular Diversity of Microbes Lab, Institut Pasteur, Université Paris Cité, INSERM, Paris, France
| | - Aude Bernheim
- Molecular Diversity of Microbes Lab, Institut Pasteur, Université Paris Cité, INSERM, Paris, France.
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31
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Silpe JE, Duddy OP, Johnson GE, Beggs GA, Hussain FA, Forsberg KJ, Bassler BL. Small protein modules dictate prophage fates during polylysogeny. Nature 2023; 620:625-633. [PMID: 37495698 PMCID: PMC10432266 DOI: 10.1038/s41586-023-06376-y] [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: 09/16/2022] [Accepted: 06/27/2023] [Indexed: 07/28/2023]
Abstract
Most bacteria in the biosphere are predicted to be polylysogens harbouring multiple prophages1-5. In studied systems, prophage induction from lysogeny to lysis is near-universally driven by DNA-damaging agents6. Thus, how co-residing prophages compete for cell resources if they respond to an identical trigger is unknown. Here we discover regulatory modules that control prophage induction independently of the DNA-damage cue. The modules bear little resemblance at the sequence level but share a regulatory logic by having a transcription factor that activates the expression of a neighbouring gene that encodes a small protein. The small protein inactivates the master repressor of lysis, which leads to induction. Polylysogens that harbour two prophages exposed to DNA damage release mixed populations of phages. Single-cell analyses reveal that this blend is a consequence of discrete subsets of cells producing one, the other or both phages. By contrast, induction through the DNA-damage-independent module results in cells producing only the phage sensitive to that specific cue. Thus, in the polylysogens tested, the stimulus used to induce lysis determines phage productivity. Considering the lack of potent DNA-damaging agents in natural habitats, additional phage-encoded sensory pathways to lysis likely have fundamental roles in phage-host biology and inter-prophage competition.
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Affiliation(s)
- Justin E Silpe
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Olivia P Duddy
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Grace E Johnson
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Grace A Beggs
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Fatima A Hussain
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kevin J Forsberg
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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Gonzales MEM, Ureta JC, Shrestha AMS. Protein embeddings improve phage-host interaction prediction. PLoS One 2023; 18:e0289030. [PMID: 37486915 PMCID: PMC10365317 DOI: 10.1371/journal.pone.0289030] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/07/2023] [Indexed: 07/26/2023] Open
Abstract
With the growing interest in using phages to combat antimicrobial resistance, computational methods for predicting phage-host interactions have been explored to help shortlist candidate phages. Most existing models consider entire proteomes and rely on manual feature engineering, which poses difficulty in selecting the most informative sequence properties to serve as input to the model. In this paper, we framed phage-host interaction prediction as a multiclass classification problem that takes as input the embeddings of a phage's receptor-binding proteins, which are known to be the key machinery for host recognition, and predicts the host genus. We explored different protein language models to automatically encode these protein sequences into dense embeddings without the need for additional alignment or structural information. We show that the use of embeddings of receptor-binding proteins presents improvements over handcrafted genomic and protein sequence features. The highest performance was obtained using the transformer-based protein language model ProtT5, resulting in a 3% to 4% increase in weighted F1 and recall scores across different prediction confidence thresholds, compared to using selected handcrafted sequence features.
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Affiliation(s)
- Mark Edward M Gonzales
- Bioinformatics Laboratory, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, Philippines
- Department of Software Technology, College of Computer Studies, De La Salle University, Manila, Philippines
| | - Jennifer C Ureta
- Bioinformatics Laboratory, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, Philippines
- Department of Software Technology, College of Computer Studies, De La Salle University, Manila, Philippines
| | - Anish M S Shrestha
- Bioinformatics Laboratory, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, Philippines
- Systems and Computational Biology Research Unit, Center for Natural Sciences and Environmental Research, De La Salle University, Manila, Philippines
- Department of Software Technology, College of Computer Studies, De La Salle University, Manila, Philippines
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Nguyen TVP, Wu Y, Yao T, Trinh JT, Zeng L, Chemla YR, Golding I. CO-INFECTING PHAGES IMPEDE EACH OTHER'S ENTRY INTO THE CELL. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543643. [PMID: 37333217 PMCID: PMC10274716 DOI: 10.1101/2023.06.05.543643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Bacteriophage lambda tunes its propensity to lysogenize based on the number of viral genome copies inside the infected cell. Viral self-counting is believed to serve as a way of inferring the abundance of available hosts in the environment. This interpretation is premised on an accurate mapping between the extracellular phage-to-bacteria ratio and the intracellular multiplicity of infection (MOI). However, here we show this premise to be untrue. By simultaneously labeling phage capsids and genomes, we find that, while the number of phages landing on each cell reliably samples the population ratio, the number of phages entering the cell does not. Single-cell infections, followed in a microfluidic device and interpreted using a stochastic model, reveal that the probability and rate of individual phage entries decrease with MOI. This decrease reflects an MOI-dependent perturbation to host physiology caused by phage landing, evidenced by compromised membrane integrity and loss of membrane potential. The dependence of phage entry dynamics on the surrounding medium is found to result in a strong impact of environmental conditions on the infection outcome, while the protracted entry of co-infecting phages increases the cell-to-cell variability in infection outcome at a given MOI. Our findings demonstrate the previously unappreciated role played by entry dynamics in determining the outcome of bacteriophage infection.
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Affiliation(s)
- Thu Vu Phuc Nguyen
- Department of Physics, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, TX 77030, USA
| | - Yuchen Wu
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Tianyou Yao
- Department of Physics, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Jimmy T. Trinh
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Yann R. Chemla
- Department of Physics, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Ido Golding
- Department of Physics, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, TX 77030, USA
- Department of Microbiology, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
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Zhang Y, Song X, Chen C, Liu L, Xu Y, Zhang N, Huang W, Zheng J, Yuan W, Tang L, Lin Z. Structural insights of the toxin-antitoxin system VPA0770-VPA0769 in Vibrio parahaemolyticus. Int J Biol Macromol 2023:124755. [PMID: 37164131 DOI: 10.1016/j.ijbiomac.2023.124755] [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: 02/24/2023] [Revised: 04/13/2023] [Accepted: 05/02/2023] [Indexed: 05/12/2023]
Abstract
Toxin-antitoxin (TA) systems are involved in both normal bacterial physiology and pathogenicity, including gene regulation, antibiotic resistance, and bacteria persistence under stressful environments. In pathogenic Vibrio parahaemolyticus, however, TA interaction and assembly remain largely unknown. In this work, we identified a new RES-Xre type II TA module, encoded by gene cluster vpa0770-vpa0769 on chromosome II of V. parahaemolyticus. Ectopic expression of the VPA0770 toxin rapidly arrests the growth of E. coli cells, which can be neutralized by co-expression of the VPA0769 antitoxin. To decipher the action mechanism, we determined the crystal structure of the VPA0770-VPA0769 TA complex. VPA0770 and VPA0769 proteins can assemble into two types of large complexes, a W-shaped hetero-hexamer and a donut-like hetero-dodecamer, in a concentration-dependent manner in solution. Disruption of the TA interface results in a loss of the antitoxic phenotype. The toxicity of the VPA0770 toxin, which harbors a NAD+-binding pocket, may be largely ascribed to its highly effective capability to degrade intracellular NAD+. Our study provides a structural basis for a better understanding of diverse molecular mechanisms employed by human pathogens.
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Affiliation(s)
- Yan Zhang
- School of Life Sciences, Tianjin University, Tianjin 300073, China
| | - Xiaojie Song
- School of Life Sciences, Tianjin University, Tianjin 300073, China
| | - Cheng Chen
- School of Life Sciences, Tianjin University, Tianjin 300073, China
| | - Lin Liu
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou 515041, China
| | - Yangyang Xu
- School of Life Sciences, Tianjin University, Tianjin 300073, China
| | - Ning Zhang
- School of Life Sciences, Tianjin University, Tianjin 300073, China
| | - Weidong Huang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Ningxia Medical University, 750004, China
| | - Jun Zheng
- Faculty of Health Sciences, University of Macau, Macao
| | - Wensu Yuan
- School of Life Sciences, Tianjin University, Tianjin 300073, China.
| | - Le Tang
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou 515041, China.
| | - Zhi Lin
- School of Life Sciences, Tianjin University, Tianjin 300073, China.
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Silpe JE, Duddy OP, Bassler BL. Induction mechanisms and strategies underlying interprophage competition during polylysogeny. PLoS Pathog 2023; 19:e1011363. [PMID: 37200239 DOI: 10.1371/journal.ppat.1011363] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Affiliation(s)
- Justin E Silpe
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Olivia P Duddy
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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Wang S, Mirmiran SD, Li X, Li X, Zhang F, Duan X, Gao D, Chen Y, Chen H, Qian P. Temperate phage influence virulence and biofilm-forming of Salmonella Typhimurium and enhance the ability to contaminate food product. Int J Food Microbiol 2023; 398:110223. [PMID: 37120944 DOI: 10.1016/j.ijfoodmicro.2023.110223] [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: 12/25/2022] [Revised: 04/05/2023] [Accepted: 04/18/2023] [Indexed: 05/02/2023]
Abstract
Salmonella is a food-borne zoonotic pathogen that threatens food safety and public health security. Temperate phages can influence bacterial virulence and phenotype and play an important role in bacterial evolution. However, most studies on Salmonella temperate phages focus on prophage induced by bacteria, with few reports on Salmonella temperate phages isolated in the environment. Moreover, whether temperate phages drive bacterial virulence and biofilm formation in food and animal models remains unknown. In this study, Salmonella temperate phage vB_Sal_PHB48 was isolated from sewage. TEM and phylogenetic analysis indicated that phage PHB48 belongs to the Myoviridae family. Additionally, Salmonella Typhimurium integrating PHB48 was screened and designated as Sal013+. Whole genome sequencing revealed that the integration site was specific and we confirmed that the integration of PHB48 did not change the O-antigen and coding sequences of Sal013. Our in vitro and in vivo studies showed that the integration of PHB48 could significantly enhance the virulence and biofilm formation of S. Typhimurium. More importantly, the integration of PHB48 significantly improved the colonization and contamination ability of bacteria in food samples. In conclusion, we isolated Salmonella temperate phage directly from the environment and systematically clarified that PHB48 enhanced the virulence and biofilm-forming ability of Salmonella. In addition, we found that PHB48 increased the colonization and contamination ability of Salmonella in food samples. These results indicated that the highly pathogenic Salmonella induced by temperate phage was more harmful to food matrices and public health security. Our results could enhance the understanding of the evolutionary relationship between bacteriophages and bacteria, and raise public awareness of large-scale outbreaks resulting from Salmonella virulence enhancement in food industry.
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Affiliation(s)
- Shuang Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070 Wuhan, China; The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, 430070 Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, 430070 Wuhan, China
| | - Seyyed Danial Mirmiran
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070 Wuhan, China; The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, 430070 Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, 430070 Wuhan, China
| | - Xiangmin Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070 Wuhan, China; The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, 430070 Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, 430070 Wuhan, China
| | - Xinxin Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070 Wuhan, China; The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, 430070 Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, 430070 Wuhan, China
| | - Fenqiang Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070 Wuhan, China; The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, 430070 Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, 430070 Wuhan, China
| | - Xiaochao Duan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070 Wuhan, China; The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, 430070 Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, 430070 Wuhan, China
| | - Dongyang Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070 Wuhan, China; The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, 430070 Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yibao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070 Wuhan, China; The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, 430070 Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, 430070 Wuhan, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070 Wuhan, China; The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, 430070 Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, 430070 Wuhan, China
| | - Ping Qian
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070 Wuhan, China; The Cooperative Innovation Centre for Sustainable Pig Production, Huazhong Agricultural University, 430070 Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, 430070 Wuhan, China.
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Hochhauser D, Millman A, Sorek R. The defense island repertoire of the Escherichia coli pan-genome. PLoS Genet 2023; 19:e1010694. [PMID: 37023146 PMCID: PMC10121019 DOI: 10.1371/journal.pgen.1010694] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/21/2023] [Accepted: 03/06/2023] [Indexed: 04/08/2023] Open
Abstract
It has become clear in recent years that anti-phage defense systems cluster non-randomly within bacterial genomes in so-called "defense islands". Despite serving as a valuable tool for the discovery of novel defense systems, the nature and distribution of defense islands themselves remain poorly understood. In this study, we comprehensively mapped the defense system repertoire of >1,300 strains of Escherichia coli, the most widely studied organism for phage-bacteria interactions. We found that defense systems are usually carried on mobile genetic elements including prophages, integrative conjugative elements and transposons, which preferentially integrate at several dozens of dedicated hotspots in the E. coli genome. Each mobile genetic element type has a preferred integration position but can carry a diverse variety of defensive cargo. On average, an E. coli genome has 4.7 hotspots occupied by defense system-containing mobile elements, with some strains possessing up to eight defensively occupied hotspots. Defense systems frequently co-localize with other systems on the same mobile genetic element, in agreement with the observed defense island phenomenon. Our data show that the overwhelming majority of the E. coli pan-immune system is carried on mobile genetic elements, explaining why the immune repertoire varies substantially between different strains of the same species.
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Affiliation(s)
- Dina Hochhauser
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Millman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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38
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Jia PP, Yang YF, Junaid M, Jia HJ, Li WG, Pei DS. Bacteriophage-based techniques for elucidating the function of zebrafish gut microbiota. Appl Microbiol Biotechnol 2023; 107:2039-2059. [PMID: 36847856 DOI: 10.1007/s00253-023-12439-x] [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: 12/03/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 03/01/2023]
Abstract
Bacteriophages (or phages) are unique viruses that can specifically infect bacteria. Since their discovery by Twort and d'Herelle, phages with bacterial specificity have played important roles in microbial regulation. The intestinal microbiota and host health are intimately linked with nutrient, metabolism, development, and immunity aspects. However, the mechanism of interactions between the composition of the microbiota and their functions in maintaining host health still needs to be further explored. To address the lack of methodology and functions of intestinal microbiota in the host, we first proposed that, with the regulations of special intestinal microbiota and applications of germ-free (GF) zebrafish model, phages would be used to infect and reduce/eliminate the defined gut bacteria in the conventionally raised (CR) zebrafish and compared with the GF zebrafish colonized with defined bacterial strains. Thus, this review highlighted the background and roles of phages and their functional characteristics, and we also summarized the phage-specific infection of target microorganisms, methods to improve the phage specificity, and their regulation within the zebrafish model and gut microbial functional study. Moreover, the primary protocol of phage therapy to control the intestinal microbiota in zebrafish models from larvae to adults was recommended including phage screening from natural sources, identification of host ranges, and experimental design in the animal. A well understanding of the interaction and mechanism between phages and gut bacteria in the host can potentially provide powerful strategies or techniques for preventing bacteria-related human diseases by precisely regulating in vitro and in vivo, which will provide novel insights for phages' application and combined research in the future. KEY POINTS: • Zebrafish models for clarifying the microbial and phages' functions were discussed • Phages infect host bacteria with exquisite specificity and efficacy • Phages can reduce/eliminate the defined gut bacteria to clarify their function.
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Affiliation(s)
- Pan-Pan Jia
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China
| | - Yi-Fan Yang
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China
- College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - Muhammad Junaid
- Joint Laboratory of Guangdong Province and Hong Kong Region On Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Huang-Jie Jia
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China
| | - Wei-Guo Li
- College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - De-Sheng Pei
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China.
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do Socorro Fôro Ramos E, Bahia SL, de Oliveira Ribeiro G, Villanova F, de Pádua Milagres FA, Brustulin R, Pandey RP, Deng X, Delwart E, da Costa AC, Leal É. Characterization of Phietavirus Henu 2 in the virome of individuals with acute gastroenteritis. Virus Genes 2023; 59:464-472. [PMID: 37004601 DOI: 10.1007/s11262-023-01990-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/15/2023] [Indexed: 04/04/2023]
Abstract
There is a growing interest in phages as potential biotechnological tools in human health owing to the antibacterial activity of these viruses. In this study, we characterized a new member (named PhiV_005_BRA/2016) of the recently identified phage species Phietavirus Henu 2. PhiV_005_BRA/2016 was detected through metagenomic analysis of stool samples of individuals with acute gastroenteritis. PhiV_005_BRA/2016 contains double-stranded linear DNA (dsDNA), it has a genome of 43,513 base pairs (bp), with a high identity score (99%) with phage of the genus Phietavirus, species of Phietavirus Henu 2. Life style prediction indicated that PhiV_005_BRA/2016 is a lysogenic phage whose the main host is methicillin-resistant Staphylococcus aureus (MRSA). Indeed, we found PhiV_005_BRA/2016 partially integrated in the genome of distinct MRSA strains. Our findings highlights the importance of large-scale screening of bacteriophages to better understand the emergence of multi-drug resistant bacterial.
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Affiliation(s)
- Endrya do Socorro Fôro Ramos
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicais, Universidade Federal do Pará, Belém, Pará, 66075-000, Brazil
| | - Santana Lobato Bahia
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicais, Universidade Federal do Pará, Belém, Pará, 66075-000, Brazil
| | - Geovani de Oliveira Ribeiro
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicais, Universidade Federal do Pará, Belém, Pará, 66075-000, Brazil
| | - Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicais, Universidade Federal do Pará, Belém, Pará, 66075-000, Brazil
| | - Flávio Augusto de Pádua Milagres
- Secretaria de Saúde do Tocantins, Palmas, Tocantins, 77453-000, Brazil
- Laboratório Central de Saúde Pública do Tocantins (LACEN/TO), Palmas, Tocantins, 77016-330, Brazil
| | - Rafael Brustulin
- Secretaria de Saúde do Tocantins, Palmas, Tocantins, 77453-000, Brazil
- Laboratório Central de Saúde Pública do Tocantins (LACEN/TO), Palmas, Tocantins, 77016-330, Brazil
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), SRM University Delhi-NCR, Rajiv Gandhi Education City, Sonepat, Haryana, 131029, India
| | - Xutao Deng
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, 94118-4417, USA
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Eric Delwart
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, 94118-4417, USA
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | | | - Élcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicais, Universidade Federal do Pará, Belém, Pará, 66075-000, Brazil.
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40
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Intestinal colonization with multidrug-resistant Enterobacterales: screening, epidemiology, clinical impact, and strategies to decolonize carriers. Eur J Clin Microbiol Infect Dis 2023; 42:229-254. [PMID: 36680641 PMCID: PMC9899200 DOI: 10.1007/s10096-023-04548-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/11/2023] [Indexed: 01/22/2023]
Abstract
The clinical impact of infections due to extended-spectrum β-lactamase (ESBL)- and/or carbapenemase-producing Enterobacterales (Ent) has reached dramatic levels worldwide. Infections due to these multidrug-resistant (MDR) pathogens-especially Escherichia coli and Klebsiella pneumoniae-may originate from a prior asymptomatic intestinal colonization that could also favor transmission to other subjects. It is therefore desirable that gut carriers are rapidly identified to try preventing both the occurrence of serious endogenous infections and potential transmission. Together with the infection prevention and control countermeasures, any strategy capable of effectively eradicating the MDR-Ent from the intestinal tract would be desirable. In this narrative review, we present a summary of the different aspects linked to the intestinal colonization due to MDR-Ent. In particular, culture- and molecular-based screening techniques to identify carriers, data on prevalence and risk factors in different populations, clinical impact, length of colonization, and contribution to transmission in various settings will be overviewed. We will also discuss the standard strategies (selective digestive decontamination, fecal microbiota transplant) and those still in development (bacteriophages, probiotics, microcins, and CRISPR-Cas-based) that might be used to decolonize MDR-Ent carriers.
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41
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Prediction of Phage Virion Proteins Using Machine Learning Methods. Molecules 2023; 28:molecules28052238. [PMID: 36903484 PMCID: PMC10004995 DOI: 10.3390/molecules28052238] [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: 01/02/2023] [Revised: 01/27/2023] [Accepted: 02/20/2023] [Indexed: 03/04/2023] Open
Abstract
Antimicrobial resistance (AMR) is a major problem and an immediate alternative to antibiotics is the need of the hour. Research on the possible alternative products to tackle bacterial infections is ongoing worldwide. One of the most promising alternatives to antibiotics is the use of bacteriophages (phage) or phage-driven antibacterial drugs to cure bacterial infections caused by AMR bacteria. Phage-driven proteins, including holins, endolysins, and exopolysaccharides, have shown great potential in the development of antibacterial drugs. Likewise, phage virion proteins (PVPs) might also play an important role in the development of antibacterial drugs. Here, we have developed a machine learning-based prediction method to predict PVPs using phage protein sequences. We have employed well-known basic and ensemble machine learning methods with protein sequence composition features for the prediction of PVPs. We found that the gradient boosting classifier (GBC) method achieved the best accuracy of 80% on the training dataset and an accuracy of 83% on the independent dataset. The performance on the independent dataset is better than other existing methods. A user-friendly web server developed by us is freely available to all users for the prediction of PVPs from phage protein sequences. The web server might facilitate the large-scale prediction of PVPs and hypothesis-driven experimental study design.
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Karczewska M, Strzelecki P, Szalewska-Pałasz A, Nowicki D. How to Tackle Bacteriophages: The Review of Approaches with Mechanistic Insight. Int J Mol Sci 2023; 24:ijms24054447. [PMID: 36901878 PMCID: PMC10003480 DOI: 10.3390/ijms24054447] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/26/2023] Open
Abstract
Bacteriophage-based applications have a renaissance today, increasingly marking their use in industry, medicine, food processing, biotechnology, and more. However, phages are considered resistant to various harsh environmental conditions; besides, they are characterized by high intra-group variability. Phage-related contaminations may therefore pose new challenges in the future due to the wider use of phages in industry and health care. Therefore, in this review, we summarize the current knowledge of bacteriophage disinfection methods, as well as highlight new technologies and approaches. We discuss the need for systematic solutions to improve bacteriophage control, taking into account their structural and environmental diversity.
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Affiliation(s)
- Monika Karczewska
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Patryk Strzelecki
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
- Institut de Physique et Chimie des Matériaux de Strasbourg, Université de Strasbourg, CNRS, UMR7504, 23 rue du Loess, CEDEX 2, F-67034 Strasbourg, France
| | - Agnieszka Szalewska-Pałasz
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Dariusz Nowicki
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
- Correspondence: ; Tel.: +48-58-523-6065
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Schackart KE, Graham JB, Ponsero AJ, Hurwitz BL. Evaluation of computational phage detection tools for metagenomic datasets. Front Microbiol 2023; 14:1078760. [PMID: 36760501 PMCID: PMC9902911 DOI: 10.3389/fmicb.2023.1078760] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/09/2023] [Indexed: 01/25/2023] Open
Abstract
Introduction As new computational tools for detecting phage in metagenomes are being rapidly developed, a critical need has emerged to develop systematic benchmarks. Methods In this study, we surveyed 19 metagenomic phage detection tools, 9 of which could be installed and run at scale. Those 9 tools were assessed on several benchmark challenges. Fragmented reference genomes are used to assess the effects of fragment length, low viral content, phage taxonomy, robustness to eukaryotic contamination, and computational resource usage. Simulated metagenomes are used to assess the effects of sequencing and assembly quality on the tool performances. Finally, real human gut metagenomes and viromes are used to assess the differences and similarities in the phage communities predicted by the tools. Results We find that the various tools yield strikingly different results. Generally, tools that use a homology approach (VirSorter, MARVEL, viralVerify, VIBRANT, and VirSorter2) demonstrate low false positive rates and robustness to eukaryotic contamination. Conversely, tools that use a sequence composition approach (VirFinder, DeepVirFinder, Seeker), and MetaPhinder, have higher sensitivity, including to phages with less representation in reference databases. These differences led to widely differing predicted phage communities in human gut metagenomes, with nearly 80% of contigs being marked as phage by at least one tool and a maximum overlap of 38.8% between any two tools. While the results were more consistent among the tools on viromes, the differences in results were still significant, with a maximum overlap of 60.65%. Discussion: Importantly, the benchmark datasets developed in this study are publicly available and reusable to enable the future comparability of new tools developed.
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Affiliation(s)
- Kenneth E. Schackart
- Department of Biosystems Engineering, The University of Arizona, Tucson, AZ, United States
| | - Jessica B. Graham
- BIO5 Institute, The University of Arizona, Tucson, AZ, United States
| | - Alise J. Ponsero
- Department of Biosystems Engineering, The University of Arizona, Tucson, AZ, United States
- BIO5 Institute, The University of Arizona, Tucson, AZ, United States
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Bonnie L. Hurwitz
- Department of Biosystems Engineering, The University of Arizona, Tucson, AZ, United States
- BIO5 Institute, The University of Arizona, Tucson, AZ, United States
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Yang Y, Du H, Zou G, Song Z, Zhou Y, Li H, Tan C, Chen H, Fischetti VA, Li J. Encapsulation and delivery of phage as a novel method for gut flora manipulation in situ: A review. J Control Release 2023; 353:634-649. [PMID: 36464065 DOI: 10.1016/j.jconrel.2022.11.048] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/27/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022]
Abstract
Intestinal flora regulation is an effective method to intervene and treat diseases associated with microbiome imbalance. In addition to conventional probiotic supplement, phage delivery has recently exhibited great prospect in modifying gut flora composition and regulating certain gene expression of gut bacteria. However, the protein structure of phage is vulnerable to external factors during storage and delivery, which leads to the loss of infection ability and flora regulation function. Encapsulation strategy provides an effective solution for improving phage stability and precisely controlling delivery dosage. Different functional materials including enzyme-responsive and pH-responsive polymers have been used to construct encapsulation carriers to protect phages from harsh conditions and release them in the colon. Meanwhile, diverse carriers showed different characteristics in structure and function, which influenced their protective effect and delivery efficiency. This review systematically summarizes recent research progress on the phage encapsulation and delivery, with an emphasis on function properties of carrier systems in the protection effect and colon-targeted delivery. The present review may provide a theoretical reference for the encapsulation and delivery of phage as microbiota modulator, so as to expedite the development of functional material and delivery carrier, as well as the advances in practical application of intestinal flora regulation.
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Affiliation(s)
- Yufan Yang
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Hu Du
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Geng Zou
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhiyong Song
- College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Zhou
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Li
- Faculty of Bioscience Engineering, Ghent University, Gent 9000, Belgium
| | - Chen Tan
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Huanchun Chen
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Vincent A Fischetti
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York 10065, USA
| | - Jinquan Li
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China; Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York 10065, USA; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China.
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W B Jr M, A S R, P M, F B. Cellular and Natural Viral Engineering in Cognition-Based Evolution. Commun Integr Biol 2023; 16:2196145. [PMID: 37153718 PMCID: PMC10155641 DOI: 10.1080/19420889.2023.2196145] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Neo-Darwinism conceptualizes evolution as the continuous succession of predominately random genetic variations disciplined by natural selection. In that frame, the primary interaction between cells and the virome is relegated to host-parasite dynamics governed by selective influences. Cognition-Based Evolution regards biological and evolutionary development as a reciprocating cognition-based informational interactome for the protection of self-referential cells. To sustain cellular homeorhesis, cognitive cells collaborate to assess the validity of ambiguous biological information. That collective interaction involves coordinate measurement, communication, and active deployment of resources as Natural Cellular Engineering. These coordinated activities drive multicellularity, biological development, and evolutionary change. The virome participates as the vital intercessory among the cellular domains to ensure their shared permanent perpetuation. The interactions between the virome and the cellular domains represent active virocellular cross-communications for the continual exchange of resources. Modular genetic transfers between viruses and cells carry bioactive potentials. Those exchanges are deployed as nonrandom flexible tools among the domains in their continuous confrontation with environmental stresses. This alternative framework fundamentally shifts our perspective on viral-cellular interactions, strengthening established principles of viral symbiogenesis. Pathogenesis can now be properly appraised as one expression of a range of outcomes between cells and viruses within a larger conceptual framework of Natural Viral Engineering as a co-engineering participant with cells. It is proposed that Natural Viral Engineering should be viewed as a co-existent facet of Natural Cellular Engineering within Cognition-Based Evolution.
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Affiliation(s)
- Miller W B Jr
- Banner Health Systems - Medicine, Paradise Valley, Arizona, AZ, USA
- CONTACT Miller W B Jr Paradise Valley, Arizona, AZ85253, USA
| | - Reber A S
- Department of Psychology, University of British Columbia, Vancouver, BC, Canada
| | - Marshall P
- Department of Engineering, Evolution 2.0, Oak Park, IL, USA
| | - Baluška F
- Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
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46
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Ding Y, Huang C, Zhang Y, Wang J, Wang X. Magnetic microbead enzyme-linked immunoassay based on phage encoded protein RBP 41-mediated for rapid and sensitive detection of Salmonella in food matrices. Food Res Int 2023; 163:112212. [PMID: 36596140 DOI: 10.1016/j.foodres.2022.112212] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/07/2022] [Accepted: 11/15/2022] [Indexed: 11/27/2022]
Abstract
Rapid and sensitive quantitative detection methods are required to monitor and detect Salmonella throughout the food supply chain and early prevention of foodborne disease outbreaks. In this study, a magnetic microbead enzyme-linked immunoassay (MELISA) based on phage receptor binding protein was developed for rapid enrichment and detection of Salmonella in complex food matrices. RBP 41 from phage T102 acted as a species-specific recognition element for Salmonella by exploiting its strong binding capacity to Salmonella surface receptors. RBP 41-MBs were prepared by coupling recombinant RBP 41 with MBs and used to separate and enrich Salmonella cells from spiked food samples. The captured complexes were further integrated with ELISA procedures by HRP-labeled anti-Salmonella antibody for rapid and accurate detection of Salmonella. The whole method took <1.5 h and the detection limit was 10 CFU/mL. Therefore, MELISA was successfully developed for the detection of Salmonella in various spiked food samples (skim milk, lettuce, and chicken breast). The ELISA reaction process of this method was carried out on magnetic beads. It simplified the process of the traditional ELISA method and reduces the reaction time. This study expanded the use of phage-associated proteins and demonstrated the promising prospects for practical applications in the detection of foodborne pathogens.
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Affiliation(s)
- Yifeng Ding
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan 430070, China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Chenxi Huang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yiming Zhang
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan 430070, China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jia Wang
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan 430070, China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xiaohong Wang
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan 430070, China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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Cui Y, Su X, Wang C, Xu H, Hu D, Wang J, Pei K, Sun M, Zou T. Bacterial MazF/MazE toxin-antitoxin suppresses lytic propagation of arbitrium-containing phages. Cell Rep 2022; 41:111752. [PMID: 36476854 DOI: 10.1016/j.celrep.2022.111752] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 05/18/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022] Open
Abstract
Temperate phages dynamically switch between lysis and lysogeny in their full life cycle. Some Bacillus-infecting phages utilize a quorum-sensing-like intercellular communication system, the "arbitrium," to mediate lysis-lysogeny decisions. However, whether additional factors participate in the arbitrium signaling pathway remains largely elusive. Here, we find that the arbitrium signal induces the expression of a functionally conserved operon downstream of the arbitrium module in SPbeta-like phages. SPbeta yopM and yopR (as well as phi3T phi3T_93 and phi3T_97) in the operon play roles in suppressing phage lytic propagation and promoting lysogeny, respectively. We further focus on phi3T_93 and demonstrate that it directly binds antitoxin MazE in the host MazF/MazE toxin-antitoxin (TA) module and facilitates the activation of MazF's toxicity, which is required for phage suppression. These findings show events regulated by the arbitrium system and shed light on how the interplay between phages and the host TA module affects phage-host co-survival.
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Affiliation(s)
- Yongqing Cui
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiang Su
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Chen Wang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Han Xu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Delei Hu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Wang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Kai Pei
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingting Zou
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
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Nicholls P, Aslam S. Role of bacteriophage therapy for resistant infections in transplant recipients. Curr Opin Organ Transplant 2022; 27:546-553. [PMID: 36222821 PMCID: PMC9613597 DOI: 10.1097/mot.0000000000001029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
PURPOSE OF REVIEW Multidrug-resistant organisms (MDROs) are prevalent in transplant recipients and associated with poor outcomes. We review recent cases of phage therapy used to treat recalcitrant infections in transplant recipients and explore the future role of such therapy in this setting. RECENT FINDINGS Individual case reports and small case series suggest possible efficacy of phage therapy for the treatment of MDRO infections in pre and posttransplant patients. Importantly, there have been no serious safety concerns in the reported cases that we reviewed. There are no applicable randomized controlled trials (RCTs) to better guide phage therapy at this time. SUMMARY Given the safety and possibility of successful salvage therapy of MDRO infections using bacteriophages, it is reasonable to pursue phage therapy for difficult-to-treat infections on a compassionate use basis, but RCT data are critically needed to better inform management.
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Affiliation(s)
- Paul Nicholls
- Section of Infectious Diseases, Department of Medicine, Baylor College of Medicine, Houston, TX
| | - Saima Aslam
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA
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Shaidullina A, Harms A. Toothpicks, logic, and next-generation sequencing: systematic investigation of bacteriophage-host interactions. Curr Opin Microbiol 2022; 70:102225. [PMID: 36327691 DOI: 10.1016/j.mib.2022.102225] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/27/2022] [Accepted: 10/01/2022] [Indexed: 01/25/2023]
Abstract
Bacteriophages are abundant and diverse predators that drive community dynamics in many ecosystems and hold great potential for biotechnology and as therapeutics for bacterial infections. Previous research has largely explored phage-host interactions one-by-one, which limited our ability to observe phenotypic patterns, to uncover their genetic basis, and to unravel the underlying molecular mechanisms. However, the famous 'toothpicks and logic' were recently joined by large-scale sequencing of phage genomes and bacterial genome-wide screens that enable us to systematically investigate phage-host interactions. In this article, we highlight recent breakthroughs from the molecular basis of phage host range and receptor recognition over new insights into bacterial immunity to the serendipitous discovery of a new bacterial surface glycan. Future work will enable the understanding, prediction, and engineering of more complicated phage traits for new applications and extend the scope of these studies from simple test tube experiments to natural communities of phages and hosts.
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50
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Millman A, Melamed S, Leavitt A, Doron S, Bernheim A, Hör J, Garb J, Bechon N, Brandis A, Lopatina A, Ofir G, Hochhauser D, Stokar-Avihail A, Tal N, Sharir S, Voichek M, Erez Z, Ferrer JLM, Dar D, Kacen A, Amitai G, Sorek R. An expanded arsenal of immune systems that protect bacteria from phages. Cell Host Microbe 2022; 30:1556-1569.e5. [DOI: 10.1016/j.chom.2022.09.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/15/2022] [Accepted: 09/28/2022] [Indexed: 01/16/2023]
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