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Guo X, Luo G, Hou F, Zhou C, Liu X, Lei Z, Niu D, Ran T, Tan Z. A review of bacteriophage and their application in domestic animals in a post-antibiotic era. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174931. [PMID: 39043300 DOI: 10.1016/j.scitotenv.2024.174931] [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: 05/09/2024] [Revised: 07/17/2024] [Accepted: 07/19/2024] [Indexed: 07/25/2024]
Abstract
Bacteriophages (phages for short) are the most abundant biological entities on Earth and are natural enemies of bacteria. Genomics and molecular biology have identified subtle and complex relationships among phages, bacteria and their animal hosts. This review covers composition, diversity and factors affecting gut phage, their lifecycle in the body, and interactions with bacteria and hosts. In addition, research regarding phage in poultry, aquaculture and livestock are summarized, and application of phages in antibiotic substitution, phage therapy and food safety are reviewed.
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Affiliation(s)
- Xinyu Guo
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Guowang Luo
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Fujiang Hou
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Chuanshe Zhou
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutrition Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Xiu Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhaomin Lei
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Dongyan Niu
- Faculty of Veterinary Medicine, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada
| | - Tao Ran
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Zhiliang Tan
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutrition Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
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2
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Lee Y, Kim K, Choi M, Seo SW. Natural transformation of Vibrio natriegens with large genetic cluster enables alginate assimilation for isopentenol production. BIORESOURCE TECHNOLOGY 2024; 406:130988. [PMID: 38885723 DOI: 10.1016/j.biortech.2024.130988] [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: 03/20/2024] [Revised: 06/14/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024]
Abstract
Alginate is a major component of brown macroalgae, and its efficient utilization is critical for developing sustainable technologies. Vibrio natriegens is a fast-growing marine bacterium that has gained massive attention due to its potential as an alternative industrial chassis. However, V. natriegens cannot naturally metabolize alginate, limiting its usage in marine biomass conversion. In this study, V. natriegens was engineered to utilize marine biomass, kelp, as a carbon source. A total of 33.8 kb of the genetic cluster for alginate assimilation from Vibrio sp. dhg was integrated into V. natriegens by natural transformation. Engineered V. natriegens was further modified to produce 1.8 mg/L of isopentenol from 16 g/L of crude kelp powder. This study not only presents the very first case in which V. natriegens can be naturally transformed with large DNA fragments but also highlights the potential of this strain for converting marine biomass into valuable products.
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Affiliation(s)
- Yungyu Lee
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Keonwoo Kim
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Mincheol Choi
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; Bio-MAX Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; Institute of Bio Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
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3
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Meidaninikjeh S, Mohammadi P, Elikaei A. Bacteriophages and bacterial extracellular vesicles, threat or opportunity? Life Sci 2024; 350:122749. [PMID: 38821215 DOI: 10.1016/j.lfs.2024.122749] [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: 12/04/2023] [Revised: 03/25/2024] [Accepted: 05/23/2024] [Indexed: 06/02/2024]
Abstract
Emergence of antimicrobial-resistant bacteria (AMR) is one of the health major problems worldwide. The scientists are looking for a novel method to treat infectious diseases. Phage therapy is considered a suitable approach for treating infectious diseases. However, there are different challenges in this way. Some biological aspects can probably influence on therapeutic results and further investigations are necessary to reach a successful phage therapy. Bacteriophage activity can influence by bacterial defense system. Bacterial extracellular vesicles (BEVs) are one of the bacterial defense mechanisms which can modify the results of bacteriophage activity. BEVs have the significant roles in the gene transferring, invasion, escape, and spreading of bacteriophages. In this review, the defense mechanisms of bacteria against bacteriophages, especially BEVs secretion, the hidden linkage of BEVs and bacteriophages, and its possible consequences on the bacteriophage activity as well phage therapy will be discussed.
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Affiliation(s)
- Sepideh Meidaninikjeh
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Parisa Mohammadi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran; Research Center for Applied Microbiology and Microbial Biotechnology, Alzahra University, Tehran, Iran.
| | - Ameneh Elikaei
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran; Research Center for Applied Microbiology and Microbial Biotechnology, Alzahra University, Tehran, Iran.
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4
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Cocorullo M, Stelitano G, Chiarelli LR. Phage Therapy: An Alternative Approach to Combating Multidrug-Resistant Bacterial Infections in Cystic Fibrosis. Int J Mol Sci 2024; 25:8321. [PMID: 39125890 PMCID: PMC11313351 DOI: 10.3390/ijms25158321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/25/2024] [Accepted: 07/27/2024] [Indexed: 08/12/2024] Open
Abstract
Patients with cystic fibrosis (CF) are prone to developing life-threatening lung infections with a variety of pathogens that are difficult to eradicate, such as Burkholderia cepacia complex (Bcc), Hemophilus influenzae, Mycobacterium abscessus (Mab), Pseudomonas aeruginosa, and Staphylococcus aureus. These infections still remain an important issue, despite the therapy for CF having considerably improved in recent years. Moreover, prolonged exposure to antibiotics in combination favors the development and spread of multi-resistant bacteria; thus, the development of alternative strategies is crucial to counter antimicrobial resistance. In this context, phage therapy, i.e., the use of phages, viruses that specifically infect bacteria, has become a promising strategy. In this review, we aim to address the current status of phage therapy in the management of multidrug-resistant infections, from compassionate use cases to ongoing clinical trials, as well as the challenges this approach presents in the particular context of CF patients.
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Affiliation(s)
| | | | - Laurent Robert Chiarelli
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via A. Ferrata 9, 27100 Pavia, Italy; (M.C.); (G.S.)
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Dieppa-Colón E, Martin C, Anantharaman K. Prophage-DB: A comprehensive database to explore diversity, distribution, and ecology of prophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.603044. [PMID: 39071402 PMCID: PMC11275716 DOI: 10.1101/2024.07.11.603044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Background Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact microbial community dynamics, microbial ecology, and evolution. Efforts to document the diversity, host range, infection dynamics, and effects of bacteriophage infection on host cell metabolism are extremely underexplored. Phages are classified as virulent or temperate based on their life cycles. Temperate phages adopt the lysogenic mode of infection, where the genome integrates into the host cell genome forming a prophage. Prophages enable viral genome replication without host cell lysis, and often contribute novel and beneficial traits to the host genome. Current phage research predominantly focuses on lytic phages, leaving a significant gap in knowledge regarding prophages, including their biology, diversity, and ecological roles. Results Here we develop and describe Prophage-DB, a database of prophages, their proteins, and associated metadata that will serve as a resource for viral genomics and microbial ecology. To create the database, we identified and characterized prophages from genomes in three of the largest publicly available databases. We applied several state-of-the-art tools in our pipeline to annotate these viruses, cluster and taxonomically classify them, and detect their respective auxiliary metabolic genes. In total, we identify and characterize over 350,000 prophages and 35,000 auxiliary metabolic genes. Our prophage database is highly representative based on statistical results and contains prophages from a diverse set of archaeal and bacterial hosts which show a wide environmental distribution. Conclusion Prophages are particularly overlooked in viral ecology and merit increased attention due to their vital implications for microbiomes and their hosts. Here, we created Prophage-DB to advance our comprehension of prophages in microbiomes through a comprehensive characterization of prophages in publicly available genomes. We propose that Prophage-DB will serve as a valuable resource for advancing phage research, offering insights into viral taxonomy, host relationships, auxiliary metabolic genes, and environmental distribution.
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Affiliation(s)
- Etan Dieppa-Colón
- Department of Bacteriology, University of Wisconsin-Madison
- Microbiology Doctoral Training Program, University of Wisconsin-Madison
| | - Cody Martin
- Department of Bacteriology, University of Wisconsin-Madison
- Microbiology Doctoral Training Program, University of Wisconsin-Madison
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison
- Department of Integrative Biology, University of Wisconsin-Madison
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6
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Babar TK, Glare TR, Hampton JG, Hurst MRH, Narciso J. Biochemical characterisation and production kinetics of high molecular-weight (HMW) putative antibacterial proteins of insect pathogenic Brevibacillus laterosporus isolates. BMC Microbiol 2024; 24:259. [PMID: 38997685 PMCID: PMC11245835 DOI: 10.1186/s12866-024-03340-2] [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: 08/15/2023] [Accepted: 05/16/2024] [Indexed: 07/14/2024] Open
Abstract
BACKGROUND Bacterial genomes often encode structures similar to phage capsids (encapsulins) and phage tails which can be induced spontaneously or using genotoxic compounds such as mitomycin C. These high molecular-weight (HMW) putative antibacterial proteins (ABPs) are used against the competitive strains under natural environment. Previously, it was unknown whether these HMW putative ABPs originating from the insect pathogenic Gram-positive, spore-forming bacterium Brevibacillus laterosporus (Bl) isolates (1821L, 1951) are spontaneously induced during the growth and pose a detrimental effect on their own survival. Furthermore, no prior work has been undertaken to determine their biochemical characteristics. RESULTS Using a soft agar overlay method with polyethylene glycol precipitation, a narrow spectrum of bioactivity was found from the precipitated lysate of Bl 1951. Electron micrographs of mitomycin C- induced filtrates showed structures similar to phage capsids and contractile tails. Bioactivity assays of cell free supernatants (CFS) extracted during the growth of Bl 1821L and Bl 1951 suggested spontaneous induction of these HMW putative ABPs with an autocidal activity. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis of spontaneously induced putative ABPs showed appearance of ~ 30 kDa and ~ 48 kDa bands of varying intensity across all the time intervals during the bacterial growth except in the initial hours. Statistically, spontaneously induced HMW putative ABPs of Bl 1951 exhibited a significant decrease in the number of viable cells of its producer strain after 18 h of growth in liquid. In addition, a significant change in pH and prominent bioactivity of the CFS of this particular time period was noted. Biochemically, the filtered supernatant derived from either Bl 1821L or Bl 1951 maintained bioactivity over a wide range of pH and temperature. CONCLUSION This study reports the spontaneous induction of HMW putative ABPs (bacteriocins) of Bl 1821L and Bl 1951 isolates during the course of growth with potential autocidal activity which is critically important during production as a potential biopesticide. A narrow spectrum of putative antibacterial activity of Bl 1951 precipitate was found. The stability of HMW putative ABPs of Bl 1821L and Bl 1951 over a wide range of pH and temperature can be useful in expanding the potential of this useful bacterium beyond the insecticidal value.
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Affiliation(s)
- Tauseef K Babar
- Bioprotection Research Centre, Lincoln University, Lincoln, Canterbury, 7647, New Zealand.
- Department of Entomology, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, 60000, Pakistan.
| | - Travis R Glare
- Bioprotection Research Centre, Lincoln University, Lincoln, Canterbury, 7647, New Zealand
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Canterbury, 7647, New Zealand
| | - John G Hampton
- Bioprotection Research Centre, Lincoln University, Lincoln, Canterbury, 7647, New Zealand
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Canterbury, 7647, New Zealand
| | - Mark R H Hurst
- Resilient agriculture, AgResearch, Lincoln Research Centre, Christchurch, New Zealand
| | - Josefina Narciso
- Bioprotection Research Centre, Lincoln University, Lincoln, Canterbury, 7647, New Zealand
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Canterbury, 7647, New Zealand
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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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8
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Zhu Y, Yan S, Chen X, Li Y, Xie S. Thallium spill shifts the structural and functional characteristics of viral communities with different lifestyles in river sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174531. [PMID: 38971241 DOI: 10.1016/j.scitotenv.2024.174531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/10/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
Thallium (Tl), a highly toxic heavy metal, can affect microbial community, while little is known about its effect on viral community. The present study investigated the variation of viral communities, as well as their interactions with microbial hosts under Tl stress. Tl in sediments significantly altered the composition and diversity of the viral communities, but showed no significant links with the prokaryotic communities, which may reveal a potential discrepancy in the sensitivity of the viral and prokaryotic communities to heavy metal stress. Auxiliary metabolic genes (AMGs) involved in denitrification, methane oxidation and organic sulfur transformation were enriched at T1-contaminated sites, while the abundance of AMGs related to methanogenesis and sulfate reduction were higher at pristine sites. Specially, the enrichment of AMGs involved in assimilatory sulfate reduction in Tl-contaminated sites could possibly reduce Tl bioavailability by enhancing the microbially-driven sulfur cycling to generate sulfides that could be complexed with Tl. Moreover, there was a significantly positive correlation between virus-carrying metal resistant genes and the sedimentary Tl concentration, implying that Tl contamination might enhance the metal resistant potential of the viruses. Serving as the functional gene reservoir, the response of viral AMGs to Tl stress could represent a potential pathway for microorganisms to be adapted to the metal-polluted environments. Our study provided novel insights into the impact of Tl spill on viral communities, shedding light on functional characteristics and the links of virus-host interaction with Tl level.
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Affiliation(s)
- Ying Zhu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Shuang Yan
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Xiuli Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yangyang Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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Lewis JM, Williams J, Sagona AP. Making the leap from technique to treatment - genetic engineering is paving the way for more efficient phage therapy. Biochem Soc Trans 2024; 52:1373-1384. [PMID: 38716972 DOI: 10.1042/bst20231289] [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: 01/16/2024] [Revised: 03/30/2024] [Accepted: 04/29/2024] [Indexed: 06/27/2024]
Abstract
Bacteriophages (phages) are viruses specific to bacteria that target them with great efficiency and specificity. Phages were first studied for their antibacterial potential in the early twentieth century; however, their use was largely eclipsed by the popularity of antibiotics. Given the surge of antimicrobial-resistant strains worldwide, there has been a renaissance in harnessing phages as therapeutics once more. One of the key advantages of phages is their amenability to modification, allowing the generation of numerous derivatives optimised for specific functions depending on the modification. These enhanced derivatives could display higher infectivity, expanded host range or greater affinity to human tissues, where some bacterial species exert their pathogenesis. Despite this, there has been a noticeable discrepancy between the generation of derivatives in vitro and their clinical application in vivo. In most instances, phage therapy is only used on a compassionate-use basis, where all other treatment options have been exhausted. A lack of clinical trials and numerous regulatory hurdles hamper the progress of phage therapy and in turn, the engineered variants, in becoming widely used in the clinic. In this review, we outline the various types of modifications enacted upon phages and how these modifications contribute to their enhanced bactericidal function compared with wild-type phages. We also discuss the nascent progress of genetically modified phages in clinical trials along with the current issues these are confronted with, to validate it as a therapy in the clinic.
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Affiliation(s)
- Jessica M Lewis
- School of Life Sciences, University of Warwick, Coventry, U.K
| | - Joshua Williams
- School of Life Sciences, University of Warwick, Coventry, U.K
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10
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Yates CR, Nguyen A, Liao J, Cheng RA. What's on a prophage: analysis of Salmonella spp. prophages identifies a diverse range of cargo with multiple virulence- and metabolism-associated functions. mSphere 2024; 9:e0003124. [PMID: 38775467 DOI: 10.1128/msphere.00031-24] [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: 01/13/2024] [Accepted: 04/22/2024] [Indexed: 06/26/2024] Open
Abstract
The gain of mobile elements, such as prophages, can introduce cargo to the recipient bacterium that could facilitate its persistence in or expansion to a new environment, such as a host. While previous studies have focused on identifying and characterizing the genetic diversity of prophages, analyses characterizing the cargo that prophages carry have not been extensively explored. We characterized prophage regions from 303 Salmonella spp. genomes (representing 254 unique serovars) to assess the distribution of prophages in diverse Salmonella. On average, prophages accounted for 3.7% (0.1%-8.8%) of the total genomic content of each isolate. Prophage regions annotated as Gifsy 1 and Salmon Fels 1 were the most commonly identified intact prophages, suggesting that they are common throughout the Salmonella genus. Among 21,687 total coding sequences (CDSs) from intact prophage regions in subsp. enterica genomes, 7.5% (median; range: 1.1%-47.6%) were categorized as having a function not related to prophage integration or phage structure, some of which could potentially provide a functional attribute to the host Salmonella cell. These predicted functions could be broadly categorized into CDSs involved in: (i) modification of cell surface structures (i.e., glycosyltransferases); (ii) modulation of host responses (e.g., SodC/SodA, SopE, ArtAB, and typhoid toxin); (iii) conferring resistance to heavy metals and antimicrobials; (iv) metabolism of carbohydrates, amino acids, and nucleotides; and (v) DNA replication, repair, and regulation. Overall, our systematic analysis of prophage cargo highlights a broader role for prophage cargo in influencing the metabolic, virulence, and resistance characteristics of Salmonella. IMPORTANCE Lysogenic bacteriophages (phages) can integrate their genome into a bacterial host's genome, potentially introducing genetic elements that can affect the fitness of the host bacterium. The functions of prophage-encoded genes are important to understand as these genes could be mobilized and transferred to a new host. Using a large genomic dataset representing >300 isolates from all known subspecies and species of Salmonella, our study contributes important new findings on the distribution of prophages and the types of cargo that diverse Salmonella prophages carry. We identified a number of coding sequences (CDSs) annotated as having cell surface-modifying attributes, suggesting that prophages may have played an important role in shaping Salmonella's diverse surface antigen repertoire. Furthermore, our characterization of prophages suggests that they play a broader role in facilitating the acquisition and transfer of CDSs associated with metabolism, DNA replication and repair, virulence factors, and to a lesser extent, antimicrobial resistance.
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Affiliation(s)
- Caroline R Yates
- Department of Food Science and Technology, Virginia Tech, Blacksburg, Virginia, USA
| | - Anthony Nguyen
- Computational Modeling and Data Analytics Program, Virginia Tech, Blacksburg, Virginia, USA
| | - Jingqiu Liao
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia, USA
| | - Rachel A Cheng
- Department of Food Science and Technology, Virginia Tech, Blacksburg, Virginia, USA
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11
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Ji M, Li Y, Zhou J, Song W, Zhou Y, Ma K, Wang M, Liu X, Li Y, Gong X, Tu Q. Temporal turnover of viral biodiversity and functional potential in intertidal wetlands. NPJ Biofilms Microbiomes 2024; 10:48. [PMID: 38898104 PMCID: PMC11186824 DOI: 10.1038/s41522-024-00522-8] [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: 11/25/2023] [Accepted: 06/07/2024] [Indexed: 06/21/2024] Open
Abstract
As the central members of the microbiome networks, viruses regulate the composition of microbial communities and drive the nutrient cycles of ecosystems by lysing host cells. Therefore, uncovering the dynamic patterns and the underlying ecological mechanisms mediating the tiniest viral communities across space and through time in natural ecosystems is of crucial importance for better understanding the complex microbial world. Here, the temporal dynamics of intertidal viral communities were investigated via a time-series sampling effort. A total of 1911 viral operational taxonomic units were recovered from 36 bimonthly collected shotgun metagenomes. Functionally important auxiliary metabolic genes involved in carbohydrate, sulfur, and phosphorus metabolism were detected, some of which (e.g., cysH gene) were stably present within viral genomes over time. Over the sampling period, strong and comparable temporal turnovers were observed for intertidal viromes and their host microbes. Winter was determined as the pivotal point for the shifts in viral diversity patterns. Notably, the viral micro-diversity covaried with the macro-diversity, following similar temporal patterns. The relative abundances of viral taxa also covaried with their host prokaryotes. Meanwhile, the virus-host relationships at the whole community level were relatively stable. Further statistical analyses demonstrated that the dynamic patterns of viral communities were highly deterministic, for which temperature was the major driver. This study provided valuable mechanistic insights into the temporal turnover of viral communities in complex ecosystems such as intertidal wetlands.
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Affiliation(s)
- Mengzhi Ji
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong Province, China
| | - Yan Li
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong Province, China
| | - Jiayin Zhou
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong Province, China
| | - Wen Song
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong Province, China
| | - Yuqi Zhou
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong Province, China
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Kai Ma
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong Province, China
| | - Mengqi Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong Province, China
| | - Xia Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong Province, China
| | - Yueyue Li
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong Province, China
| | - Xiaofan Gong
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong Province, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong Province, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangzhou, China.
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12
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Ortiz de Ora L, Wiles ET, Zünd M, Bañuelos MS, Haro-Ramirez N, Suder DS, Ujagar N, Angulo JA, Trinh C, Knitter C, Gonen S, Nicholas DA, Wiles TJ. Phollow: Visualizing Gut Bacteriophage Transmission within Microbial Communities and Living Animals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598711. [PMID: 38915633 PMCID: PMC11195241 DOI: 10.1101/2024.06.12.598711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Bacterial viruses (known as "phages") shape the ecology and evolution of microbial communities, making them promising targets for microbiome engineering. However, knowledge of phage biology is constrained because it remains difficult to study phage transmission dynamics within multi-member communities and living animal hosts. We therefore created "Phollow": a live imaging-based approach for tracking phage replication and spread in situ with single-virion resolution. Combining Phollow with optically transparent zebrafish enabled us to directly visualize phage outbreaks within the vertebrate gut. We observed that virions can be rapidly taken up by intestinal tissues, including by enteroendocrine cells, and quickly disseminate to extraintestinal sites, including the liver and brain. Moreover, antibiotics trigger waves of interbacterial transmission leading to sudden shifts in spatial organization and composition of defined gut communities. Phollow ultimately empowers multiscale investigations connecting phage transmission to transkingdom interactions that have the potential to open new avenues for viral-based microbiome therapies.
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Affiliation(s)
- Lizett Ortiz de Ora
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California, USA
| | - Elizabeth T Wiles
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California, USA
| | - Mirjam Zünd
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California, USA
| | - Maria S Bañuelos
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California, USA
| | - Nancy Haro-Ramirez
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California, USA
| | - Diana S Suder
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California, USA
| | - Naveena Ujagar
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California, USA
| | - Julio Ayala Angulo
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California, USA
| | - Calvin Trinh
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California, USA
| | - Courtney Knitter
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California, USA
| | - Shane Gonen
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California, USA
| | - Dequina A Nicholas
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California, USA
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, USA
- Center for Epigenetics and Metabolism, School of Medicine, University of California, Irvine, California, USA
| | - Travis J Wiles
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California, USA
- Center for Virus Research, University of California, Irvine, California, USA
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13
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Al-Anany AM, Fatima R, Nair G, Mayol JT, Hynes AP. Temperate phage-antibiotic synergy across antibiotic classes reveals new mechanism for preventing lysogeny. mBio 2024; 15:e0050424. [PMID: 38757974 PMCID: PMC11237771 DOI: 10.1128/mbio.00504-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
A recent demonstration of synergy between a temperate phage and the antibiotic ciprofloxacin suggested a scalable approach to exploiting temperate phages in therapy, termed temperate phage-antibiotic synergy, which specifically interacted with the lysis-lysogeny decision. To determine whether this would hold true across antibiotics, we challenged Escherichia coli with the phage HK97 and a set of 13 antibiotics spanning seven classes. As expected, given the conserved induction pathway, we observed synergy with classes of drugs known to induce an SOS response: a sulfa drug, other quinolones, and mitomycin C. While some β-lactams exhibited synergy, this appeared to be traditional phage-antibiotic synergy, with no effect on the lysis-lysogeny decision. Curiously, we observed a potent synergy with antibiotics not known to induce the SOS response: protein synthesis inhibitors gentamicin, kanamycin, tetracycline, and azithromycin. The synergy results in an eightfold reduction in the effective minimum inhibitory concentration of gentamicin, complete eradication of the bacteria, and, when administered at sub-optimal doses, drastically decreases the frequency of lysogens emerging from the combined challenge. However, lysogens exhibit no increased sensitivity to the antibiotic; synergy was maintained in the absence of RecA; and the antibiotic reduced the initial frequency of lysogeny rather than selecting against formed lysogens. Our results confirm that SOS-inducing antibiotics broadly result in temperate-phage-specific synergy, but that other antibiotics can interact with temperate phages specifically and result in synergy. This is the first report of a means of chemically blocking entry into lysogeny, providing a new means for manipulating the key lysis-lysogeny decision.IMPORTANCEThe lysis-lysogeny decision is made by most bacterial viruses (bacteriophages, phages), determining whether to kill their host or go dormant within it. With over half of the bacteria containing phages waiting to wake, this is one of the most important behaviors in all of biology. These phages are also considered unusable for therapy because of this behavior. In this paper, we show that many antibiotics bias this behavior to "wake" the dormant phages, forcing them to kill their host, but some also prevent dormancy in the first place. These will be important tools to study this critical decision point and may enable the therapeutic use of these phages.
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Affiliation(s)
- Amany M Al-Anany
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Rabia Fatima
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Gayatri Nair
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jordan T Mayol
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Alexander P Hynes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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14
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Chen PWY, Olivia M, Gong GC, Jan S, Tsai AY. Viral Dynamics in the Tropical Pacific Ocean: A Comparison between Within and Outside a Warm Eddy. Viruses 2024; 16:937. [PMID: 38932229 PMCID: PMC11209615 DOI: 10.3390/v16060937] [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: 03/30/2024] [Revised: 06/02/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
In mesoscale eddies, the chemical properties and biological composition are different from those in the surrounding water due to their unique physical processes. The mechanism of physical-biological coupling in warm-core eddies is unclear, especially because no studies have examined the effects of environmental factors on bacteria and viruses. The purpose of the present study was to examine the influence of an anticyclonic warm eddy on the relationship between bacterial and viral abundances, as well as viral activity (viral production), at different depths. At the core of the warm eddy, the bacterial abundance (0.48 to 2.82 × 105 cells mL-1) fluctuated less than that outside the eddy (1.12 to 7.03 × 105 cells mL-1). In particular, there was a four-fold higher viral-bacterial abundance ratio (VBR) estimated within the eddy, below the layer of the deep chlorophyll maximum, than outside the eddy. An anticyclonic warm eddy with downwelling at its center may contribute to viruses being transmitted directly into the deep ocean through adsorption on particulate organic matter while sinking. Overall, our findings provide valuable insights into the interaction between bacterial and viral abundances and their ecological mechanisms within a warm eddy.
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Affiliation(s)
- Patrichka Wei-Yi Chen
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung 202-24, Taiwan; (P.W.-Y.C.); (M.O.); (G.-C.G.)
- Doctoral Degree Program in Ocean Resource and Environmental Changes, National Taiwan Ocean University, Keelung 202-24, Taiwan
| | - Madeline Olivia
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung 202-24, Taiwan; (P.W.-Y.C.); (M.O.); (G.-C.G.)
- Doctoral Degree Program in Ocean Resource and Environmental Changes, National Taiwan Ocean University, Keelung 202-24, Taiwan
| | - Gwo-Ching Gong
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung 202-24, Taiwan; (P.W.-Y.C.); (M.O.); (G.-C.G.)
- Doctoral Degree Program in Ocean Resource and Environmental Changes, National Taiwan Ocean University, Keelung 202-24, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202-24, Taiwan
| | - Sen Jan
- Institute of Oceanography, National Taiwan University, Taipei 106319, Taiwan;
| | - An-Yi Tsai
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung 202-24, Taiwan; (P.W.-Y.C.); (M.O.); (G.-C.G.)
- Doctoral Degree Program in Ocean Resource and Environmental Changes, National Taiwan Ocean University, Keelung 202-24, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202-24, Taiwan
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15
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Copeland CJ, Roddy JW, Schmidt AK, Secor P, Wheeler T. VIBES: a workflow for annotating and visualizing viral sequences integrated into bacterial genomes. NAR Genom Bioinform 2024; 6:lqae030. [PMID: 38584872 PMCID: PMC10993291 DOI: 10.1093/nargab/lqae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/05/2024] [Accepted: 03/18/2024] [Indexed: 04/09/2024] Open
Abstract
Bacteriophages are viruses that infect bacteria. Many bacteriophages integrate their genomes into the bacterial chromosome and become prophages. Prophages may substantially burden or benefit host bacteria fitness, acting in some cases as parasites and in others as mutualists. Some prophages have been demonstrated to increase host virulence. The increasing ease of bacterial genome sequencing provides an opportunity to deeply explore prophage prevalence and insertion sites. Here we present VIBES (Viral Integrations in Bacterial genomES), a workflow intended to automate prophage annotation in complete bacterial genome sequences. VIBES provides additional context to prophage annotations by annotating bacterial genes and viral proteins in user-provided bacterial and viral genomes. The VIBES pipeline is implemented as a Nextflow-driven workflow, providing a simple, unified interface for execution on local, cluster and cloud computing environments. For each step of the pipeline, a container including all necessary software dependencies is provided. VIBES produces results in simple tab-separated format and generates intuitive and interactive visualizations for data exploration. Despite VIBES's primary emphasis on prophage annotation, its generic alignment-based design allows it to be deployed as a general-purpose sequence similarity search manager. We demonstrate the utility of the VIBES prophage annotation workflow by searching for 178 Pf phage genomes across 1072 Pseudomonas spp. genomes.
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Affiliation(s)
- Conner J Copeland
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Jack W Roddy
- R. Ken Coit College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA
| | - Amelia K Schmidt
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Patrick R Secor
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Travis J Wheeler
- R. Ken Coit College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA
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16
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Casters Y, Bäcker LE, Broux K, Aertsen A. Phage transmission strategies: are phages farming their host? Curr Opin Microbiol 2024; 79:102481. [PMID: 38677076 DOI: 10.1016/j.mib.2024.102481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/29/2024]
Abstract
Extensive coevolution has led to utterly intricate interactions between phages and their bacterial hosts. While both the (short-term) intracellular molecular host-subversion mechanisms during a phage infection cycle and the (long-term) mutational arms race between phages and host cells have traditionally received a lot of attention, there has been an underestimating neglect of (mid-term) transmission strategies by which phages manage to cautiously spread throughout their host population. However, recent findings underscore that phages encode mechanisms to avoid host cell scarcity and promote coexistence with the host, giving the impression that some phages manage to 'farm' their host population to ensure access to host cells for lytic consumption. Given the tremendous impact of phages on bacterial ecology, charting and understanding the complexity of such transmission strategies is of key importance.
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Affiliation(s)
- Yorben Casters
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 23 - bus 2457, 3001, Belgium
| | - Leonard E Bäcker
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 23 - bus 2457, 3001, Belgium
| | - Kevin Broux
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 23 - bus 2457, 3001, Belgium
| | - Abram Aertsen
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 23 - bus 2457, 3001, Belgium.
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17
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Gilman RT, Muldoon MR, Megremis S, Robertson DL, Chanishvili N, Papadopoulos NG. Lysogeny destabilizes computationally simulated microbiomes. Ecol Lett 2024; 27:e14464. [PMID: 38923281 DOI: 10.1111/ele.14464] [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: 01/03/2024] [Revised: 05/06/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
Microbiomes are ecosystems, and their stability can impact the health of their hosts. Theory predicts that predators influence ecosystem stability. Phages are key predators of bacteria in microbiomes, but phages are unusual predators because many have lysogenic life cycles. It has been hypothesized that lysogeny can destabilize microbiomes, but lysogeny has no direct analog in classical ecological theory, and no formal theory exists. We studied the stability of computationally simulated microbiomes with different numbers of temperate (lysogenic) and virulent (obligate lytic) phage species. Bacterial populations were more likely to fluctuate over time when there were more temperate phages species. After disturbances, bacterial populations returned to their pre-disturbance densities more slowly when there were more temperate phage species, but cycles engendered by disturbances dampened more slowly when there were more virulent phage species. Our work offers the first formal theory linking lysogeny to microbiome stability.
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Affiliation(s)
- R Tucker Gilman
- Department of Earth and Environmental Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, UK
| | - Mark R Muldoon
- Department of Mathematics, Faculty of Science and Engineering, University of Manchester, Manchester, UK
| | - Spyridon Megremis
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Department of Genetics and Genome Biology, Centre for Phage Research, Institute for Precision Health, University of Leicester, Leicester, UK
| | | | - Nina Chanishvili
- George Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, Georgia
- Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
- NewVision University, Tbilisi, Georgia
| | - Nikolaos G Papadopoulos
- Allergy Department, 2nd Pediatric Clinic, University of Athens, Athens, Greece
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK
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18
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Iwanicki A, Roskwitalska M, Frankowska N, Wultańska D, Kabała M, Pituch H, Obuchowski M, Hinc K. Insight into the Mechanism of Lysogeny Control of phiCDKH01 Bacteriophage Infecting Clinical Isolate of Clostridioides difficile. Int J Mol Sci 2024; 25:5662. [PMID: 38891850 PMCID: PMC11172241 DOI: 10.3390/ijms25115662] [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: 04/26/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
Clostridioides difficile is a causative agent of antibiotic-associated diarrhea as well as pseudomembranous colitis. So far, all known bacteriophages infecting these bacteria are temperate, which means that instead of prompt lysis of host cells, they can integrate into the host genome or replicate episomally. While C. difficile phages are capable of spontaneous induction and entering the lytic pathway, very little is known about the regulation of their maintenance in the state of lysogeny. In this study, we investigated the properties of a putative major repressor of the recently characterized C. difficile phiCDKH01 bacteriophage. A candidate protein belongs to the XRE family and controls the transcription of genes encoding putative phage antirepressors, known to be involved in the regulation of lytic development. Hence, the putative major phage repressor is likely to be responsible for maintenance of the lysogeny.
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Affiliation(s)
- Adam Iwanicki
- Division of Molecular Bacteriology, Medical University of Gdańsk, 80-211 Gdańsk, Poland; (A.I.); (M.R.); (N.F.); (M.O.)
| | - Małgorzata Roskwitalska
- Division of Molecular Bacteriology, Medical University of Gdańsk, 80-211 Gdańsk, Poland; (A.I.); (M.R.); (N.F.); (M.O.)
| | - Natalia Frankowska
- Division of Molecular Bacteriology, Medical University of Gdańsk, 80-211 Gdańsk, Poland; (A.I.); (M.R.); (N.F.); (M.O.)
- Intercollegiate Faculty of Biotechnology, University of Gdańsk, 80-307 Gdańsk, Poland
| | - Dorota Wultańska
- Department of Medical Microbiology, Medical University of Warsaw, 02-004 Warsaw, Poland; (D.W.); (H.P.)
| | - Monika Kabała
- Department of Medical Microbiology, Medical University of Silesia, 40-055 Katowice, Poland;
| | - Hanna Pituch
- Department of Medical Microbiology, Medical University of Warsaw, 02-004 Warsaw, Poland; (D.W.); (H.P.)
| | - Michał Obuchowski
- Division of Molecular Bacteriology, Medical University of Gdańsk, 80-211 Gdańsk, Poland; (A.I.); (M.R.); (N.F.); (M.O.)
| | - Krzysztof Hinc
- Division of Molecular Bacteriology, Medical University of Gdańsk, 80-211 Gdańsk, Poland; (A.I.); (M.R.); (N.F.); (M.O.)
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19
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Kang Y, Wang J, Wang Y, Li Z. Profiles of phage in global hospital wastewater: Association with microbial hosts, antibiotic resistance genes, metal resistance genes, and mobile genetic elements. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171766. [PMID: 38513871 DOI: 10.1016/j.scitotenv.2024.171766] [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: 12/24/2023] [Revised: 02/28/2024] [Accepted: 03/15/2024] [Indexed: 03/23/2024]
Abstract
Hospital wastewater (HWW) is known to host taxonomically diverse microbial communities, yet limited information is available on the phages infecting these microorganisms. To fill this knowledge gap, we conducted an in-depth analysis using 377 publicly available HWW metagenomic datasets from 16 countries across 4 continents in the NCBI SRA database to elucidate phage-host dynamics and phage contributions to resistance gene transmission. We first assembled a metagenomic HWW phage catalog comprising 13,812 phage operational taxonomic units (pOTUs). The majority of these pOTUs belonged to the Caudoviricetes order, representing 75.29 % of this catalog. Based on the lifestyle of phages, we found that potentially virulent phages predominated in HWW. Specifically, 583 pOTUs have been predicted to have the capability to lyse 81 potentially pathogenic bacteria, suggesting the promising role of HWW phages as a viable alternative to antibiotics. Among all pOTUs, 1.56 % of pOTUs carry 108 subtypes of antibiotic resistance genes (ARGs), 0.96 % of pOTUs carry 76 subtypes of metal resistance genes (MRGs), and 0.96 % of pOTUs carry 22 subtypes of non-phage mobile genetic elements (MGEs). Predictions indicate that certain phages carrying ARGs, MRGs, and non-phage MGEs could infect bacteria hosts, even potential pathogens. This suggests that phages in HWW may contribute to the dissemination of resistance-associated genes in the environment. This meta-analysis provides the first global catalog of HWW phages, revealing their correlations with microbial hosts and pahge-associated ARGs, MRG, and non-phage MGEs. The insights gained from this research hold promise for advancing the applications of phages in medical and industrial contexts.
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Affiliation(s)
- Yutong Kang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102200, China
| | - Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Yuan Wang
- North China University of Science and Technology, Basic Medical College, Tangshan, Hebei 063210, P.R. China
| | - Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102200, China.
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20
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Irby I, Broddrick JT. Microbial adaptation to spaceflight is correlated with bacteriophage-encoded functions. Nat Commun 2024; 15:3474. [PMID: 38750067 PMCID: PMC11096397 DOI: 10.1038/s41467-023-42104-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 09/27/2023] [Indexed: 05/18/2024] Open
Abstract
Evidence from the International Space Station suggests microbial populations are rapidly adapting to the spacecraft environment; however, the mechanism of this adaptation is not understood. Bacteriophages are prolific mediators of bacterial adaptation on Earth. Here we survey 245 genomes sequenced from bacterial strains isolated on the International Space Station for dormant (lysogenic) bacteriophages. Our analysis indicates phage-associated genes are significantly different between spaceflight strains and their terrestrial counterparts. In addition, we identify 283 complete prophages, those that could initiate bacterial lysis and infect additional hosts, of which 21% are novel. These prophage regions encode functions that correlate with increased persistence in extreme environments, such as spaceflight, to include antimicrobial resistance and virulence, DNA damage repair, and dormancy. Our results correlate microbial adaptation in spaceflight to bacteriophage-encoded functions that may impact human health in spaceflight.
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Affiliation(s)
- Iris Irby
- Space Biosciences Research Branch, NASA Ames Research Center, Moffett Field, CA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jared T Broddrick
- Space Biosciences Research Branch, NASA Ames Research Center, Moffett Field, CA, USA.
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21
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Ralhan K, Iyer KA, Diaz LL, Bird R, Maind A, Zhou QA. Navigating Antibacterial Frontiers: A Panoramic Exploration of Antibacterial Landscapes, Resistance Mechanisms, and Emerging Therapeutic Strategies. ACS Infect Dis 2024; 10:1483-1519. [PMID: 38691668 PMCID: PMC11091902 DOI: 10.1021/acsinfecdis.4c00115] [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: 02/10/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 05/03/2024]
Abstract
The development of effective antibacterial solutions has become paramount in maintaining global health in this era of increasing bacterial threats and rampant antibiotic resistance. Traditional antibiotics have played a significant role in combating bacterial infections throughout history. However, the emergence of novel resistant strains necessitates constant innovation in antibacterial research. We have analyzed the data on antibacterials from the CAS Content Collection, the largest human-curated collection of published scientific knowledge, which has proven valuable for quantitative analysis of global scientific knowledge. Our analysis focuses on mining the CAS Content Collection data for recent publications (since 2012). This article aims to explore the intricate landscape of antibacterial research while reviewing the advancement from traditional antibiotics to novel and emerging antibacterial strategies. By delving into the resistance mechanisms, this paper highlights the need to find alternate strategies to address the growing concern.
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Affiliation(s)
| | | | - Leilani Lotti Diaz
- CAS,
A Division of the American Chemical Society, Columbus, Ohio 43210, United States
| | - Robert Bird
- CAS,
A Division of the American Chemical Society, Columbus, Ohio 43210, United States
| | - Ankush Maind
- ACS
International India Pvt. Ltd., Pune 411044, India
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22
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Kobakhidze S, Koulouris S, Kakabadze N, Kotetishvili M. Genetic recombination-mediated evolutionary interactions between phages of potential industrial importance and prophages of their hosts within or across the domains of Escherichia, Listeria, Salmonella, Campylobacter, and Staphylococcus. BMC Microbiol 2024; 24:155. [PMID: 38704526 PMCID: PMC11069274 DOI: 10.1186/s12866-024-03312-6] [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: 06/25/2023] [Accepted: 04/23/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND The in-depth understanding of the role of lateral genetic transfer (LGT) in phage-prophage interactions is essential to rationalizing phage applications for human and animal therapy, as well as for food and environmental safety. This in silico study aimed to detect LGT between phages of potential industrial importance and their hosts. METHODS A large array of genetic recombination detection algorithms, implemented in SplitsTree and RDP4, was applied to detect LGT between various Escherichia, Listeria, Salmonella, Campylobacter, Staphylococcus, Pseudomonas, and Vibrio phages and their hosts. PHASTER and RAST were employed respectively to identify prophages across the host genome and to annotate LGT-affected genes with unknown functions. PhageAI was used to gain deeper insights into the life cycle history of recombined phages. RESULTS The split decomposition inferences (bootstrap values: 91.3-100; fit: 91.433-100), coupled with the Phi (0.0-2.836E-12) and RDP4 (P being well below 0.05) statistics, provided strong evidence for LGT between certain Escherichia, Listeria, Salmonella, and Campylobacter virulent phages and prophages of their hosts. The LGT events entailed mainly the phage genes encoding for hypothetical proteins, while some of these genetic loci appeared to have been affected even by intergeneric recombination in specific E. coli and S. enterica virulent phages when interacting with their host prophages. Moreover, it is shown that certain L. monocytogenes virulent phages could serve at least as the donors of the gene loci, involved in encoding for the basal promoter specificity factor, for L. monocytogenes. In contrast, the large genetic clusters were determined to have been simultaneously exchanged by many S. aureus prophages and some Staphylococcus temperate phages proposed earlier as potential therapeutic candidates (in their native or modified state). The above genetic clusters were found to encompass multiple genes encoding for various proteins, such as e.g., phage tail proteins, the capsid and scaffold proteins, holins, and transcriptional terminator proteins. CONCLUSIONS It is suggested that phage-prophage interactions, mediated by LGT (including intergeneric recombination), can have a far-reaching impact on the co-evolutionary trajectories of industrial phages and their hosts especially when excessively present across microbially rich environments.
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Affiliation(s)
- Saba Kobakhidze
- Hygiene and Medical Ecology, G. Natadze Scientific-Research Institute of Sanitary, 78 D. Uznadze St. 0102, Tbilisi, Georgia
- Faculty of Medicine, Iv. Javakhishvili Tbilisi State University, 1 Ilia Chavchavadze Ave. 0179, Tbilisi, Georgia
| | - Stylianos Koulouris
- Directorate General for Health and Food Safety (DG-SANTE), European Commission, 1049, Bruxelles/Brussel, Belgium
| | - Nata Kakabadze
- Hygiene and Medical Ecology, G. Natadze Scientific-Research Institute of Sanitary, 78 D. Uznadze St. 0102, Tbilisi, Georgia
| | - Mamuka Kotetishvili
- Hygiene and Medical Ecology, G. Natadze Scientific-Research Institute of Sanitary, 78 D. Uznadze St. 0102, Tbilisi, Georgia.
- Scientific Research Institute, School of Science and Technology, the University of Georgia, 77a M. Kostava St., 0171, Tbilisi, Georgia.
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23
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Wang Y, Gao Y, Wang X, Lin Y, Xu G, Yang F, Ni K. Insights into the phage community structure and potential function in silage fermentation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 358:120837. [PMID: 38593737 DOI: 10.1016/j.jenvman.2024.120837] [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: 02/01/2024] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/11/2024]
Abstract
The virus that infects bacteria known as phage, plays a crucial role in the biogeochemical cycling of nutrients. However, the community structure and potential functions of phages in silage fermentation remain largely unexplored. In this study, we utilized viral metagenomics (viromics) to investigate the types, lifestyles, functions, and nutrient utilization patterns of phages in silage. Our findings indicated a high prevalence of annotated phages belonging to Caudovirales and Geplafuvirales, as well as unclassified phages in silage. The predominant host types for these phages were Campylobacterales and Enterobacterales. Virulent phages dominated the silage environment due to their broader range of hosts and enhanced survival capabilities. All identified phages present in silage were found to be non-pathogenic. Although temperate and virulent phages carried distinct genes associated with nutrient cycling processes, the shared genes (prsA) involved in carbon metabolism underscore the potential significance of phages in regulating carbon metabolism in silage. Overall, our findings provide a valuable foundation for further exploring the complex interactions between phages and microorganisms in regulating silage fermentation quality.
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Affiliation(s)
- Yuan Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China
| | - Yu Gao
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China
| | - Xin Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China
| | - Yanli Lin
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China
| | - Gang Xu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China
| | - Fuyu Yang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China; College of Animal Science, Guizhou University, Guiyang, 550025, PR China.
| | - Kuikui Ni
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, PR China.
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24
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Jensen RO, Schulz F, Roux S, Klingeman DM, Mitchell WP, Udwary D, Moraïs S, Reynoso V, Winkler J, Nagaraju S, De Tissera S, Shapiro N, Ivanova N, Reddy TBK, Mizrahi I, Utturkar SM, Bayer EA, Woyke T, Mouncey NJ, Jewett MC, Simpson SD, Köpke M, Jones DT, Brown SD. Phylogenomics and genetic analysis of solvent-producing Clostridium species. Sci Data 2024; 11:432. [PMID: 38693191 PMCID: PMC11063209 DOI: 10.1038/s41597-024-03210-6] [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: 10/15/2023] [Accepted: 04/02/2024] [Indexed: 05/03/2024] Open
Abstract
The genus Clostridium is a large and diverse group within the Bacillota (formerly Firmicutes), whose members can encode useful complex traits such as solvent production, gas-fermentation, and lignocellulose breakdown. We describe 270 genome sequences of solventogenic clostridia from a comprehensive industrial strain collection assembled by Professor David Jones that includes 194 C. beijerinckii, 57 C. saccharobutylicum, 4 C. saccharoperbutylacetonicum, 5 C. butyricum, 7 C. acetobutylicum, and 3 C. tetanomorphum genomes. We report methods, analyses and characterization for phylogeny, key attributes, core biosynthetic genes, secondary metabolites, plasmids, prophage/CRISPR diversity, cellulosomes and quorum sensing for the 6 species. The expanded genomic data described here will facilitate engineering of solvent-producing clostridia as well as non-model microorganisms with innately desirable traits. Sequences could be applied in conventional platform biocatalysts such as yeast or Escherichia coli for enhanced chemical production. Recently, gene sequences from this collection were used to engineer Clostridium autoethanogenum, a gas-fermenting autotrophic acetogen, for continuous acetone or isopropanol production, as well as butanol, butanoic acid, hexanol and hexanoic acid production.
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Affiliation(s)
| | - Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | | | - Daniel Udwary
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sarah Moraïs
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | | | | | | | | | - Nicole Shapiro
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Natalia Ivanova
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - T B K Reddy
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Sagar M Utturkar
- Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Edward A Bayer
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California Merced, Life and Environmental Sciences, Merced, CA, USA
| | - Nigel J Mouncey
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michael C Jewett
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | | | - David T Jones
- Department of Microbiology, University of Otago, Dunedin, New Zealand.
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25
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Zhang C, Quan X, Lian W, Liu R, Wen Q, Chen X. Phenotypic characterization and genomic analysis of Limosilactobacillus fermentum phage. Curr Res Food Sci 2024; 8:100748. [PMID: 38764976 PMCID: PMC11098726 DOI: 10.1016/j.crfs.2024.100748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 04/14/2024] [Accepted: 04/22/2024] [Indexed: 05/21/2024] Open
Abstract
Limosilactobacillus (L.) fermentum is widely utilized for its beneficial properties, but lysogenic phages can integrate into its genome and can be induced to enter the lysis cycle under certain conditions, thus accomplishing lysis of host cells, resulting in severe economic losses. In this study, a lysogenic phage, LFP03, was induced from L. fermentum IMAU 32510 by UV irradiation for 70 s. The electron microscopy showed that this phage belonged to Caudoviricetes class. Its genome size was 39,556 bp with a GC content of 46.08%, which includes 20 functional proteins. Compared with other L. fermentum phages, the genome of phage LFP03 exhibited deletions, inversions and translocations. Biological analysis showed that its optimal multiplicity of infection was 0.1, with a burst size of 133.5 ± 4.9 PFU/infective cell. Phage LFP03 was sensitive to temperature and pH value, with a survival rate of 48.98% at 50 °C. It could be completely inactivated under pH 2. The adsorption ability of this phage was minimally affected by temperature and pH value, with adsorption rates reaching 80% under all treated conditions. Divalent cations could accelerate phage adsorption, while chloramphenicol expressed little influence. This study might expand the related knowledge of L. fermentum phages, and provide some theoretical basis for improving the stability of related products and establishing phage control measures.
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Affiliation(s)
- Can Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, 010018, PR China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, 010018, PR China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, 010018, PR China
| | - Xingyu Quan
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, 010018, PR China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, 010018, PR China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, 010018, PR China
| | - Weiqi Lian
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, 010018, PR China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, 010018, PR China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, 010018, PR China
| | - Runze Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, 010018, PR China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, 010018, PR China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, 010018, PR China
| | - Qiannan Wen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, 010018, PR China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, 010018, PR China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, 010018, PR China
| | - Xia Chen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, 010018, PR China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, 010018, PR China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, 010018, PR China
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26
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Zheng Y, Gao Z, Wu S, Ruan A. Community Structure, Drivers, and Potential Functions of Different Lifestyle Viruses in Chaohu Lake. Viruses 2024; 16:590. [PMID: 38675931 PMCID: PMC11053968 DOI: 10.3390/v16040590] [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: 03/22/2024] [Revised: 04/06/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Viruses, as the most prolific entities on Earth, constitute significant ecological groups within freshwater lakes, exerting pivotal ecological roles. In this study, we selected Chaohu Lake, a representative eutrophic freshwater lake in China, as our research site to explore the community distribution, driving mechanisms, and potential ecological functions of diverse viral communities, the intricate virus-host interaction systems, and the overarching influence of viruses on global biogeochemical cycling.
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Affiliation(s)
- Yu Zheng
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210024, China; (Y.Z.); (Z.G.); (S.W.)
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Zihao Gao
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210024, China; (Y.Z.); (Z.G.); (S.W.)
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Shuai Wu
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210024, China; (Y.Z.); (Z.G.); (S.W.)
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Aidong Ruan
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210024, China; (Y.Z.); (Z.G.); (S.W.)
- College of Geography and Remote Sensing, Hohai University, Nanjing 210098, China
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27
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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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28
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Flores VS, Amgarten DE, Iha BKV, Ryon KA, Danko D, Tierney BT, Mason C, da Silva AM, Setubal JC. Discovery and description of novel phage genomes from urban microbiomes sampled by the MetaSUB consortium. Sci Rep 2024; 14:7913. [PMID: 38575625 PMCID: PMC10994904 DOI: 10.1038/s41598-024-58226-0] [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: 06/08/2023] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
Bacteriophages are recognized as the most abundant members of microbiomes and have therefore a profound impact on microbial communities through the interactions with their bacterial hosts. The International Metagenomics and Metadesign of Subways and Urban Biomes Consortium (MetaSUB) has sampled mass-transit systems in 60 cities over 3 years using metagenomics, throwing light into these hitherto largely unexplored urban environments. MetaSUB focused primarily on the bacterial community. In this work, we explored MetaSUB metagenomic data in order to recover and analyze bacteriophage genomes. We recovered and analyzed 1714 phage genomes with size at least 40 kbp, from the class Caudoviricetes, the vast majority of which (80%) are novel. The recovered genomes were predicted to belong to temperate (69%) and lytic (31%) phages. Thirty-three of these genomes have more than 200 kbp, and one of them reaches 572 kbp, placing it among the largest phage genomes ever found. In general, the phages tended to be site-specific or nearly so, but 194 genomes could be identified in every city from which phage genomes were retrieved. We predicted hosts for 48% of the phages and observed general agreement between phage abundance and the respective bacterial host abundance, which include the most common nosocomial multidrug-resistant pathogens. A small fraction of the phage genomes are carriers of antibiotic resistance genes, and such genomes tended to be particularly abundant in the sites where they were found. We also detected CRISPR-Cas systems in five phage genomes. This study expands the previously reported MetaSUB results and is a contribution to the knowledge about phage diversity, global distribution, and phage genome content.
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Affiliation(s)
- Vinicius S Flores
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil
| | - Deyvid E Amgarten
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Bruno Koshin Vázquez Iha
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil
| | | | | | - Braden T Tierney
- Weill Cornell Medicine, New York, NY, USA
- Harvard Medical School, Cambridge, MA, USA
| | | | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil.
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil.
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29
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Babkin IV, Tikunov AY, Baykov IK, Morozova VV, Tikunova NV. Genome Analysis of Epsilon CrAss-like Phages. Viruses 2024; 16:513. [PMID: 38675856 PMCID: PMC11054128 DOI: 10.3390/v16040513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
CrAss-like phages play an important role in maintaining ecological balance in the human intestinal microbiome. However, their genetic diversity and lifestyle are still insufficiently studied. In this study, a novel CrAssE-Sib phage genome belonging to the epsilon crAss-like phage genomes was found. Comparative analysis indicated that epsilon crAss-like phages are divided into two putative genera, which were proposed to be named Epsilonunovirus and Epsilonduovirus; CrAssE-Sib belongs to the former. The crAssE-Sib genome contains a diversity-generating retroelement (DGR) cassette with all essential elements, including the reverse transcriptase (RT) and receptor binding protein (RBP) genes. However, this RT contains the GxxxSP motif in its fourth domain instead of the usual GxxxSQ motif found in all known phage and bacterial DGRs. RBP encoded by CrAssE-Sib and other Epsilonunoviruses has an unusual structure, and no similar phage proteins were found. In addition, crAssE-Sib and other Epsilonunoviruses encode conserved prophage repressor and anti-repressors that could be involved in lysogenic-to-lytic cycle switches. Notably, DNA primase sequences of epsilon crAss-like phages are not included in the monophyletic group formed by the DNA primases of all other crAss-like phages. Therefore, epsilon crAss-like phage substantially differ from other crAss-like phages, indicating the need to classify these phages into a separate family.
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Affiliation(s)
- Igor V. Babkin
- Federal State Public Scientific Institution «Institute of Chemical Biology and Fundamental Medicine», Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (I.K.B.); (V.V.M.)
| | - Artem Y. Tikunov
- Federal State Public Scientific Institution «Institute of Chemical Biology and Fundamental Medicine», Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (I.K.B.); (V.V.M.)
| | - Ivan K. Baykov
- Federal State Public Scientific Institution «Institute of Chemical Biology and Fundamental Medicine», Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (I.K.B.); (V.V.M.)
- Shared Research Facility “Siberian Circular Photon Source” (SRF “SKIF”) of Boreskov Institute of Catalysis SB RAS, 630090 Novosibirsk, Russia
| | - Vera V. Morozova
- Federal State Public Scientific Institution «Institute of Chemical Biology and Fundamental Medicine», Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (I.K.B.); (V.V.M.)
| | - Nina V. Tikunova
- Federal State Public Scientific Institution «Institute of Chemical Biology and Fundamental Medicine», Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (I.K.B.); (V.V.M.)
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30
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Li Y, Huo Y, Liang L, Li D, Zhang Z, Yang H. Bacillus phage phi18-2 is a novel temperate virus with an unintegrated genome present in the cytoplasm of lysogenic cells as a linear phage-plasmid. Arch Virol 2024; 169:81. [PMID: 38519716 DOI: 10.1007/s00705-024-06014-6] [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: 07/14/2023] [Accepted: 02/01/2024] [Indexed: 03/25/2024]
Abstract
Bacillus subtilis is a Gram-positive bacterium that is widely used in fermentation and in the pharmaceutical industry. Phage contamination occasionally occurs in various fermentation processes and causes significant economic loss. Here, we report the isolation and characterization of a temperate B. subtilis phage, termed phi18-2, from spore powder manufactured in a fermentation plant. Transmission electron microscopy showed that phi18-2 has a symmetrical polyhedral head and a long noncontractile tail. Receptor analysis showed that phi18-2 recognizes wall teichoic acid (WTA) for infection. The phage virions have a linear double-stranded DNA genome of 64,467 bp with identical direct repeat sequences of 309 bp at each end of the genome. In lysogenic cells, the phage genome was found to be present in the cytoplasm without integration into the host cell chromosome, and possibly as a linear phage-plasmid with unmodified ends. Our data may provide some insight into the molecular basis of the unique lysogenic cycle of phage phi18-2.
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Affiliation(s)
- Yutong Li
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Yansheng Huo
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Li Liang
- Shandong Vland Biotech Co., Ltd., Shandong, 251700, China
| | - Donghang Li
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Zhiqiang Zhang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Hongjiang Yang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China.
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31
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Yu X, Cheng L, Yi X, Li B, Li X, Liu X, Liu Z, Kong X. Gut phageome: challenges in research and impact on human microbiota. Front Microbiol 2024; 15:1379382. [PMID: 38585689 PMCID: PMC10995246 DOI: 10.3389/fmicb.2024.1379382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/11/2024] [Indexed: 04/09/2024] Open
Abstract
The human gut microbiome plays a critical role in maintaining our health. Fluctuations in the diversity and structure of the gut microbiota have been implicated in the pathogenesis of several metabolic and inflammatory conditions. Dietary patterns, medication, smoking, alcohol consumption, and physical activity can all influence the abundance of different types of microbiota in the gut, which in turn can affect the health of individuals. Intestinal phages are an essential component of the gut microbiome, but most studies predominantly focus on the structure and dynamics of gut bacteria while neglecting the role of phages in shaping the gut microbiome. As bacteria-killing viruses, the distribution of bacteriophages in the intestine, their role in influencing the intestinal microbiota, and their mechanisms of action remain elusive. Herein, we present an overview of the current knowledge of gut phages, their lifestyles, identification, and potential impact on the gut microbiota.
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Affiliation(s)
- Xiao Yu
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, The First Hospital of Shanxi Medical University, Taiyuan, China
| | - Li Cheng
- Department of Clinical Laboratory and Pathology, Hospital of Shanxi People’s Armed Police, Taiyuan, China
| | - Xin Yi
- Academy of Medical Sciences, Shanxi Medical University, Taiyuan, China
| | - Bing Li
- Academy of Medical Sciences, Shanxi Medical University, Taiyuan, China
| | - Xueqin Li
- Department of Pulmonary and Critical Care Medicine, The General Hospital of Jincheng Coal Industry Group, Jincheng, China
| | - Xiang Liu
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, The First Hospital of Shanxi Medical University, Taiyuan, China
| | - Zhihong Liu
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, The First Hospital of Shanxi Medical University, Taiyuan, China
| | - Xiaomei Kong
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, The First Hospital of Shanxi Medical University, Taiyuan, China
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32
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Castledine M, Buckling A. Critically evaluating the relative importance of phage in shaping microbial community composition. Trends Microbiol 2024:S0966-842X(24)00057-X. [PMID: 38604881 DOI: 10.1016/j.tim.2024.02.014] [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: 01/17/2024] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 04/13/2024]
Abstract
The ubiquity of bacteriophages (phages) and the major evolutionary and ecological impacts they can have on their microbial hosts has resulted in phages often cited as key drivers shaping microbial community composition (the relative abundances of species). However, the evidence for the importance of phages is mixed. Here, we critically review the theory and data exploring the role of phages in communities, identifying the conditions when phages are likely to be important drivers of community composition. At ecological scales, we conclude that phages are often followers rather than drivers of microbial population and community dynamics. While phages can affect strain diversity within species, there is yet to be strong evidence suggesting that fluctuations in species' strains affects community composition.
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Affiliation(s)
- Meaghan Castledine
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK.
| | - Angus Buckling
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
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Huang D, Xia R, Chen C, Liao J, Chen L, Wang D, Alvarez PJJ, Yu P. Adaptive strategies and ecological roles of phages in habitats under physicochemical stress. Trends Microbiol 2024:S0966-842X(24)00042-8. [PMID: 38433027 DOI: 10.1016/j.tim.2024.02.002] [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: 12/04/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 03/05/2024]
Abstract
Bacteriophages (phages) play a vital role in ecosystem functions by influencing the composition, genetic exchange, metabolism, and environmental adaptation of microbial communities. With recent advances in sequencing technologies and bioinformatics, our understanding of the ecology and evolution of phages in stressful environments has substantially expanded. Here, we review the impact of physicochemical environmental stress on the physiological state and community dynamics of phages, the adaptive strategies that phages employ to cope with environmental stress, and the ecological effects of phage-host interactions in stressful environments. Specifically, we highlight the contributions of phages to the adaptive evolution and functioning of microbiomes and suggest that phages and their hosts can maintain a mutualistic relationship in response to environmental stress. In addition, we discuss the ecological consequences caused by phages in stressful environments, encompassing biogeochemical cycling. Overall, this review advances an understanding of phage ecology in stressful environments, which could inform phage-based strategies to improve microbiome performance and ecosystem resilience and resistance in natural and engineering systems.
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Affiliation(s)
- Dan Huang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Rong Xia
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chengyi Chen
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jingqiu Liao
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Linxing Chen
- Department of Earth and Planetary Sciences, University of California Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94720, USA
| | - Dongsheng Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, USA
| | - Pingfeng Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, 314100, China.
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Nordstrom HR, Griffith MP, Rangachar Srinivasa V, Wallace NR, Li A, Cooper VS, Shields RK, Van Tyne D. Harnessing the Diversity of Burkholderia spp. Prophages for Therapeutic Potential. Cells 2024; 13:428. [PMID: 38474392 PMCID: PMC10931425 DOI: 10.3390/cells13050428] [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: 01/22/2024] [Revised: 02/24/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Burkholderia spp. are often resistant to antibiotics, and infections with these organisms are difficult to treat. A potential alternative treatment for Burkholderia spp. infections is bacteriophage (phage) therapy; however, it can be difficult to locate phages that target these bacteria. Prophages incorporated into the bacterial genome have been identified within Burkholderia spp. and may represent a source of useful phages for therapy. Here, we investigate whether prophages within Burkholderia spp. clinical isolates can kill conspecific and heterospecific isolates. Thirty-two Burkholderia spp. isolates were induced for prophage release, and harvested phages were tested for lytic activity against the same 32 isolates. Temperate phages were passaged and their host ranges were determined, resulting in four unique phages of prophage origin that showed different ranges of lytic activity. We also analyzed the prophage content of 35 Burkholderia spp. clinical isolate genomes and identified several prophages present in the genomes of multiple isolates of the same species. Finally, we observed that Burkholdera cenocepacia isolates were more phage-susceptible than Burkholderia multivorans isolates. Overall, our findings suggest that prophages present within Burkholderia spp. genomes are a potentially useful starting point for the isolation and development of novel phages for use in phage therapy.
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Affiliation(s)
- Hayley R. Nordstrom
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Marissa P. Griffith
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | | | - Nathan R. Wallace
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Anna Li
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Vaughn S. Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Ryan K. Shields
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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Winans JB, Garcia SL, Zeng L, Nadell CD. Spatial propagation of temperate phages within and among biofilms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.20.571119. [PMID: 38187755 PMCID: PMC10769212 DOI: 10.1101/2023.12.20.571119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Bacteria form groups comprised of cells and secreted adhesive matrix that controls their spatial organization. These groups - termed biofilms - can act as refuges from environmental disturbance and from biotic threats, including phages. Despite the ubiquity of temperate phages and bacterial biofilms, temperate phage propagation within biofilms has never been characterized on multicellular spatial scales. Here, we leverage several approaches to track temperate phages and distinguish between lytic and lysogenic infections. We determine that lysogeny within E. coli biofilms most often occurs within a predictable region of cell group architecture. Because lysogens are generally found on the periphery of large groups, where lytic viral activity also reduces local structural integrity, lysogens are predisposed to disperse and are over-represented in biofilms formed downstream of the original biofilm-phage system. Comparing our results with those for virulent phages reveals that the temperate phages possess previously unknown advantages for propagation in architecturally heterogeneous biofilm communities.
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Tan X, Zhang M, Liu S, Xiao X, Zhang Y, Jian H. Prophage enhances the ability of deep-sea bacterium Shewanella psychrophila WP2 to utilize D-amino acid. Microbiol Spectr 2024; 12:e0326323. [PMID: 38170979 PMCID: PMC10845958 DOI: 10.1128/spectrum.03263-23] [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: 09/01/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024] Open
Abstract
Prophages are prevalent in the marine bacterial genomes and reshape the physiology and metabolism of their hosts. However, whether and how prophages influence the microbial degradation of D-amino acids (D-AAs), which is one of the widely distributed recalcitrant dissolved organic matters (RDOMs) in the ocean, remain to be explored. In this study, we addressed this issue in a representative marine bacterium, Shewanella psychrophila WP2 (WP2), and its integrated prophage SP1. Notably, compared to the WP2 wild-type strain, the SP1 deletion mutant of WP2 (WP2ΔSP1) exhibited a significantly lower D-glutamate (D-Glu) consumption rate and longer lag phase when D-Glu was used as the sole nitrogen source. The subsequent transcriptome analysis identified 1,523 differentially expressed genes involved in diverse cellular processes, especially that multiple genes related to inorganic nitrogen metabolism were highly upregulated. In addition, the dynamic profiles of ammonium, nitrate, and nitrite were distinct between the culture media of WP2 and WP2ΔSP1. Finally, we provide evidence that SP1 conferred a competitive advantage to WP2 when D-Glu was used as the sole nitrogen source and SP1-like phages may be widely distributed in the global ocean. Taken together, these findings offer novel insight into the influences of prophages on host metabolism and RDOM cycling in marine environments.IMPORTANCEThis work represents the first exploration of the impact of prophages on the D-amino acid (D-AA) metabolism of deep-sea bacteria. By using S. psychrophila WP2 and its integrated prophage SP1 as a representative system, we found that SP1 can significantly increase the catabolism rate of WP2 to D-glutamate and produce higher concentrations of ammonium, resulting in faster growth and competitive advantages. Our findings not only deepen our understanding of the interaction between deep-sea prophages and hosts but also provide new insights into the ecological role of prophages in refractory dissolved organic matter and the nitrogen cycle in deep oceans.
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Affiliation(s)
- Xiaoli Tan
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Mujie Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Shunzhang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Yu Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
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Nweze JE, Schweichhart JS, Angel R. Viral communities in millipede guts: Insights into the diversity and potential role in modulating the microbiome. Environ Microbiol 2024; 26:e16586. [PMID: 38356108 DOI: 10.1111/1462-2920.16586] [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: 09/08/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Millipedes are important detritivores harbouring a diverse microbiome. Previous research focused on bacterial and archaeal diversity, while the virome remained neglected. We elucidated the DNA and RNA viral diversity in the hindguts of two model millipede species with distinct microbiomes: the tropical Epibolus pulchripes (methanogenic, dominated by Bacillota) and the temperate Glomeris connexa (non-methanogenic, dominated by Pseudomonadota). Based on metagenomic and metatranscriptomic assembled viral genomes, the viral communities differed markedly and preferentially infected the most abundant prokaryotic taxa. The majority of DNA viruses were Caudoviricetes (dsDNA), Cirlivirales (ssDNA) and Microviridae (ssDNA), while RNA viruses consisted of Leviviricetes (ssRNA), Potyviridae (ssRNA) and Eukaryotic viruses. A high abundance of subtypes I-C, I-B and II-C CRISPR-Cas systems was found, primarily from Pseudomonadota, Bacteroidota and Bacillota. In addition, auxiliary metabolic genes that modulate chitin degradation, vitamins and amino acid biosynthesis and sulphur metabolism were also detected. Lastly, we found low virus-to-microbe-ratios and a prevalence of lysogenic viruses, supporting a Piggyback-the-Winner dynamic in both hosts.
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Affiliation(s)
- Julius Eyiuche Nweze
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czechia
| | - Johannes Sergej Schweichhart
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czechia
| | - Roey Angel
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia
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38
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Kim KE, Joo HM, Kim YJ, Kang D, Lee TK, Jung SW, Ha SY. Ecological Interaction between Bacteriophages and Bacteria in Sub-Arctic Kongsfjorden Bay, Svalbard, Norway. Microorganisms 2024; 12:276. [PMID: 38399681 PMCID: PMC10893223 DOI: 10.3390/microorganisms12020276] [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: 12/30/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Marine virus diversity and their relationships with their hosts in the marine environment remain unclear. This study investigated the co-occurrence of marine DNA bacteriophages (phages) and bacteria in the sub-Arctic area of Kongsfjorden Bay in Svalbard (Norway) in April and June 2018 using metagenomics tools. Of the marine viruses identified, 48-81% were bacteriophages of the families Myoviridae, Siphoviridae, and Podoviridae. Puniceispirillum phage HMO-2011 was dominant (7.61%) in April, and Puniceispirillum phage HMO-2011 (3.32%) and Pelagibacter phage HTVC008M (3.28%) were dominant in June. Gammaproteobacteria (58%), including Eionea flava (14.3%) and Pseudomonas sabulinigri (12.2%), were dominant in April, whereas Alphaproteobacteria (87%), including Sulfitobacter profundi (51.5%) and Loktanella acticola (32.4%), were dominant in June. The alpha diversity of the bacteriophages and bacterial communities exhibited opposite patterns. The diversity of the bacterial community was higher in April and lower in June. Changes in water temperature and light can influence the relationship between bacteria and bacteriophages.
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Affiliation(s)
- Kang Eun Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (K.E.K.); (Y.J.K.)
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea;
| | - Hyoung Min Joo
- Unit of Next Generation IBRV Building Program, Korea Polar Research Institute, Incheon 21990, Republic of Korea;
| | - Yu Jin Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (K.E.K.); (Y.J.K.)
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea;
| | - Donhyug Kang
- Marine Domain & Security Research Department, Korea Institute of Ocean Science & Technology, Busan 49111, Republic of Korea;
| | - Taek-Kyun Lee
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea;
- Risk Assessment Research Center, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea
| | - Seung Won Jung
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (K.E.K.); (Y.J.K.)
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea;
| | - Sun-Yong Ha
- Division of Polar Ocean Science Research, Korea Polar Research Institute, Incheon 21990, Republic of Korea
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39
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Nordstrom HR, Griffith MP, Srinivasa VR, Wallace NR, Li A, Cooper VS, Shields RK, Van Tyne D. Harnessing the diversity of Burkholderia spp. prophages for therapeutic potential. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577087. [PMID: 38328162 PMCID: PMC10849711 DOI: 10.1101/2024.01.24.577087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Burkholderia spp. are often resistant to antibiotics, and infections with these organisms are difficult to treat. A potential alternative treatment for Burkholderia spp. infections is bacteriophage (phage) therapy; however, it can be difficult to locate phages that target these bacteria. Prophages incorporated into the bacterial genome have been identified within Burkholderia spp. and may represent a source of useful phages for therapy. Here we investigate whether prophages within Burkholderia spp. clinical isolates can kill conspecific and heterospecific isolates. Thirty-two Burkholderia spp. isolates were induced for prophage release, and harvested prophages were tested for lytic activity against the same 32 isolates. Lytic phages were passaged and their host ranges were determined, resulting in four unique phages of prophage origin that showed different ranges of lytic activity. We also analyzed the prophage content of 35 Burkholderia spp. clinical isolate genomes, and identified several prophages present in the genomes of multiple isolates of the same species. Finally, we observed that B. cenocepacia isolates were more phage-susceptible than Burkholderia multivorans isolates. Overall, our findings suggest that prophages present within Burkholderia spp. genomes are a potentially useful starting point for the isolation and development of novel phages for use in phage therapy.
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Affiliation(s)
- Hayley R. Nordstrom
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Marissa P. Griffith
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | | | - Nathan R. Wallace
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Anna Li
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Vaughn S. Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Ryan K. Shields
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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40
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Zheng R, Wang C, Liu R, Cai R, Sun C. Physiological and metabolic insights into the first cultured anaerobic representative of deep-sea Planctomycetes bacteria. eLife 2024; 12:RP89874. [PMID: 38265071 PMCID: PMC10945688 DOI: 10.7554/elife.89874] [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] [Indexed: 01/25/2024] Open
Abstract
Planctomycetes bacteria are ubiquitously distributed across various biospheres and play key roles in global element cycles. However, few deep-sea Planctomycetes members have been cultivated, limiting our understanding of Planctomycetes in the deep biosphere. Here, we have successfully cultured a novel strain of Planctomycetes (strain ZRK32) from a deep-sea cold seep sediment. Our genomic, physiological, and phylogenetic analyses indicate that strain ZRK32 is a novel species, which we propose be named: Poriferisphaera heterotrophicis. We show that strain ZRK32 replicates using a budding mode of division. Based on the combined results from growth assays and transcriptomic analyses, we found that rich nutrients, or supplementation with NO3- or NH4+ promoted the growth of strain ZRK32 by facilitating energy production through the tricarboxylic acid cycle and the Embden-Meyerhof-Parnas glycolysis pathway. Moreover, supplementation with NO3- or NH4+ induced strain ZRK32 to release a bacteriophage in a chronic manner, without host cell lysis. This bacteriophage then enabled strain ZRK32, and another marine bacterium that we studied, to metabolize nitrogen through the function of auxiliary metabolic genes. Overall, these findings expand our understanding of deep-sea Planctomycetes bacteria, while highlighting their ability to metabolize nitrogen when reprogrammed by chronic viruses.
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Affiliation(s)
- Rikuan Zheng
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center of Ocean Mega-Science, Chinese Academy of SciencesQingdaoChina
| | - Chong Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center of Ocean Mega-Science, Chinese Academy of SciencesQingdaoChina
| | - Rui Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center of Ocean Mega-Science, Chinese Academy of SciencesQingdaoChina
| | - Ruining Cai
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center of Ocean Mega-Science, Chinese Academy of SciencesQingdaoChina
- College of Earth Science, University of Chinese Academy of SciencesBeijingChina
| | - Chaomin Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center of Ocean Mega-Science, Chinese Academy of SciencesQingdaoChina
- College of Earth Science, University of Chinese Academy of SciencesBeijingChina
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41
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Zhou K, Zhang T, Chen XW, Xu Y, Zhang R, Qian PY. Viruses in Marine Invertebrate Holobionts: Complex Interactions Between Phages and Bacterial Symbionts. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:467-485. [PMID: 37647612 DOI: 10.1146/annurev-marine-021623-093133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Marine invertebrates are ecologically and economically important and have formed holobionts by evolving symbiotic relationships with cellular and acellular microorganisms that reside in and on their tissues. In recent decades, significant focus on symbiotic cellular microorganisms has led to the discovery of various functions and a considerable expansion of our knowledge of holobiont functions. Despite this progress, our understanding of symbiotic acellular microorganisms remains insufficient, impeding our ability to achieve a comprehensive understanding of marine holobionts. In this review, we highlight the abundant viruses, with a particular emphasis on bacteriophages; provide an overview of their diversity, especially in extensively studied sponges and corals; and examine their potential life cycles. In addition, we discuss potential phage-holobiont interactions of various invertebrates, including participating in initial bacterial colonization, maintaining symbiotic relationships, and causing or exacerbating the diseases of marine invertebrates. Despite the importance of this subject, knowledge of how viruses contribute to marine invertebrate organisms remains limited. Advancements in technology and greater attention to viruses will enhance our understanding of marine invertebrate holobionts.
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Affiliation(s)
- Kun Zhou
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China;
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Ting Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen, Fujian, China
| | - Xiao-Wei Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen, Fujian, China
| | - Ying Xu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China;
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, China;
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China;
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
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42
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Chaudhary V, Kajla P, Lather D, Chaudhary N, Dangi P, Singh P, Pandiselvam R. Bacteriophages: a potential game changer in food processing industry. Crit Rev Biotechnol 2024:1-25. [PMID: 38228500 DOI: 10.1080/07388551.2023.2299768] [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: 02/25/2023] [Accepted: 10/03/2023] [Indexed: 01/18/2024]
Abstract
In the food industry, despite the widespread use of interventions such as preservatives and thermal and non-thermal processing technologies to improve food safety, incidences of foodborne disease continue to happen worldwide, prompting the search for alternative strategies. Bacteriophages, commonly known as phages, have emerged as a promising alternative for controlling pathogenic bacteria in food. This review emphasizes the potential applications of phages in biological sciences, food processing, and preservation, with a particular focus on their role as biocontrol agents for improving food quality and preservation. By shedding light on recent developments and future possibilities, this review highlights the significance of phages in the food industry. Additionally, it addresses crucial aspects such as regulatory status and safety concerns surrounding the use of bacteriophages. The inclusion of up-to-date literature further underscores the relevance of phage-based strategies in reducing foodborne pathogenic bacteria's presence in both food and the production environment. As we look ahead, new phage products are likely to be targeted against emerging foodborne pathogens. This will further advance the efficacy of approaches that are based on phages in maintaining the safety and security of food.
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Affiliation(s)
- Vandana Chaudhary
- Department of Dairy Technology, College of Dairy Science and Technology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Priyanka Kajla
- Department of Food Technology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, India
| | - Deepika Lather
- Department of Veterinary Pathology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Nisha Chaudhary
- Department of Food Science and Technology, College of Agriculture, Agriculture University, Jodhpur, Rajasthan, India
| | - Priya Dangi
- Department of Food and Nutrition and Food Technology, Institute of Home Economics, University of Delhi, New Delhi, India
| | - Punit Singh
- Department of Mechanical Engineering, Institute of Engineering and Technology, GLA University Mathura, Mathura, Uttar Pradesh, India
| | - Ravi Pandiselvam
- Physiology, Biochemistry and Post-Harvest Technology Division, ICAR -Central Plantation Crops Research Institute, Kasaragod, Kerala, India
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43
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Samson R, Dharne M, Khairnar K. Bacteriophages: Status quo and emerging trends toward one health approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168461. [PMID: 37967634 DOI: 10.1016/j.scitotenv.2023.168461] [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: 08/21/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 11/17/2023]
Abstract
The alarming rise in antimicrobial resistance (AMR) among the drug-resistant pathogens has been attributed to the ESKAPEE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, Enterobacter sp., and Escherichia coli). Recently, these AMR microbes have become difficult to treat, as they have rendered the existing therapeutics ineffective. Thus, there is an urgent need for effective alternatives to lessen or eliminate the current infections and limit the spread of emerging diseases under the "One Health" framework. Bacteriophages (phages) are naturally occurring biological resources with extraordinary potential for biomedical, agriculture/food safety, environmental protection, and energy production. Specific unique properties of phages, such as their bactericidal activity, host specificity, potency, and biocompatibility, make them desirable candidates in therapeutics. The recent biotechnological advancement has broadened the repertoire of phage applications in nanoscience, material science, physical chemistry, and soft-matter research. Herein, we present a comprehensive review, coupling the substantial aspects of phages with their applicability status and emerging opportunities in several interdependent areas under one health concept. Consolidating the recent state-of-the-art studies that integrate human, animal, plant, and environment health, the following points have been highlighted: (i) The biomedical and pharmacological advantages of phages and their antimicrobial derivatives with particular emphasis on in-vivo and clinical studies. (ii) The remarkable potential of phages to be altered, improved, and applied for drug delivery, biosensors, biomedical imaging, tissue engineering, energy, and catalysis. (iii) Resurgence of phages in biocontrol of plant, food, and animal-borne pathogens. (iv) Commercialization of phage-based products, current challenges, and perspectives.
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Affiliation(s)
- Rachel Samson
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Mahesh Dharne
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India.
| | - Krishna Khairnar
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Environmental Virology Cell (EVC), CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India.
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [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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Howard-Varona C, Lindback MM, Fudyma JD, Krongauz A, Solonenko NE, Zayed AA, Andreopoulos WB, Olson HM, Kim YM, Kyle JE, Glavina del Rio T, Adkins JN, Tfaily MM, Paul S, Sullivan MB, Duhaime MB. Environment-specific virocell metabolic reprogramming. THE ISME JOURNAL 2024; 18:wrae055. [PMID: 38552150 PMCID: PMC11170926 DOI: 10.1093/ismejo/wrae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/23/2023] [Accepted: 03/28/2024] [Indexed: 06/14/2024]
Abstract
Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a "virocell," is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that abound in nature are poorly understood. Here we used a systems biology approach to investigate virocell metabolic reprogramming under nutrient limitation. Using transcriptomics, proteomics, lipidomics, and endo- and exo-metabolomics, we assessed how low phosphate (low-P) conditions impacted virocells of a marine Pseudoalteromonas host when independently infected by two unrelated phages (HP1 and HS2). With the combined stresses of infection and nutrient limitation, a set of nested responses were observed. First, low-P imposed common cellular responses on all cells (virocells and uninfected cells), including activating the canonical P-stress response, and decreasing transcription, translation, and extracellular organic matter consumption. Second, low-P imposed infection-specific responses (for both virocells), including enhancing nitrogen assimilation and fatty acid degradation, and decreasing extracellular lipid relative abundance. Third, low-P suggested virocell-specific strategies. Specifically, HS2-virocells regulated gene expression by increasing transcription and ribosomal protein production, whereas HP1-virocells accumulated host proteins, decreased extracellular peptide relative abundance, and invested in broader energy and resource acquisition. These results suggest that although environmental conditions shape metabolism in common ways regardless of infection, virocell-specific strategies exist to support viral replication during nutrient limitation, and a framework now exists for identifying metabolic strategies of nutrient-limited virocells in nature.
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Affiliation(s)
- Cristina Howard-Varona
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
| | - Morgan M Lindback
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109, United States
| | - Jane D Fudyma
- Department of Environmental Science, University of Arizona, 1177 E 4th St, Tucson, AZ 85719, United States
- Present address: Department of Plant Pathology, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Azriel Krongauz
- Department of Statistics, The Ohio State University, 1958 Neil Ave, Columbus, OH 43210, United States
| | - Natalie E Solonenko
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
| | - William B Andreopoulos
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, United States
- Present address: Department of Computer Science, San Jose State University, One Washington Square, San Jose CA 95192, United States
| | - Heather M Olson
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
| | - Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
| | - Tijana Glavina del Rio
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, United States
| | - Joshua N Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, United States
| | - Malak M Tfaily
- Department of Environmental Science, University of Arizona, 1177 E 4th St, Tucson, AZ 85719, United States
| | - Subhadeep Paul
- Department of Statistics, The Ohio State University, 1958 Neil Ave, Columbus, OH 43210, United States
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, 2070 Neil Ave, Columbus, OH 43210, United States
- Center for RNA Biology and Center of Microbiome Science, The Ohio State University, 484 W. 12th Ave, Columbus, OH 43210, United States
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109, United States
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Kimchi O, Meir Y, Wingreen NS. Lytic and temperate phage naturally coexist in a dynamic population model. THE ISME JOURNAL 2024; 18:wrae093. [PMID: 38818736 PMCID: PMC11187991 DOI: 10.1093/ismejo/wrae093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/14/2024] [Accepted: 05/30/2024] [Indexed: 06/01/2024]
Abstract
When phage infect their bacterial hosts, they may either lyse the cell and generate a burst of new phage, or lysogenize the bacterium, incorporating the phage genome into it. Phage lysis/lysogeny strategies are assumed to be highly optimized, with the optimal tradeoff depending on environmental conditions. However, in nature, phage of radically different lysis/lysogeny strategies coexist in the same environment, preying on the same bacteria. How can phage preying on the same bacteria coexist if one is more optimal than the other? Here, we address this conundrum within a modeling framework, simulating the population dynamics of communities of phage and their lysogens. We find that coexistence between phage of different lysis/lysogeny strategies is a natural outcome of chaotic population dynamics that arise within sufficiently diverse communities, which ensure no phage is able to absolutely dominate its competitors. Our results further suggest a bet-hedging mechanism at the level of the phage pan-genome, wherein obligate lytic (virulent) strains typically outcompete temperate strains, but also more readily fluctuate to extinction within a local community.
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Affiliation(s)
- Ofer Kimchi
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Yigal Meir
- Department of Physics, Ben-Gurion University, Be’er Sheva 84105, Israel
- Department of Physics, Princeton University, Princeton, NJ 08544, USA
| | - Ned S Wingreen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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Ye Y, Zhang L, Hong X, Chen M, Liu X, Zhou S. Interspecies ecological competition rejuvenates decayed Geobacter electroactive biofilm. THE ISME JOURNAL 2024; 18:wrae118. [PMID: 38916438 PMCID: PMC11227281 DOI: 10.1093/ismejo/wrae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/05/2024] [Accepted: 06/23/2024] [Indexed: 06/26/2024]
Abstract
Bioelectrochemical systems (BESs) exploit electroactive biofilms (EABs) for promising applications in biosensing, wastewater treatment, energy production, and chemical biosynthesis. However, during the operation of BESs, EABs inevitably decay. Seeking approaches to rejuvenate decayed EABs is critical for the sustainability and practical application of BESs. Prophage induction has been recognized as the primary reason for EAB decay. Herein, we report that introducing a competitive species of Geobacter uraniireducens suspended prophage induction in Geobacter sulfurreducens and thereby rejuvenated the decayed G. sulfurreducens EAB. The transcriptomic profile of G. sulfurreducens demonstrated that the addition of G. uraniireducens significantly affected the expression of metabolism- and stress response system-related genes and in particular suppressed the induction of phage-related genes. Mechanistic analyses revealed that interspecies ecological competition exerted by G. uraniireducens suppressed prophage induction. Our findings not only reveal a novel strategy to rejuvenate decayed EABs, which is significant for the sustainability of BESs, but also provide new knowledge for understanding phage-host interactions from an ecological perspective, with implications for developing therapies to defend against phage attack.
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Affiliation(s)
- Yin Ye
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lu Zhang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaohui Hong
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Man Chen
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xing Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Vale FF, Roberts RJ, Kobayashi I, Camargo MC, Rabkin CS. Gene content, phage cycle regulation model and prophage inactivation disclosed by prophage genomics in the Helicobacter pylori Genome Project. Gut Microbes 2024; 16:2379440. [PMID: 39132840 PMCID: PMC11321410 DOI: 10.1080/19490976.2024.2379440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 06/19/2024] [Accepted: 07/08/2024] [Indexed: 08/13/2024] Open
Abstract
Prophages can have major clinical implications through their ability to change pathogenic bacterial traits. There is limited understanding of the prophage role in ecological, evolutionary, adaptive processes and pathogenicity of Helicobacter pylori, a widespread bacterium causally associated with gastric cancer. Inferring the exact prophage genomic location and completeness requires complete genomes. The international Helicobacter pylori Genome Project (HpGP) dataset comprises 1011 H. pylori complete clinical genomes enriched with epigenetic data. We thoroughly evaluated the H. pylori prophage genomic content in the HpGP dataset. We investigated population evolutionary dynamics through phylogenetic and pangenome analyses. Additionally, we identified genome rearrangements and assessed the impact of prophage presence on bacterial gene disruption and methylome. We found that 29.5% (298) of the HpGP genomes contain prophages, of which only 32.2% (96) were complete, minimizing the burden of prophage carriage. The prevalence of H. pylori prophage sequences was variable by geography and ancestry, but not by disease status of the human host. Prophage insertion occasionally results in gene disruption that can change the global bacterial epigenome. Gene function prediction allowed the development of the first model for lysogenic-lytic cycle regulation in H. pylori. We have disclosed new prophage inactivation mechanisms that appear to occur by genome rearrangement, merger with other mobile elements, and pseudogene accumulation. Our analysis provides a comprehensive framework for H. pylori prophage biological and genomics, offering insights into lysogeny regulation and bacterial adaptation to prophages.
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Affiliation(s)
- Filipa F. Vale
- BioISI – Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | | | - Ichizo Kobayashi
- Research Center for Micro-Nano Technology, Hosei University, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Laboratory of Genome Informatics, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - M. Constanza Camargo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Charles S. Rabkin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
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Shuai X, Zhou Z, Ba X, Lin Y, Lin Z, Liu Z, Yu X, Zhou J, Zeng G, Ge Z, Chen H. Bacteriophages: Vectors of or weapons against the transmission of antibiotic resistance genes in hospital wastewater systems? WATER RESEARCH 2024; 248:120833. [PMID: 37952327 DOI: 10.1016/j.watres.2023.120833] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 10/26/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023]
Abstract
Antimicrobial resistance poses a serious threat to human health and is responsible for the death of millions of people annually. Hospital wastewater is an important hotspot for antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). However, little is known about the relationship between phages and ARGs in hospital wastewater systems (HWS). In the present study, the viral diversity of 12 HWSs using data from public metagenomic databases was investigated. Viruses were widely found in both the influent and effluent of each HWS. A total of 45 unique ARGs were carried by 85 viral contigs, which accounted for only 0.14% of the total viral populations, implying that ARGs were not commonly present in phages. Three efflux pump genes were identified as shared between phages and bacterial genomes. However, the predominant types of ARGs in HWS such as aminoglycoside- and beta-lactam-resistance genes were rarely found in phages. Based on CRISPR spacer and tRNA matches, interactions between 171 viral contigs and 60 antibiotic-resistant genomes were predicted, including interactions involving phages and vancomycin-resistant Enterococcus_B faecium or beta-lactam-resistant Klebsiella pneumoniae. More than half (56.1%) of these viral contigs indicated lytic and none of them carried ARGs. As the vOTUs in this study had few ARGs and were primarily lytic, HWS may be a valuable source for phage discovery. Future studies will be able to experimentally validate these sequence-based results to confirm the suitability of HWS phages for pathogen control measures in wastewater.
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Affiliation(s)
- Xinyi Shuai
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhenchao Zhou
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Yanhan Lin
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zejun Lin
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhe Liu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xi Yu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jinyu Zhou
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Guangshu Zeng
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ziye Ge
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hong Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; International Cooperation Base of Environmental Pollution and Ecological Health, Science and Technology Agency of Zhejiang, Zhejiang University, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China.
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50
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Muscatt G, Cook R, Millard A, Bending GD, Jameson E. Viral metagenomics reveals diverse virus-host interactions throughout the soil depth profile. mBio 2023; 14:e0224623. [PMID: 38032184 PMCID: PMC10746233 DOI: 10.1128/mbio.02246-23] [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: 08/23/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Soil viruses can moderate the roles that their host microbes play in global carbon cycling. However, given that most studies investigate the surface layer (i.e., top 20 cm) of soil, the extent to which this occurs in subsurface soil (i.e., below 20 cm) is unknown. Here, we leveraged public sequencing data to investigate the interactions between viruses and their hosts at soil depth intervals, down to 115 cm. While most viruses were detected throughout the soil depth profile, their adaptation to host microbes varied. Nonetheless, we uncovered evidence for the potential of soil viruses to encourage their hosts to recycle plant-derived carbon in both surface and subsurface soils. This work reasons that our understanding of soil viral functions requires us to continue to dig deeper and compare viruses existing throughout soil ecosystems.
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Affiliation(s)
- George Muscatt
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Ryan Cook
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, United Kingdom
| | - Andrew Millard
- Department of Genetics and Genome Biology, Leicester Centre for Phage Research, University of Leicester, Leicester, United Kingdom
| | - Gary D. Bending
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
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