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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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Torrillo PA, Lieberman TD. Reversions mask the contribution of adaptive evolution in microbiomes. eLife 2024; 13:e93146. [PMID: 39240756 PMCID: PMC11379459 DOI: 10.7554/elife.93146] [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: 09/29/2023] [Accepted: 07/30/2024] [Indexed: 09/08/2024] Open
Abstract
When examining bacterial genomes for evidence of past selection, the results depend heavily on the mutational distance between chosen genomes. Even within a bacterial species, genomes separated by larger mutational distances exhibit stronger evidence of purifying selection as assessed by dN/dS, the normalized ratio of nonsynonymous to synonymous mutations. Here, we show that the classical interpretation of this scale dependence, weak purifying selection, leads to problematic mutation accumulation when applied to available gut microbiome data. We propose an alternative, adaptive reversion model with opposite implications for dynamical intuition and applications of dN/dS. Reversions that occur and sweep within-host populations are nearly guaranteed in microbiomes due to large population sizes, short generation times, and variable environments. Using analytical and simulation approaches, we show that adaptive reversion can explain the dN/dS decay given only dozens of locally fluctuating selective pressures, which is realistic in the context of Bacteroides genomes. The success of the adaptive reversion model argues for interpreting low values of dN/dS obtained from long timescales with caution as they may emerge even when adaptive sweeps are frequent. Our work thus inverts the interpretation of an old observation in bacterial evolution, illustrates the potential of mutational reversions to shape genomic landscapes over time, and highlights the importance of studying bacterial genomic evolution on short timescales.
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Affiliation(s)
- Paul A Torrillo
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, United States
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Tami D Lieberman
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, United States
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, United States
- Broad Institute of MIT and Harvard, Cambridge, United States
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
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3
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Bonachela JA. Viral plasticity facilitates host diversity in challenging environments. Nat Commun 2024; 15:7473. [PMID: 39209841 PMCID: PMC11362530 DOI: 10.1038/s41467-024-51344-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/02/2024] [Indexed: 09/04/2024] Open
Abstract
The antagonistic coevolution of microbes and viruses influences fundamentally the diversity of microbial communities. Information on how environmental variables interact with emergent defense-counterdefense strategies and community composition is, however, still scarce. Following biological intuition, diversity should increase with improved growth conditions, which offset evolutionary costs; however, laboratory and regional data suggest that microbial diversity decreases in nutrient-rich conditions. Moreover, global oceanic data show that microbial and viral diversity decline for high latitudes, although the underlying mechanisms are unknown. This article addresses these gaps by introducing an eco-evolutionary model for bacteria-virus antagonistic coevolution. The theory presented here harmonizes the observations above and identifies negative density dependence and viral plasticity (dependence of virus performance on host physiological state) as key drivers: environmental conditions selecting for slow host growth also limit viral performance, facilitating the survival of a diverse host community; host diversity, in turn, enables viral portfolio effects and bet-hedging strategies that sustain viral diversity. From marine microbes to phage therapy against antibiotic-resistant bacteria or cancer cells, the ubiquity of antagonistic coevolution highlights the need to consider eco-evolutionary interactions across a gradient of growth conditions.
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Affiliation(s)
- Juan A Bonachela
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, 08901, USA.
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4
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Li X, Xu J, Wang Y, Gomaa SE, Zhao H, Teng T. The Biological Characteristics of Mycobacterium Phage Henu3 and the Fitness Cost Associated with Its Resistant Strains. Int J Mol Sci 2024; 25:9301. [PMID: 39273250 PMCID: PMC11394830 DOI: 10.3390/ijms25179301] [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: 07/31/2024] [Revised: 08/21/2024] [Accepted: 08/26/2024] [Indexed: 09/15/2024] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis, is an infectious disease that seriously affects human life and health. Despite centuries of efforts to control it, in recent years, the emergence of multidrug-resistant bacterial pathogens of M. tuberculosis due to various factors has exacerbated the disease, posing a serious threat to global health. Therefore, a new method to control M. tuberculosis is urgently needed. Phages, viruses that specifically infect bacteria, have emerged as potential biocontrol agents for bacterial pathogens due to their host specificity. In this study, a mycobacterium phage, Henu3, was isolated from soil around a hospital. The particle morphology, biological characteristics, genomics and phylogeny of Henu3 were characterized. Additionally, to explore the balance between phage resistance and stress response, phage Henu3-resistant strains 0G10 and 2E1 were screened by sequence passage and bidirectional validation methods, which significantly improved the sensitivity of phage to antibiotics (cefotaxime and kanamycin). By whole-genome re-sequencing of strains 0G10 and 2E1, 12 genes involved in cell-wall synthesis, transporter-encoded genes, two-component regulatory proteins and transcriptional regulatory factor-encoded genes were found to have mutations. These results suggest that phage Henu3 has the potential to control M. tuberculosis pathogens, and phage Henu3 has the potential to be a new potential solution for the treatment of M. tuberculosis infection.
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Affiliation(s)
- Xinyu Li
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Junge Xu
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Yuhan Wang
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Salwa E Gomaa
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Huijie Zhao
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Tieshan Teng
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
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5
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Xu C, Zhang J, Zhang J, Li D, Yan X, Gu Y, Zhong M, Gao H, Zhao Q, Qu X, Huang P, Zhang J. Near Infrared-Triggered Nitric Oxide-Release Nanovesicles with Mild-Photothermal Antibacterial and Immunomodulation for Healing MRSA-Infected Diabetic Wounds. Adv Healthc Mater 2024:e2402297. [PMID: 39175376 DOI: 10.1002/adhm.202402297] [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: 06/23/2024] [Revised: 08/05/2024] [Indexed: 08/24/2024]
Abstract
Bacterial infection-induced excessive inflammation is a major obstacle in diabetic wound healing. Nitric oxide (NO) exhibits significant antibacterial activity but is extremely deficient in diabetes. Hence, a near-infrared (NIR)-triggered NO release system is constructed through codelivery of polyarginine (PArg) and gold nanorods (Au) in an NIR-activatable methylene blue (MB) polypeptide-assembled nanovesicle (Au/PEL-PBA-MB/PArg). Upon NIR irradiation, the quenched MB in the nanovesicles is photoactivated to generate more reactive oxygen species (ROS) to oxidize PArg and release NO in an on-demand controlled manner. With the specific bacterial capture of phenylboronic acid (PBA), NO elevated membrane permeability and boosted bacterial vulnerability in the photothermal therapy (PTT) of the Au nanorods, which is displayed by superior mild PTT antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) at temperatures < 49.7 °C in vitro. Moreover, in vivo, the antibacterial nanovesicles greatly suppressed the burst of MRSA-induced excessive inflammation, NO relayed immunomodulated macrophage polarization from M1 to M2, and the excessive inflammatory phase is successfully transferred to the repair phase. In cooperation with angiogenesis by NO, tissue regeneration is accelerated in MRSA-infected diabetic wounds. Therefore, nanoplatform has considerable potential for accelerating the healing of infected diabetic wounds.
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Affiliation(s)
- Chang Xu
- Hebei Key Laboratory of Functional Polymers, Hebei Key Laboratory of Biomaterials and Smart Theranostics, School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
| | - Jiqing Zhang
- Department of Medical Ultrasound, the First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, 250000, China
| | - Junxian Zhang
- Hebei Key Laboratory of Functional Polymers, Hebei Key Laboratory of Biomaterials and Smart Theranostics, School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
| | - Danting Li
- Hebei Key Laboratory of Functional Polymers, Hebei Key Laboratory of Biomaterials and Smart Theranostics, School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
| | - Xiaozhe Yan
- Hebei Key Laboratory of Functional Polymers, Hebei Key Laboratory of Biomaterials and Smart Theranostics, School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
| | - Yuxuan Gu
- Hebei Key Laboratory of Functional Polymers, Hebei Key Laboratory of Biomaterials and Smart Theranostics, School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
| | - Meihui Zhong
- Hebei Key Laboratory of Functional Polymers, Hebei Key Laboratory of Biomaterials and Smart Theranostics, School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
| | - Hui Gao
- School of Materials Science and Engineering, Tianjin University of Technology, Tianjin, 300384, China
| | - Qiang Zhao
- Key Laboratory of bioactive materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xiongwei Qu
- Hebei Key Laboratory of Functional Polymers, Hebei Key Laboratory of Biomaterials and Smart Theranostics, School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
| | - Pingsheng Huang
- Tianjin Key Laboratory of Biomaterial Research, Institute of Biomedical Engineering, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300192, China
| | - Jimin Zhang
- Hebei Key Laboratory of Functional Polymers, Hebei Key Laboratory of Biomaterials and Smart Theranostics, School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
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6
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Parmar K, Fackler JR, Rivas Z, Mandrekar J, Greenwood-Quaintance KE, Patel R. A comparison of phage susceptibility testing with two liquid high-throughput methods. Front Microbiol 2024; 15:1386245. [PMID: 39171268 PMCID: PMC11335653 DOI: 10.3389/fmicb.2024.1386245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 07/09/2024] [Indexed: 08/23/2024] Open
Abstract
Phage therapy is a promising antibacterial strategy, especially given that drug-resistant bacterial infections are escalating worldwide. Because phages are not active against all strains of a given species, phages being considered for therapeutic use would ideally be tested against bacterial isolates from individual patients prior to administration. Standardized, clinically validated phage susceptibility testing (PST) methods are needed for assessing in vitro phage activity. This study compared two high-throughput liquid-based PST assays. The first, using the Biolog Omnilog™, assessed changes in microbial respiration leading to color changes based on a tetrazolium dye. The second, Agilent BioTek Cytation 7, assessed changes in optical density. Both used 96-well microtiter plate formats. A total of 55 diverse phages with activity against Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, or Enterococcus faecalis were studied against their respective susceptible bacterial hosts and non-susceptible controls, with susceptibility defined based on plaque assay. PST was performed by both assays in replicates, with results compared in terms of hold times (time through which bacterial growth is inhibited by phage compared to controls). Coefficients of variance and interclass correlation coefficients were used to assess inter- and intra-assay reproducibility. Based on a ≤50% coefficient of variance cutpoint, 87% of Biolog and 84% of Agilent assays were considered valid for susceptible bacteria, with 100% considered valid for non-susceptible bacteria by both systems. Using a 8 h hold time cutpoint, 100% of the results matched between the two assays. The interclass correlation coefficient showed 26% excellent agreement, 35% good agreement, and 17% moderate agreement between the two assays for susceptible isolates and 100% excellent agreement for non-susceptible isolates. Overall, the assays compared provided good/fair statistical reproducibility for the assessment of phage susceptibility.
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Affiliation(s)
- Krupa Parmar
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Joseph R. Fackler
- Adaptive Phage Therapeutics, Inc. (APT), Gaithersburg, MD, United States
| | - Zuriel Rivas
- Adaptive Phage Therapeutics, Inc. (APT), Gaithersburg, MD, United States
| | - Jay Mandrekar
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
| | - Kerryl E. Greenwood-Quaintance
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, MN, United States
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7
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Lyberger K, Farner J, Couper L, Mordecai EA. A Mosquito Parasite Is Locally Adapted to Its Host but Not Temperature. Am Nat 2024; 204:121-132. [PMID: 39008840 DOI: 10.1086/730522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
AbstractClimate change will alter interactions between parasites and their hosts. Warming may affect patterns of local adaptation, shifting the environment to favor the parasite or host and thus changing the prevalence of disease. We assessed local adaptation to hosts and temperature in the facultative ciliate parasite Lambornella clarki, which infects the western tree hole mosquito Aedes sierrensis. We conducted laboratory infection experiments with mosquito larvae and parasites collected from across a climate gradient, pairing sympatric or allopatric populations across three temperatures that were either matched or mismatched to the source environment. Lambornella clarki parasites were locally adapted to their hosts, with 2.6 times higher infection rates on sympatric populations compared with allopatric populations, but they were not locally adapted to temperature. Infection peaked at the intermediate temperature of 12.5°C, notably lower than the optimum temperature for free-living L. clarki growth, suggesting that the host's immune response can play a significant role in mediating the outcome of infection. Our results highlight the importance of host selective pressure on parasites, despite the impact of temperature on infection success.
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8
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Torres-Quintero MC, Santamaría RI, Martínez-Flores I, Bustos P, Girard L, Cevallos MÁ, Rodríguez-Sánchez C, González V. Role of core lipopolysaccharide biosynthetic genes in the infection and adsorption of broad-host-range bacteriophages of Rhizobium etli. Microbiol Res 2024; 285:127766. [PMID: 38788349 DOI: 10.1016/j.micres.2024.127766] [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: 03/13/2024] [Revised: 05/07/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024]
Abstract
In this study, we examined the role of the lipopolysaccharide (LPS) core of Rhizobium etli in facilitating the adsorption and infection of phages with broad host range. When the plasmid-encoded LPS biosynthesis genes, wreU and wreV, were disrupted, distinct and contrasting effects on phage infection were observed. The wreU mutant strains exhibited wild-type adsorption and infection properties, whereas the wreV mutant demonstrated resistance to phage infection, but retained the capacity to adsorb phages. Complementation of the wreV mutant strains with a recombinant plasmid containing the wreU and wreV, restored the susceptibility to the phages. However, the presence of this recombinant plasmid in a strain devoid of the native lps-encoding plasmid was insufficient to restore phage susceptibility. These results suggest that the absence of wreV impedes the proper assembly of the complete LPS core, potentially affecting the formation of UDP-KdgNAg or KDO precursors for the O-antigen. In addition, a protein not yet identified, but residing in the native lps-encoding plasmid, may be necessary for complete phage infection.
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Affiliation(s)
- Mary Carmen Torres-Quintero
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, UNAM, Av. Universidad s/n, Col. Chamilpa C.P. 62212, Cuernavaca, Mor, Apdo 565-A, Mexico
| | - Rosa Isela Santamaría
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, UNAM, Av. Universidad s/n, Col. Chamilpa C.P. 62212, Cuernavaca, Mor, Apdo 565-A, Mexico
| | - Irma Martínez-Flores
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, UNAM, Av. Universidad s/n, Col. Chamilpa C.P. 62212, Cuernavaca, Mor, Apdo 565-A, Mexico
| | - Patricia Bustos
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, UNAM, Av. Universidad s/n, Col. Chamilpa C.P. 62212, Cuernavaca, Mor, Apdo 565-A, Mexico
| | - Lourdes Girard
- Programa de Microbiología Genómica, Centro de Ciencias Genómicas, UNAM, Av. Universidad s/n, Col. Chamilpa C.P. 62212, Cuernavaca, Mor, Apdo 565-A, Mexico
| | - Miguel Ángel Cevallos
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, UNAM, Av. Universidad s/n, Col. Chamilpa C.P. 62212, Cuernavaca, Mor, Apdo 565-A, Mexico
| | - César Rodríguez-Sánchez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, UNAM, Av. Universidad s/n, Col. Chamilpa C.P. 62212, Cuernavaca, Mor, Apdo 565-A, Mexico
| | - Víctor González
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, UNAM, Av. Universidad s/n, Col. Chamilpa C.P. 62212, Cuernavaca, Mor, Apdo 565-A, Mexico.
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9
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Laine AL, Tylianakis JM. The coevolutionary consequences of biodiversity change. Trends Ecol Evol 2024; 39:745-756. [PMID: 38705768 DOI: 10.1016/j.tree.2024.04.002] [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: 10/19/2023] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 05/07/2024]
Abstract
Coevolutionary selection is a powerful process shaping species interactions and biodiversity. Anthropogenic global environmental change is reshaping planetary biodiversity, including by altering the structure and intensity of interspecific interactions. However, remarkably little is understood of how coevolutionary selection is changing in the process. Here, we outline three interrelated pathways - change in evolutionary potential, change in community composition, and shifts in interaction trait distributions - that are expected to redirect coevolutionary selection under biodiversity change. Assessing how both ecological and evolutionary rules governing species interactions are disrupted under anthropogenic global change is of paramount importance to understand the past, present, and future of Earth's biodiversity.
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Affiliation(s)
- Anna-Liisa Laine
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikinkaari 1 (PO Box 65), University of Helsinki, FI-00014 Helsinki, Finland.
| | - Jason M Tylianakis
- Bioprotection Aotearoa, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
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10
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Davies T, Cando‐Dumancela C, Liddicoat C, Dresken R, Damen RH, Edwards RA, Ramesh SA, Breed MF. Ecological phage therapy: Can bacteriophages help rapidly restore the soil microbiome? Ecol Evol 2024; 14:e70185. [PMID: 39145040 PMCID: PMC11322231 DOI: 10.1002/ece3.70185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 07/25/2024] [Accepted: 08/02/2024] [Indexed: 08/16/2024] Open
Abstract
Soil microbiota underpin ecosystem functionality yet are rarely targeted during ecosystem restoration. Soil microbiota recovery following native plant revegetation can take years to decades, while the effectiveness of soil inoculation treatments on microbiomes remains poorly explored. Therefore, innovative restoration treatments that target soil microbiota represent an opportunity to accelerate restoration outcomes. Here, we introduce the concept of ecological phage therapy-the application of phage for the targeted reduction of the most abundant and dominant bacterial taxa present in degraded ecosystems. We propose that naturally occurring bacteriophages-viruses that infect bacteria-could help rapidly shift soil microbiota towards target communities. Bacteriophages sculpt the microbiome by lysis of specific bacteria, and if followed by the addition of reference soil microbiota, such treatments could facilitate rapid reshaping of soil microbiota. Here, we experimentally tested this concept in a pilot study. We collected five replicate pre-treatment degraded soil samples, then three replicate soil samples 48 hours after phage, bacteria, and control treatments. Bacterial 16S rDNA sequencing showed that phage-treated soils had reduced bacterial diversity; however, when we combined ecological phage therapy with reference soil inoculation, we did not see a shift in soil bacterial community composition from degraded soil towards a reference-like community. Our pilot study provides early evidence that ecological phage therapy could help accelerate the reshaping of soil microbiota with the ultimate aim of reducing timeframes for ecosystem recovery. We recommend the next steps for ecological phage therapy be (a) developing appropriate risk assessment and management frameworks, and (b) focussing research effort on its practical application to maximise its accessibility to restoration practitioners.
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Affiliation(s)
- Tarryn Davies
- College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
| | | | - Craig Liddicoat
- College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
| | - Romy Dresken
- School of Biological Sciences and the Environment InstituteUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | - Rudolf H. Damen
- College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
- HAN University of Applied SciencesNijmegenNetherlands
| | - Robert A. Edwards
- College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
| | - Sunita A. Ramesh
- College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
| | - Martin F. Breed
- College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
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11
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Mason CE, Green J, Adamopoulos KI, Afshin EE, Baechle JJ, Basner M, Bailey SM, Bielski L, Borg J, Borg J, Broddrick JT, Burke M, Caicedo A, Castañeda V, Chatterjee S, Chin CR, Church G, Costes SV, De Vlaminck I, Desai RI, Dhir R, Diaz JE, Etlin SM, Feinstein Z, Furman D, Garcia-Medina JS, Garrett-Bakelman F, Giacomello S, Gupta A, Hassanin A, Houerbi N, Irby I, Javorsky E, Jirak P, Jones CW, Kamal KY, Kangas BD, Karouia F, Kim J, Kim JH, Kleinman AS, Lam T, Lawler JM, Lee JA, Limoli CL, Lucaci A, MacKay M, McDonald JT, Melnick AM, Meydan C, Mieczkowski J, Muratani M, Najjar D, Othman MA, Overbey EG, Paar V, Park J, Paul AM, Perdyan A, Proszynski J, Reynolds RJ, Ronca AE, Rubins K, Ryon KA, Sanders LM, Glowe PS, Shevde Y, Schmidt MA, Scott RT, Shirah B, Sienkiewicz K, Sierra MA, Siew K, Theriot CA, Tierney BT, Venkateswaran K, Hirschberg JW, Walsh SB, Walter C, Winer DA, Yu M, Zea L, Mateus J, Beheshti A. A second space age spanning omics, platforms and medicine across orbits. Nature 2024; 632:995-1008. [PMID: 38862027 DOI: 10.1038/s41586-024-07586-8] [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: 06/13/2023] [Accepted: 05/18/2024] [Indexed: 06/13/2024]
Abstract
The recent acceleration of commercial, private and multi-national spaceflight has created an unprecedented level of activity in low Earth orbit, concomitant with the largest-ever number of crewed missions entering space and preparations for exploration-class (lasting longer than one year) missions. Such rapid advancement into space from many new companies, countries and space-related entities has enabled a 'second space age'. This era is also poised to leverage, for the first time, modern tools and methods of molecular biology and precision medicine, thus enabling precision aerospace medicine for the crews. The applications of these biomedical technologies and algorithms are diverse, and encompass multi-omic, single-cell and spatial biology tools to investigate human and microbial responses to spaceflight. Additionally, they extend to the development of new imaging techniques, real-time cognitive assessments, physiological monitoring and personalized risk profiles tailored for astronauts. Furthermore, these technologies enable advancements in pharmacogenomics, as well as the identification of novel spaceflight biomarkers and the development of corresponding countermeasures. In this Perspective, we highlight some of the recent biomedical research from the National Aeronautics and Space Administration, Japan Aerospace Exploration Agency, European Space Agency and other space agencies, and detail the entrance of the commercial spaceflight sector (including SpaceX, Blue Origin, Axiom and Sierra Space) into aerospace medicine and space biology, the first aerospace medicine biobank, and various upcoming missions that will utilize these tools to ensure a permanent human presence beyond low Earth orbit, venturing out to other planets and moons.
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Affiliation(s)
- Christopher E Mason
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA.
- The WorldQuant Initiative for Quantitative Prediction, New York, NY, USA.
| | | | - Konstantinos I Adamopoulos
- Blue Marble Space Institute of Science, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
- Biomedical Engineering Laboratory, School of Electrical and Computer Engineering, National University of Athens, Athens, Greece
| | - Evan E Afshin
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Jordan J Baechle
- Buck Artificial Intelligence Platform, Buck Institute for Research on Aging, Novato, CA, USA
| | - Mathias Basner
- Unit for Experimental Psychiatry, Division of Sleep and Chronobiology, Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Susan M Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Luca Bielski
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Josef Borg
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta
| | - Joseph Borg
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta
| | - Jared T Broddrick
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
| | - Marissa Burke
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
- Embry-Riddle Aeronautical University, Department of Human Factors and Behavioral Neurobiology, Daytona Beach, FL, USA
| | - Andrés Caicedo
- Instituto de Investigaciones en Biomedicina iBioMed, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Escuela de Medicina, Colegio de Ciencias de la Salud COCSA, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Sistemas Médicos SIME, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Mito-Act Research Consortium, Quito, Ecuador
| | - Verónica Castañeda
- Faculty of Medicine, Universidad de los Andes, Santiago, Chile
- IMPACT, Center of Interventional Medicine for Precision and Advanced Cellular Therapy, Santiago, Chile
- Molecular Biology and Bioinformatics Lab, Program in Molecular Biology and Bioinformatics, Center for Biomedical Research and Innovation (CIIB), Universidad de los Andes, Santiago, Chile
| | | | - Christopher R Chin
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | | | - Sylvain V Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
| | - Iwijn De Vlaminck
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Rajeev I Desai
- Integrative Neurochemistry Laboratory, Behavioral Biology Program, Department of Psychiatry, Harvard Medical School, Belmont, MA, USA
| | - Raja Dhir
- Seed Health, Venice, CA, USA
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Juan Esteban Diaz
- Data Science Institute, School of Business, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Sofia M Etlin
- Department of Astrobiology, Cornell University, New York, NY, USA
| | - Zachary Feinstein
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - David Furman
- Buck Institute for Research on Aging, Novato, CA, USA
- Stanford 1000 Immunomes Project, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Research in Translational Medicine, Universidad Austral, CONICET, Pilar, Argentina
| | - J Sebastian Garcia-Medina
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Francine Garrett-Bakelman
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Stefania Giacomello
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Amira Hassanin
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Nadia Houerbi
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Iris Irby
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Emilia Javorsky
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Future of Life Institute, Campbell, CA, USA
| | - Peter Jirak
- Paracelsus Medical University, Salzburg, Austria
- Department of Internal Medicine, Hospital Gmünd, Lower Austria, Austria
| | - Christopher W Jones
- Unit for Experimental Psychiatry, Division of Sleep and Chronobiology, Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Khaled Y Kamal
- Redox Biology and Cell Signaling Laboratory, Department of Kinesiology and Sport Management, Texas A&M University, College Station, TX, USA
- Department of Kinesiology, Iowa State University, Ames, USA
| | - Brian D Kangas
- Behavioral Biology Program, Department of Psychiatry, Harvard Medical School, Belmont, MA, USA
| | - Fathi Karouia
- Blue Marble Institute of Science, Exobiology Branch NASA Ames Research Center, Moffett Field, CA, USA
- Space Research Within Reach, San Francisco, CA, USA
- Center for Space Medicine, Baylor College of Medicine, Houston, TX, USA
- BioServe Space Technologies, Smead Aerospace Engineering Science Department, University of Colorado Boulder, Boulder, CO, USA
| | - JangKeun Kim
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Joo Hyun Kim
- Redox Biology and Cell Signaling Laboratory, Department of Kinesiology and Sport Management, Texas A&M University, College Station, TX, USA
| | - Ashley S Kleinman
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Try Lam
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - John M Lawler
- Redox Biology and Cell Signaling Laboratory, Department of Kinesiology and Sport Management, Texas A&M University, College Station, TX, USA
| | - Jessica A Lee
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
| | - Charles L Limoli
- Department of Radiation Oncology, University of California, Irvine, CA, USA
| | - Alexander Lucaci
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Matthew MacKay
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - J Tyson McDonald
- Department of Radiation Medicine, Georgetown University School of Medicine, Washington, D.C., USA
| | - Ari M Melnick
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Jakub Mieczkowski
- International Research Agenda 3P-Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland
| | - Masafumi Muratani
- Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Deena Najjar
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Mariam A Othman
- Redox Biology and Cell Signaling Laboratory, Department of Kinesiology and Sport Management, Texas A&M University, College Station, TX, USA
| | - Eliah G Overbey
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- BioAstra, New York, NY, USA
| | - Vera Paar
- Department of Internal Medicine II, Division of Cardiology, Paracelsus Medical University, Salzburg, Austria
| | - Jiwoon Park
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Amber M Paul
- Blue Marble Space Institute of Science, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
- Embry-Riddle Aeronautical University, Department of Human Factors and Behavioral Neurobiology, Daytona Beach, FL, USA
| | - Adrian Perdyan
- International Research Agenda 3P-Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Jacqueline Proszynski
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Robert J Reynolds
- University of Texas Medical Branch, Galveston, TX, USA
- KBR, Inc., Houston, TX, USA
| | - April E Ronca
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
- Wake Forest Medical School, Dept of Obstetrics and Gynecology, Winston-Salem, NC, USA
| | | | - Krista A Ryon
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Lauren M Sanders
- Blue Marble Space Institute of Science, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
| | | | - Yash Shevde
- Ursa Biotechnology Corporation, Ursa Bio, New York, NY, USA
| | | | - Ryan T Scott
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
| | - Bader Shirah
- Department of Neuroscience, King Faisal Specialist Hospital and Research Centre, Jeddah, Saudi Arabia
| | - Karolina Sienkiewicz
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Maria A Sierra
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Keith Siew
- London Tubular Centre, Department of Renal Medicine, University College London, London, UK
| | | | - Braden T Tierney
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | | | - Jeremy Wain Hirschberg
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Stephen B Walsh
- London Tubular Centre, Department of Renal Medicine, University College London, London, UK
| | - Claire Walter
- Department of Physiology and Biophysics and Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Daniel A Winer
- Buck Institute for Research on Aging, Novato, CA, USA
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Division of Cellular and Molecular Biology, Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Min Yu
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Luis Zea
- Smead Aerospace Engineering Sciences Department, University of Colorado Boulder, Boulder, CO, USA
- Jaguar Space, LLC, Erie, CO, USA
| | - Jaime Mateus
- Space Exploration Technologies Corporation (SpaceX), Hawthorne, CA, USA
| | - Afshin Beheshti
- Blue Marble Space Institute of Science, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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12
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Wang Z, Yang J, Yang L, Zhong Y, Wang P. Characteristics of a pseudolysogenic phage vB_YpM_HQ103 infecting Yersinia pestis. Virus Res 2024; 346:199395. [PMID: 38782263 PMCID: PMC11177050 DOI: 10.1016/j.virusres.2024.199395] [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: 01/15/2024] [Revised: 05/09/2024] [Accepted: 05/11/2024] [Indexed: 05/25/2024]
Abstract
The plague, caused by Yersinia pestis, is a natural focal disease and the presence of Y. pestis in the environment is a critical ecological concern worldwide. The role of Y. pestis phages in the ecological life cycle of the plague is crucial. Previously, a temperature-sensitive phage named vB_YpM_HQ103 was isolated from plague foci in Yunnan province, China. Upon infecting the EV76 strain of Y. pestis, vB_YpM_HQ103 exhibits lysogenic behavior at 21 °C and lytic behavior at 37 °C. Various methods including continuous passage lysogenic tests, in vitro lysis tests, comparative genomic assays, fluorescence quantitative PCR and receptor identification tests were employed to demonstrate that the lysogenic life cycle of this phage is applicable to wild Y. pestis strains; its lysogeny is pseudolysogenic (carrying but not integrating), allowing it to replicate and proliferate within Y. pestis. Furthermore, we have identified the outer membrane protein OmpA of Y. pestis as the receptor for phage infection. In conclusion, our research provides insight into the characteristics and receptors of a novel Y. pestis phage infection with a pseudolysogenic cycle. The findings of this study enhance our understanding of Y. pestis phages and plague microecology, offering valuable insights for future studies on the conservation and genetic evolution of Y. pestis in nature.
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Affiliation(s)
- Zijian Wang
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute for Endemic Disease Control and Prevention, Dali, 671000, China
| | - Jiao Yang
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute for Endemic Disease Control and Prevention, Dali, 671000, China
| | - Lihua Yang
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute for Endemic Disease Control and Prevention, Dali, 671000, China
| | - Youhong Zhong
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute for Endemic Disease Control and Prevention, Dali, 671000, China
| | - Peng Wang
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute for Endemic Disease Control and Prevention, Dali, 671000, China.
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13
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Liébana R, Viver T, Ramos-Barbero MD, Bustos-Caparros E, Urdiain M, López C, Amoozegar MA, Antón J, Rossello-Mora R. Extremely halophilic brine community manipulation shows higher robustness of microbiomes inhabiting human-driven solar saltern than naturally driven lake. mSystems 2024; 9:e0053824. [PMID: 38934645 PMCID: PMC11324034 DOI: 10.1128/msystems.00538-24] [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: 04/16/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
Hypersaline ecosystems display taxonomically similar assemblages with low diversities and highly dense accompanying viromes. The ecological implications of viral infection on natural microbial populations remain poorly understood, especially at finer scales of diversity. Here, we sought to investigate the influence of changes in environmental physicochemical conditions and viral predation pressure by autochthonous and allochthonous viruses on host dynamics. For this purpose, we transplanted two microbiomes coming from distant hypersaline systems (solar salterns of Es Trenc in Spain and the thalassohaline lake of Aran-Bidgol lake in Iran), by exchanging the cellular fractions with the sterile-filtered accompanying brines with and without the free extracellular virus fraction. The midterm exposure (1 month) of the microbiomes to the new conditions showed that at the supraspecific taxonomic range, the assemblies from the solar saltern brine more strongly resisted the environmental changes and viral predation than that of the lake. The metagenome-assembled genomes (MAGs) analysis revealed an intraspecific transition at the ecotype level, mainly driven by changes in viral predation pressure, by both autochthonous and allochthonous viruses. IMPORTANCE Viruses greatly influence succession and diversification of their hosts, yet the effects of viral infection on the ecological dynamics of natural microbial populations remain poorly understood, especially at finer scales of diversity. By manipulating the viral predation pressure by autochthonous and allochthonous viruses, we uncovered potential phage-host interaction, and their important role in structuring the prokaryote community at an ecotype level.
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Affiliation(s)
- Raquel Liébana
- Marine Microbiology
Group, Department of Animal and Microbial Biodiversity, Mediterranean
Institute for Advanced Studies (IMEDEA,
UIB-CSIC), Esporles,
Spain
| | - Tomeu Viver
- Marine Microbiology
Group, Department of Animal and Microbial Biodiversity, Mediterranean
Institute for Advanced Studies (IMEDEA,
UIB-CSIC), Esporles,
Spain
- Department of
Molecular Ecology, Max Planck Institute for Marine
Microbiology, Bremen,
Germany
| | - María Dolores Ramos-Barbero
- Department of
Physiology, Genetics and Microbiology, University of
Alicante, Alicante,
Spain
- Department of
Genetics, Microbiology and Statistics, University of
Barcelona, Barcelona,
Spain
| | - Esteban Bustos-Caparros
- Marine Microbiology
Group, Department of Animal and Microbial Biodiversity, Mediterranean
Institute for Advanced Studies (IMEDEA,
UIB-CSIC), Esporles,
Spain
| | - Mercedes Urdiain
- Marine Microbiology
Group, Department of Animal and Microbial Biodiversity, Mediterranean
Institute for Advanced Studies (IMEDEA,
UIB-CSIC), Esporles,
Spain
| | - Cristina López
- Department of
Physiology, Genetics and Microbiology, University of
Alicante, Alicante,
Spain
| | - Mohammad Ali Amoozegar
- Extremophiles
Laboratory, Department of Microbiology, School of Biology and Center of
Excellence in Phylogeny of Living Organisms, College of Science,
University of Tehran,
Tehran, Iran
| | - Josefa Antón
- Department of
Physiology, Genetics and Microbiology, University of
Alicante, Alicante,
Spain
| | - Ramon Rossello-Mora
- Marine Microbiology
Group, Department of Animal and Microbial Biodiversity, Mediterranean
Institute for Advanced Studies (IMEDEA,
UIB-CSIC), Esporles,
Spain
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14
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Chong Qui E, Habtehyimer F, Germroth A, Grant J, Kosanovic L, Singh I, Hancock SP. Mycobacteriophage Alexphander Gene 94 Encodes an Essential dsDNA-Binding Protein during Lytic Infection. Int J Mol Sci 2024; 25:7466. [PMID: 39000573 PMCID: PMC11242194 DOI: 10.3390/ijms25137466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024] Open
Abstract
Mycobacteriophages are viruses that specifically infect bacterial species within the genera Mycobacterium and Mycolicibacterium. Over 2400 mycobacteriophages have been isolated on the host Mycolicibacterium smegmatis and sequenced. This wealth of genomic data indicates that mycobacteriophage genomes are diverse, mosaic, and contain numerous (35-60%) genes for which there is no predicted function based on sequence similarity to characterized orthologs, many of which are essential to lytic growth. To fully understand the molecular aspects of mycobacteriophage-host interactions, it is paramount to investigate the function of these genes and gene products. Here we show that the temperate mycobacteriophage, Alexphander, makes stable lysogens with a frequency of 2.8%. Alexphander gene 94 is essential for lytic infection and encodes a protein predicted to contain a C-terminal MerR family helix-turn-helix DNA-binding motif (HTH) and an N-terminal DinB/YfiT motif, a putative metal-binding motif found in stress-inducible gene products. Full-length and C-terminal gp94 constructs form high-order nucleoprotein complexes on 100-500 base pair double-stranded DNA fragments and full-length phage genomic DNA with little sequence discrimination for the DNA fragments tested. Maximum gene 94 mRNA levels are observed late in the lytic growth cycle, and gene 94 is transcribed in a message with neighboring genes 92 through 96. We hypothesize that gp94 is an essential DNA-binding protein for Alexphander during lytic growth. We proposed that gp94 forms multiprotein complexes on DNA through cooperative interactions involving its HTH DNA-binding motif at sites throughout the phage chromosome, facilitating essential DNA transactions required for lytic propagation.
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Affiliation(s)
| | | | | | | | | | | | - Stephen P. Hancock
- Department of Chemistry, Towson University, Towson, MD 21252, USA; (E.C.Q.); (F.H.); (A.G.); (J.G.); (L.K.); (I.S.)
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15
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Chakraborty S, Rohit A, Prasanthi SJ, Chauhan A. A New Casjensviridae Bacteriophage Isolated from Hospital Sewage for Inactivation of Biofilms of Carbapenem Resistant Klebsiella pneumoniae Clinical Isolates. Pharmaceutics 2024; 16:904. [PMID: 39065601 PMCID: PMC11280391 DOI: 10.3390/pharmaceutics16070904] [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: 05/27/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
Klebsiella pneumoniae, a member of the ESKAPE pathogen group, is a prominent cause of hospital-acquired infections. The WHO has recognized carbapenem-resistant K. pneumoniae as a critical-one priority pathogen. These resilient superbugs have the ability to form biofilms and present a significant global threat. In the present study, we isolated and characterized a bacteriophage SAKp02, from hospital sewage, infectious to carbapenem-resistant K. pneumoniae patient isolates. SAKp02 could infect 43 of 72 clinical isolates, indicating a broad host spectrum. Whole genome analysis classified SAKp02 within the family Casjensviridae, with a 59,343 bp genome encoding 82 ORFs. Comparative genomic analysis revealed significant differences between SAKp02 and its closest viruses, indicating a distinct genetic makeup positioning it as a novel phage strain within the lineage. The SAKp02 genome comprises bacteriolytic enzymes, including holin, endolysin, and phage depolymerase, crucial for bacterial lysis and biofilm disruption. It reduced biofilm biomass by over threefold compared to the control and eradicated 99% of viable cells within a 4 h treatment period. Scanning electron microscopy corroborated the ability of the phage to dismantle biofilm matrices and lyse bacterial cells. Safe and effective treatments are warranted, and hence, the fully characterized lytic phages with therapeutic potential against drug-resistant clinical isolates of bacteria are needed. Our study is the first to report the antibacterial and antibiofilm activity of Casjensviridae phages, and our discovery of a novel K. pneumoniae phage broadens the arsenal against the bacteria.
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Affiliation(s)
- Sambuddha Chakraborty
- Department of Microbiology, Tripura University, Suryamaninagar 799022, India
- Department of Microbiology, University of Delhi South Campus, Benito Jaurez Marg, New Delhi 110021, India
| | - Anusha Rohit
- Madras Medical Mission Hospital, Chennai 600037, India
| | | | - Ashwini Chauhan
- Department of Microbiology, Tripura University, Suryamaninagar 799022, India
- Department of Microbiology, University of Delhi South Campus, Benito Jaurez Marg, New Delhi 110021, India
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16
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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 PMCID: PMC11346441 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)
| | - Joshua Williams
- School of Life Sciences, University of Warwick, Coventry, U.K
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17
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de Melo AG, Morency C, Moineau S. Virulence-associated factors as targets for phage infection. Curr Opin Microbiol 2024; 79:102471. [PMID: 38569419 DOI: 10.1016/j.mib.2024.102471] [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: 09/27/2023] [Revised: 03/18/2024] [Accepted: 03/20/2024] [Indexed: 04/05/2024]
Abstract
Bacterial pathogens can infect a wide range of hosts and pose a threat to public and animal health as well as to agriculture. The emergence of antibiotic-resistant strains has increased this risk by making the treatment of bacterial infections even more challenging. Pathogenic bacteria thrive in various ecological niches, but they can also be specifically targeted and killed by bacteriophages (phages). Lytic phages are now investigated and even used, in some cases, as alternatives or complements to antibiotics for preventing or treating bacterial infections (phage therapy). As such, it is key to identify factors responsible for phage specificity and efficiency. Here, we review recent advances in virulence-associated factors that are targeted by phages. We highlight components of the bacterial cell surface, effector systems, and motility structures exploited by phages and the effects of phages on cell aggregation and communication. We also look at the fitness trade-off of phage resistance.
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Affiliation(s)
- Alessandra G de Melo
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Québec City, QC G1V 0A6, Canada
| | - Carlee Morency
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Québec City, QC G1V 0A6, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Québec City, QC G1V 0A6, Canada; Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, QC G1V 0A6, Canada.
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18
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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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19
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Xepapadaki P, Megremis S, Rovina N, Wardzyńska A, Pasioti M, Kritikou M, Papadopoulos NG. Exploring the Impact of Airway Microbiome on Asthma Morbidity: A Focus on the "Constructing a 'Eubiosis Reinstatement Therapy' for Asthma-CURE" Project. Pulm Ther 2024; 10:171-182. [PMID: 38814533 PMCID: PMC11282048 DOI: 10.1007/s41030-024-00261-3] [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: 02/26/2024] [Accepted: 05/02/2024] [Indexed: 05/31/2024] Open
Abstract
The asthma pandemic imposes a huge burden on patients and health systems in both developed and developing countries. Despite available treatments, symptom control is generally suboptimal, and hospitalizations and deaths remain at unacceptably high levels. A pivotal aspect of asthma that warrants further exploration is the influence of the respiratory microbiome and virome in modulating disease activity. A plethora of studies report that the respiratory microbiome is characteristically dysbiotic in asthma. In addition, our data suggest that dysbiosis is also observed on the respiratory virome, partly characterized by the reduced abundance of bacteriophages (phages). Even though phages can naturally infect and control their bacterial prey, phage therapy has been grossly neglected in the Western world, although more recently it is more widely used as a novel tool against bacterial infections. However, it has never been used for tackling microbiome dysbiosis in human non-communicable diseases. This review provides an up-to-date understanding of the microbiome and virome's role within the airways in relation to asthma morbidity. It also advances the rationale and hypothesis for the CURE project. Specifically, the CURE project suggests that managing the respiratory microbiome through phage therapy is viable and may result in restoring eubiosis within the asthmatic airway. This entails controlling immune dysregulation and the clinical manifestation of the disease. To accomplish this goal, it is crucial to predict the effects of introducing specific phage mixtures into the intricate ecology of the airways and devise suitable interventions.
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Affiliation(s)
- Paraskevi Xepapadaki
- Allergy Department, 2nd Paediatric Clinic, National and Kapodistrian University of Athens, 41, Fidippidou, 11527, Athens, Greece.
| | - Spyridon Megremis
- Department of Genetics and Genome Biology, Centre for Phage Research, University of Leicester, Leicester, UK
| | - Nikoletta Rovina
- 1st Department of Respiratory Medicine, Sotiria Hospital, School of Medicine, National and Kapodistrian University of Athens, 11527, Athens, Greece
| | | | - Maria Pasioti
- Allergy Department, 2nd Paediatric Clinic, National and Kapodistrian University of Athens, 41, Fidippidou, 11527, Athens, Greece
| | - Maria Kritikou
- Allergy Department, 2nd Paediatric Clinic, National and Kapodistrian University of Athens, 41, Fidippidou, 11527, Athens, Greece
| | - Nikolaos G Papadopoulos
- Allergy Department, 2nd Paediatric Clinic, National and Kapodistrian University of Athens, 41, Fidippidou, 11527, Athens, Greece
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20
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Kraus S, Fletcher ML, Łapińska U, Chawla K, Baker E, Attrill EL, O'Neill P, Farbos A, Jeffries A, Galyov EE, Korbsrisate S, Barnes KB, Harding SV, Tsaneva-Atanasova K, Blaskovich MAT, Pagliara S. Phage-induced efflux down-regulation boosts antibiotic efficacy. PLoS Pathog 2024; 20:e1012361. [PMID: 38941361 PMCID: PMC11239113 DOI: 10.1371/journal.ppat.1012361] [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: 11/16/2023] [Revised: 07/11/2024] [Accepted: 06/21/2024] [Indexed: 06/30/2024] Open
Abstract
The interactions between a virus and its host vary in space and time and are affected by the presence of molecules that alter the physiology of either the host or the virus. Determining the molecular mechanisms at the basis of these interactions is paramount for predicting the fate of bacterial and phage populations and for designing rational phage-antibiotic therapies. We study the interactions between stationary phase Burkholderia thailandensis and the phage ΦBp-AMP1. Although heterogeneous genetic resistance to phage rapidly emerges in B. thailandensis, the presence of phage enhances the efficacy of three major antibiotic classes, the quinolones, the beta-lactams and the tetracyclines, but antagonizes tetrahydrofolate synthesis inhibitors. We discovered that enhanced antibiotic efficacy is facilitated by reduced antibiotic efflux in the presence of phage. This new phage-antibiotic therapy allows for eradication of stationary phase bacteria, whilst requiring reduced antibiotic concentrations, which is crucial for treating infections in sites where it is difficult to achieve high antibiotic concentrations.
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Affiliation(s)
- Samuel Kraus
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Megan L Fletcher
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Urszula Łapińska
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Krina Chawla
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Evan Baker
- Department of Mathematics and Living Systems Institute, University of Exeter, Exeter, Devon, United Kingdom
- EPSRC Hub for Quantitative Modelling in Healthcare, University of Exeter, Exeter, United Kingdom
| | - Erin L Attrill
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Paul O'Neill
- Biosciences, University of Exeter, Exeter, Devon, EX4 4QD, United Kingdom
| | - Audrey Farbos
- Biosciences, University of Exeter, Exeter, Devon, EX4 4QD, United Kingdom
| | - Aaron Jeffries
- Biosciences, University of Exeter, Exeter, Devon, EX4 4QD, United Kingdom
| | - Edouard E Galyov
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, United Kingdom
| | - Sunee Korbsrisate
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok Thailand
| | - Kay B Barnes
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Sarah V Harding
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Krasimira Tsaneva-Atanasova
- Department of Mathematics and Living Systems Institute, University of Exeter, Exeter, Devon, United Kingdom
- EPSRC Hub for Quantitative Modelling in Healthcare, University of Exeter, Exeter, United Kingdom
| | - Mark A T Blaskovich
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Stefano Pagliara
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon, United Kingdom
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21
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Auzat I, Ouldali M, Jacquet E, Fauler B, Mielke T, Tavares P. Dual function of a highly conserved bacteriophage tail completion protein essential for bacteriophage infectivity. Commun Biol 2024; 7:590. [PMID: 38755280 PMCID: PMC11099176 DOI: 10.1038/s42003-024-06221-6] [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: 08/28/2023] [Accepted: 04/19/2024] [Indexed: 05/18/2024] Open
Abstract
Infection of bacteria by phages is a complex multi-step process that includes specific recognition of the host cell, creation of a temporary breach in the host envelope, and ejection of viral DNA into the bacterial cytoplasm. These steps must be perfectly regulated to ensure efficient infection. Here we report the dual function of the tail completion protein gp16.1 of bacteriophage SPP1. First, gp16.1 has an auxiliary role in assembly of the tail interface that binds to the capsid connector. Second, gp16.1 is necessary to ensure correct routing of phage DNA to the bacterial cytoplasm. Viral particles assembled without gp16.1 are indistinguishable from wild-type virions and eject DNA normally in vitro. However, they release their DNA to the extracellular space upon interaction with the host bacterium. The study shows that a highly conserved tail completion protein has distinct functions at two essential steps of the virus life cycle in long-tailed phages.
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Affiliation(s)
- Isabelle Auzat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Malika Ouldali
- Université Paris-Saclay, CEA, CNRS, Cryo-Electron Microscopy Facility, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Eric Jacquet
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
| | - Beatrix Fauler
- Microscopy and Cryo-electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195, Berlin, Germany
| | - Thorsten Mielke
- Microscopy and Cryo-electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195, Berlin, Germany
| | - Paulo Tavares
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
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22
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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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23
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Yan M, Yu Z. Viruses contribute to microbial diversification in the rumen ecosystem and are associated with certain animal production traits. MICROBIOME 2024; 12:82. [PMID: 38725064 PMCID: PMC11080232 DOI: 10.1186/s40168-024-01791-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/09/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND The rumen microbiome enables ruminants to digest otherwise indigestible feedstuffs, thereby facilitating the production of high-quality protein, albeit with suboptimal efficiency and producing methane. Despite extensive research delineating associations between the rumen microbiome and ruminant production traits, the functional roles of the pervasive and diverse rumen virome remain to be determined. RESULTS Leveraging a recent comprehensive rumen virome database, this study analyzes virus-microbe linkages, at both species and strain levels, across 551 rumen metagenomes, elucidating patterns of microbial and viral diversity, co-occurrence, and virus-microbe interactions. Additionally, this study assesses the potential role of rumen viruses in microbial diversification by analyzing prophages found in rumen metagenome-assembled genomes. Employing CRISPR-Cas spacer-based matching and virus-microbe co-occurrence network analysis, this study suggests that the viruses in the rumen may regulate microbes at strain and community levels through both antagonistic and mutualistic interactions. Moreover, this study establishes that the rumen virome demonstrates responsiveness to dietary shifts and associations with key animal production traits, including feed efficiency, lactation performance, weight gain, and methane emissions. CONCLUSIONS These findings provide a substantive framework for further investigations to unravel the functional roles of the virome in the rumen in shaping the microbiome and influencing overall animal production performance. Video Abstract.
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Affiliation(s)
- Ming Yan
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA.
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA.
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24
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Oyejobi GK, Zhang X, Xiong D, Xue H, Shi M, Yang H, Wei H. Phage-Bacterial Interaction Alters Phenotypes Associated with Virulence in Acinetobacter baumannii. Viruses 2024; 16:743. [PMID: 38793624 PMCID: PMC11125765 DOI: 10.3390/v16050743] [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: 03/27/2024] [Revised: 04/30/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Bacteriophages exert strong selection on their bacterial hosts to evolve resistance. At the same time, the fitness costs on bacteria following phage resistance may change their virulence, which may affect the therapeutic outcomes of phage therapy. In this study, we set out to assess the costs of phage resistance on the in vitro virulence of priority 1 nosocomial pathogenic bacterium, Acinetobacter baumannii. By subjecting phage-resistant variant Ev5-WHG of A. baumannii WHG40004 to several in vitro virulence profiles, we found that its resistance to phage is associated with reduced fitness in host microenvironments. Also, the mutant exhibited impaired adhesion and invasion to mammalian cells, as well as increased susceptibility to macrophage phagocytosis. Furthermore, the whole-genome sequencing of the mutant revealed that there exist multiple mutations which may play a role in phage resistance and altered virulence. Altogether, this study demonstrates that resistance to phage can significantly alter phenotypes associated with virulence in Acinetobacter baumannii.
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Affiliation(s)
- Greater Kayode Oyejobi
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (G.K.O.); (X.Z.); (D.X.); (H.X.); (M.S.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoxu Zhang
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (G.K.O.); (X.Z.); (D.X.); (H.X.); (M.S.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongyan Xiong
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (G.K.O.); (X.Z.); (D.X.); (H.X.); (M.S.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Heng Xue
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (G.K.O.); (X.Z.); (D.X.); (H.X.); (M.S.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengjuan Shi
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (G.K.O.); (X.Z.); (D.X.); (H.X.); (M.S.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hang Yang
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (G.K.O.); (X.Z.); (D.X.); (H.X.); (M.S.)
| | - Hongping Wei
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (G.K.O.); (X.Z.); (D.X.); (H.X.); (M.S.)
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25
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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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26
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Yarahmadi A, Zare M, Aghayari M, Afkhami H, Jafari GA. Therapeutic bacteria and viruses to combat cancer: double-edged sword in cancer therapy: new insights for future. Cell Commun Signal 2024; 22:239. [PMID: 38654309 PMCID: PMC11040964 DOI: 10.1186/s12964-024-01622-w] [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] [Accepted: 04/17/2024] [Indexed: 04/25/2024] Open
Abstract
Cancer, ranked as the second leading cause of mortality worldwide, leads to the death of approximately seven million people annually, establishing itself as one of the most significant health challenges globally. The discovery and identification of new anti-cancer drugs that kill or inactivate cancer cells without harming normal and healthy cells and reduce adverse effects on the immune system is a potential challenge in medicine and a fundamental goal in Many studies. Therapeutic bacteria and viruses have become a dual-faceted instrument in cancer therapy. They provide a promising avenue for cancer treatment, but at the same time, they also create significant obstacles and complications that contribute to cancer growth and development. This review article explores the role of bacteria and viruses in cancer treatment, examining their potential benefits and drawbacks. By amalgamating established knowledge and perspectives, this review offers an in-depth examination of the present research landscape within this domain and identifies avenues for future investigation.
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Affiliation(s)
- Aref Yarahmadi
- Department of Biology, Khorramabad Branch, Islamic Azad University, Khorramabad, Iran
| | - Mitra Zare
- Department of Microbiology, Faculty of Sciences, Kerman Branch, Islamic Azad University, Kerman, Iran
| | - Masoomeh Aghayari
- Department of Microbiology, Faculty of Sciences, Urmia Branch, Islamic Azad University, Urmia, Iran
| | - Hamed Afkhami
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran.
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran.
- Department of Medical Microbiology, Faculty of Medicine, Shahed University, Tehran, Iran.
| | - Gholam Ali Jafari
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran.
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27
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Chitboonthavisuk C, Martin C, Huss P, Peters JM, Anantharaman K, Raman S. Systematic genome-wide discovery of host factors governing bacteriophage infectivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.20.590424. [PMID: 38659955 PMCID: PMC11042327 DOI: 10.1101/2024.04.20.590424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Bacterial host factors regulate the infection cycle of bacteriophages. Except for some well-studied host factors (e.g., receptors or restriction-modification systems), the contribution of the rest of the host genome on phage infection remains poorly understood. We developed PHAGEPACK, a pooled assay that systematically and comprehensively measures each host-gene impact on phage fitness. PHAGEPACK combines CRISPR interference with phage packaging to link host perturbation to phage fitness during active infection. Using PHAGEPACK, we constructed a genome-wide map of genes impacting T7 phage fitness in permissive E. coli, revealing pathways previously unknown to affect phage packaging. When applied to the non-permissive E. coli O121, PHAGEPACK identified pathways leading to host resistance; their removal increased phage susceptibility up to a billion-fold. Bioinformatic analysis indicates phage genomes carry homologs or truncations of key host factors, potentially for fitness advantage. In summary, PHAGEPACK offers valuable insights into phage-host interactions, phage evolution, and bacterial resistance.
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28
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Gucwa K, Wons E, Wisniewska A, Jakalski M, Dubiak Z, Kozlowski LP, Mruk I. Lethal perturbation of an Escherichia coli regulatory network is triggered by a restriction-modification system's regulator and can be mitigated by excision of the cryptic prophage Rac. Nucleic Acids Res 2024; 52:2942-2960. [PMID: 38153127 PMCID: PMC11014345 DOI: 10.1093/nar/gkad1234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 12/29/2023] Open
Abstract
Bacterial gene regulatory networks orchestrate responses to environmental challenges. Horizontal gene transfer can bring in genes with regulatory potential, such as new transcription factors (TFs), and this can disrupt existing networks. Serious regulatory perturbations may even result in cell death. Here, we show the impact on Escherichia coli of importing a promiscuous TF that has adventitious transcriptional effects within the cryptic Rac prophage. A cascade of regulatory network perturbations occurred on a global level. The TF, a C regulatory protein, normally controls a Type II restriction-modification system, but in E. coli K-12 interferes with expression of the RacR repressor gene, resulting in de-repression of the normally-silent Rac ydaT gene. YdaT is a prophage-encoded TF with pleiotropic effects on E. coli physiology. In turn, YdaT alters expression of a variety of bacterial regulons normally controlled by the RcsA TF, resulting in deficient lipopolysaccharide biosynthesis and cell division. At the same time, insufficient RacR repressor results in Rac DNA excision, halting Rac gene expression due to loss of the replication-defective Rac prophage. Overall, Rac induction appears to counteract the lethal toxicity of YdaT. We show here that E. coli rewires its regulatory network, so as to minimize the adverse regulatory effects of the imported C TF. This complex set of interactions may reflect the ability of bacteria to protect themselves by having robust mechanisms to maintain their regulatory networks, and/or suggest that regulatory C proteins from mobile operons are under selection to manipulate their host's regulatory networks for their own benefit.
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Affiliation(s)
- Katarzyna Gucwa
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ewa Wons
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Aleksandra Wisniewska
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Marcin Jakalski
- 3P-Medicine Laboratory, Medical University of Gdansk, Debinki 7, 80-211 Gdansk, Poland
| | - Zuzanna Dubiak
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Lukasz Pawel Kozlowski
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
| | - Iwona Mruk
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
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Kunz Coyne AJ, Stamper K, Bleick C, Kebriaei R, Lehman SM, Rybak MJ. Synergistic bactericidal effects of phage-enhanced antibiotic therapy against MRSA biofilms. Microbiol Spectr 2024; 12:e0321223. [PMID: 38411110 PMCID: PMC10986480 DOI: 10.1128/spectrum.03212-23] [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: 08/30/2023] [Accepted: 01/10/2024] [Indexed: 02/28/2024] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) causes biofilm-related medical device infections. Phage-antibiotic combinations offer potential therapy due to proven in vitro antibiofilm efficacy. We evaluated phage-antibiotic synergy against biofilms using modified checkerboard and 24-h time-kill assays. Humanized-simulated daptomycin (DAP) (10, 8, and 6 mg/kg q24h) and ceftaroline (CPT) (600 mg q12h) were combined with Intesti13, Sb-1, and Romulus phages (tMOI 1, q12h). Assays were conducted in 168-h biofilm reactor models against DAP non-susceptible (DNS) vancomycin intermediate S. aureus (VISA) MRSA D712 and DAP-susceptible MRSA 8014. Synergistic activity and bactericidal activity were defined as ≥2log10 CFU/mL reduction from antibiotic-only regimens and ≥3log10 CFU/mL decrease from baseline at 24 h. Differences were analyzed by one-way analysis of variance with Tukey's post hoc test (P ≤ 0.05 is considered significant). Surviving bacteria were examined for antibiotic minimum biofilm inhibitory concentration (MBIC) changes and phage susceptibility. In 168-h biofilm models, humanized DAP 10 mg/kg + CPT, combined with a 2-phage cocktail (Intesti13 + Sb-1) against D712, and a 3-phage cocktail (Intesti13 + Sb-1 + Romulus) against 8014, demonstrated synergistic bactericidal activity. At 168 h, bacteria were minimally detectable [2log10 CFU/cm2 (-Δ4.23 and -Δ4.42 log10 CFU/cm2; both P < 0.001)]. Antibiotic MBIC remained unchanged compared to baseline across various time points. None of the tested bacteria at 168 h exhibited complete phage resistance. This study reveals bactericidal efficacy of DAP + CPT with 2-phage and 3-phage cocktails against DNS VISA and MRSA isolates (D712 and 8014) in biofilm models, maintaining susceptibility. Further research is needed for diverse strains and durations, aligning with infection care. IMPORTANCE The prevalence of biofilm-associated medical device infections caused by methicillin-resistant Staphylococcus aureus (MRSA) presents a pressing medical challenge. The latest research demonstrates the potential of phage-antibiotic combinations (PACs) as a promising solution, notably in vitro antibiofilm efficacy. By adopting modified checkerboard and 24-h time-kill assays, the study investigated the synergistic action of phages combined with humanized-simulated doses of daptomycin (DAP) and ceftaroline (CPT). The results were promising: a combination of DAP, CPT, and either a 2-phage or 3-phage cocktail effectively exhibited bactericidal activity against both DAP non-susceptible vancomycin intermediate S. aureus MRSA and DAP-susceptible MRSA strains within 168-h biofilm models. Moreover, post-treatment evaluations revealed no discernible rise in antibiotic resistance or complete phage resistance. This pioneering work suggests the potential of PACs in addressing MRSA biofilm infections, setting the stage for further expansive research tailored to diverse bacterial strains and treatment durations.
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Affiliation(s)
- Ashlan J. Kunz Coyne
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan, USA
| | - Kyle Stamper
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan, USA
| | - Callan Bleick
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan, USA
| | - Razieh Kebriaei
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan, USA
| | - Susan M. Lehman
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Michael J. Rybak
- Anti-Infective Research Laboratory, Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan, USA
- Department of Pharmacy Services, Detroit Receiving Hospital, Detroit Medical Center, Detroit, Michigan, USA
- Department of Medicine, Division of Infectious Diseases, Wayne State University, Detroit, Michigan, USA
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30
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O’Connor PBF, Mahony J, Casey E, Baranov PV, van Sinderen D, Yordanova MM. Ribosome profiling reveals downregulation of UMP biosynthesis as the major early response to phage infection. Microbiol Spectr 2024; 12:e0398923. [PMID: 38451091 PMCID: PMC10986495 DOI: 10.1128/spectrum.03989-23] [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: 11/23/2023] [Accepted: 02/14/2024] [Indexed: 03/08/2024] Open
Abstract
Bacteria have evolved diverse defense mechanisms to counter bacteriophage attacks. Genetic programs activated upon infection characterize phage-host molecular interactions and ultimately determine the outcome of the infection. In this study, we applied ribosome profiling to monitor protein synthesis during the early stages of sk1 bacteriophage infection in Lactococcus cremoris. Our analysis revealed major changes in gene expression within 5 minutes of sk1 infection. Notably, we observed a specific and severe downregulation of several pyr operons which encode enzymes required for uridine monophosphate biosynthesis. Consistent with previous findings, this is likely an attempt of the host to starve the phage of nucleotides it requires for propagation. We also observed a gene expression response that we expect to benefit the phage. This included the upregulation of 40 ribosome proteins that likely increased the host's translational capacity, concurrent with a downregulation of genes that promote translational fidelity (lepA and raiA). In addition to the characterization of host-phage gene expression responses, the obtained ribosome profiling data enabled us to identify two putative recoding events as well as dozens of loci currently annotated as pseudogenes that are actively translated. Furthermore, our study elucidated alterations in the dynamics of the translation process, as indicated by time-dependent changes in the metagene profile, suggesting global shifts in translation rates upon infection. Additionally, we observed consistent modifications in the ribosome profiles of individual genes, which were apparent as early as 2 minutes post-infection. The study emphasizes our ability to capture rapid alterations of gene expression during phage infection through ribosome profiling. IMPORTANCE The ribosome profiling technology has provided invaluable insights for understanding cellular translation and eukaryotic viral infections. However, its potential for investigating host-phage interactions remains largely untapped. Here, we applied ribosome profiling to Lactococcus cremoris cultures infected with sk1, a major infectious agent in dairy fermentation processes. This revealed a profound downregulation of genes involved in pyrimidine nucleotide synthesis at an early stage of phage infection, suggesting an anti-phage program aimed at restricting nucleotide availability and, consequently, phage propagation. This is consistent with recent findings and contributes to our growing appreciation for the role of nucleotide limitation as an anti-viral strategy. In addition to capturing rapid alterations in gene expression levels, we identified translation occurring outside annotated regions, as well as signatures of non-standard translation mechanisms. The gene profiles revealed specific changes in ribosomal densities upon infection, reflecting alterations in the dynamics of the translation process.
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Affiliation(s)
- Patrick B. F. O’Connor
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
- EIRNA Bio, Bioinnovation Hub, Cork, Ireland
| | - Jennifer Mahony
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Eoghan Casey
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Pavel V. Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
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31
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Zhang M, Zhou Y, Cui X, Zhu L. The Potential of Co-Evolution and Interactions of Gut Bacteria-Phages in Bamboo-Eating Pandas: Insights from Dietary Preference-Based Metagenomic Analysis. Microorganisms 2024; 12:713. [PMID: 38674657 PMCID: PMC11051890 DOI: 10.3390/microorganisms12040713] [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: 01/16/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Bacteria and phages are two of the most abundant biological entities in the gut microbiome, and diet and host phylogeny are two of the most critical factors influencing the gut microbiome. A stable gut bacterial community plays a pivotal role in the host's physiological development and immune health. A phage is a virus that directly infects bacteria, and phages' close associations and interactions with bacteria are essential for maintaining the stability of the gut bacterial community and the entire microbial ecosystem. Here, we utilized 99 published metagenomic datasets from 38 mammalian species to investigate the relationship (diversity and composition) and potential interactions between gut bacterial and phage communities and the impact of diet and phylogeny on these communities. Our results highlight the co-evolutionary potential of bacterial-phage interactions within the mammalian gut. We observed a higher alpha diversity in gut bacteria than in phages and identified positive correlations between bacterial and phage compositions. Furthermore, our study revealed the significant influence of diet and phylogeny on mammalian gut bacterial and phage communities. We discovered that the impact of dietary factors on these communities was more pronounced than that of phylogenetic factors at the order level. In contrast, phylogenetic characteristics had a more substantial influence at the family level. The similar omnivorous dietary preference and closer phylogenetic relationship (family Ursidae) may contribute to the similarity of gut bacterial and phage communities between captive giant panda populations (GPCD and GPYA) and omnivorous animals (OC; including Sun bear, brown bear, and Asian black bear). This study employed co-occurrence microbial network analysis to reveal the potential interaction patterns between bacteria and phages. Compared to other mammalian groups (carnivores, herbivores, and omnivores), the gut bacterial and phage communities of bamboo-eating species (giant pandas and red pandas) exhibited a higher level of interaction. Additionally, keystone species and modular analysis showed the potential role of phages in driving and maintaining the interaction patterns between bacteria and phages in captive giant pandas. In sum, gaining a comprehensive understanding of the interaction between the gut microbiota and phages in mammals is of great significance, which is of great value in promoting healthy and sustainable mammals and may provide valuable insights into the conservation of wildlife populations, especially endangered animal species.
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Affiliation(s)
| | | | | | - Lifeng Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing 210098, China; (M.Z.); (Y.Z.); (X.C.)
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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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33
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Li W, Liang H, He W, Gao X, Wu Z, Hu T, Lin X, Wang M, Zhong Y, Zhang H, Ge L, Jin X, Xiao L, Zou Y. Genomic and functional diversity of cultivated Bifidobacterium from human gut microbiota. Heliyon 2024; 10:e27270. [PMID: 38463766 PMCID: PMC10923715 DOI: 10.1016/j.heliyon.2024.e27270] [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: 08/27/2023] [Revised: 02/14/2024] [Accepted: 02/27/2024] [Indexed: 03/12/2024] Open
Abstract
The genus Bifidobacterium widely exists in human gut and has been increasingly used as the adjuvant probiotics for the prevention and treatment of diseases. However, the functional differences of Bifidobacterium genomes from different regions of the world remain unclear. We here describe an extensive study on the genomic characteristics and function annotations of 1512 genomes (clustered to 849 non-redundant genomes) of Bifidobacterium cultured from human gut. The distribution of some carbohydrate-active enzymes varied among different Bifidobacterium species and continents. More than 36% of the genomes of B. pseudocatenulatum harbored biosynthetic gene clusters of lanthipeptide-class-iv. 99.76% of the cultivated genomes of Bifidobacterium harbored genes of bile salt hydrolase. Most genomes of B. adolescentis, and all genomes of B. dentium harbored genes involved in gamma-aminobutyric acid synthesis. B. longum subsp. infantis were characterized harboring most genes related to human milk oligosaccharide utilization. Significant differences between the distribution of antibiotic resistance genes among different species and continents revealed the importance to use antibiotics precisely in the clinical treatment. Phages infecting Bifidobacterium and horizontal gene transfers occurring in genomes of Bifidobacterium were dependent on species and region sources, and might help Bifidobacterium adapt to the environment. In addition, the distribution of Bifidobacterium in human gut was found varied from different regions of the world. This study represents a comprehensive view of characteristics and functions of genomes of cultivated Bifidobacterium from human gut, and enables clinical advances in the future.
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Affiliation(s)
- Wenxi Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
- BGI Research, Shenzhen, 518083, China
| | | | - Wenxin He
- BGI Research, Shenzhen, 518083, China
| | | | - Zhinan Wu
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Xiaoqian Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
- BGI Research, Shenzhen, 518083, China
| | - Mengmeng Wang
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiyi Zhong
- BGI Research, Shenzhen, 518083, China
- BGI Precision Nutrition (Shenzhen) Technology Co., Ltd, Shenzhen, China
| | - Haifeng Zhang
- BGI Research, Shenzhen, 518083, China
- BGI Precision Nutrition (Shenzhen) Technology Co., Ltd, Shenzhen, China
| | - Lan Ge
- BGI Research, Shenzhen, 518083, China
- BGI Precision Nutrition (Shenzhen) Technology Co., Ltd, Shenzhen, China
| | - Xin Jin
- BGI Research, Shenzhen, 518083, China
| | - Liang Xiao
- BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI Research, Qingdao, 266555, China
- Shenzhen Engineering Laboratory of Detection and Intervention of human intestinal microbiome, BGI-Shenzhen, Shenzhen, China
| | - Yuanqiang Zou
- BGI Research, Shenzhen, 518083, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark
- BGI Research, Qingdao, 266555, China
- Shenzhen Engineering Laboratory of Detection and Intervention of human intestinal microbiome, BGI-Shenzhen, Shenzhen, China
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34
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Ji Y, Xi H, Chen C, Sun C, Feng X, Lei L, Han W, Gu J. The pig intestinal phageome is an important reservoir and transfer vector for virulence genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170076. [PMID: 38220020 DOI: 10.1016/j.scitotenv.2024.170076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/16/2024]
Abstract
Bacteriophages (phages) can significantly influence the composition and functions of their host communities, and enhance host pathogenicity via the transport of phage-encoded virulence genes. Phages are the main component of animal gut viruses, however, there are few reports on the piglet gut phageome and its contribution to virulence genes. Here, a total of 185 virulence genes from 59,955 predicted genes of gut phages in weaned piglets were identified, with 0.688 % of the phage contigs coding for at least one virulence gene. The virulence gene pblA was the most abundant, with various virulence genes significantly correlated with gut phages and their encoded mobile gene element (MGE) genes. Importantly, multiple virulence genes and MGE genes coexist in some phage sequences, and up to 12 virulence genes were detected in a single phage sequence, greatly increasing the risk of phage-mediated transmission of virulence genes into the bacterial genome. In addition, diarrhoea has driven changes in the composition and structure of phage and bacterial communities in the intestinal tract of weaned piglets, significantly increasing the abundance of phage contigs encoding both virulence genes and MGE genes in faecal samples, which potentially increases the risk of phage-mediated virulence genes being transfected into the gut bacterial genome. In summary, this study expands our understanding of the gut microbiome of piglets, advances our understanding of the potential role of phages in driving host pathogenesis in the gut system, and provides new insights into the sources of virulence genes and genetic evolution of bacteria in pig farm environments.
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Affiliation(s)
- Yalu Ji
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Hengyu Xi
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Chong Chen
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Changjiang Sun
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xin Feng
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Liancheng Lei
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Wenyu Han
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jingmin Gu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China.
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35
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Stante M, Weiland-Bräuer N, von Hoyningen-Huene AJE, Schmitz RA. Marine bacteriophages disturb the associated microbiota of Aurelia aurita with a recoverable effect on host morphology. Front Microbiol 2024; 15:1356337. [PMID: 38533338 PMCID: PMC10964490 DOI: 10.3389/fmicb.2024.1356337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/21/2024] [Indexed: 03/28/2024] Open
Abstract
The concept of the metaorganism describes a multicellular host and its diverse microbial community, which form one biological unit with a combined genetic repertoire that significantly influences health and survival of the host. The present study delved into the emerging field of bacteriophage research within metaorganisms, focusing on the moon jellyfish Aurelia aurita as a model organism. The previously isolated Pseudomonas phage BSwM KMM1 and Citrobacter phages BSwM KMM2 - KMM4 demonstrated potent infectivity on bacteria present in the A. aurita-associated microbiota. In a host-fitness experiment, Baltic Sea subpopulation polyps were exposed to individual phages and a phage cocktail, monitoring polyp survival and morphology, as well as microbiome changes. The following effects were obtained. First, phage exposure in general led to recoverable malformations in polyps without affecting their survival. Second, analyses of the community structure, using 16S rRNA amplicon sequencing, revealed alterations in the associated microbial community in response to phage exposure. Third, the native microbiota is dominated by an uncultured likely novel Mycoplasma species, potentially specific to A. aurita. Notably, this main colonizer showed resilience through the recovery after initial declines, which aligned with abundance changes in Bacteroidota and Proteobacteria, suggesting a dynamic and adaptable microbial community. Overall, this study demonstrates the resilience of the A. aurita metaorganism facing phage-induced perturbations, emphasizing the importance of understanding host-phage interactions in metaorganism biology. These findings have implications for ecological adaptation and conservation in the rapidly changing marine environment, particularly regarding the regulation of blooming species and the health of marine ecosystems during ongoing environmental changes.
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Affiliation(s)
| | | | | | - Ruth Anne Schmitz
- Institute of General Microbiology, Christian-Albrechts University Kiel, Kiel, Germany
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36
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del Arco A, Fischer MG, Becks L. Evolution of exploitation and replication of giant viruses and virophages. Virus Evol 2024; 10:veae021. [PMID: 38562952 PMCID: PMC10984621 DOI: 10.1093/ve/veae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 01/05/2024] [Accepted: 02/22/2024] [Indexed: 04/04/2024] Open
Abstract
Tripartite biotic interactions are inherently complex, and the strong interdependence of species and often one-sided exploitation can make these systems vulnerable to extinction. The persistence of species depends then on the balance between exploitation and avoidance of exploitation beyond the point where sustainable resource use is no longer possible. We used this general prediction to test the potential role of trait evolution for persistence in a tripartite microbial system consisting of a marine heterotrophic flagellate preyed upon by a giant virus, which in turn is parasitized by a virophage. Host and virophage may benefit from this interaction because the virophage reduces the harmful effects of the giant virus on the host population and the virophage can persist integrated into the host genome when giant viruses are scarce. We grew hosts and virus in the presence and absence of the virophage over ∼280 host generations and tested whether levels of exploitation and replication in the giant virus and/or virophage population evolved over the course of the experiment, and whether the changes were such that they could avoid overexploitation and extinction. We found that the giant virus evolved toward lower levels of replication and the virophage evolved toward increased replication but decreased exploitation of the giant virus. These changes reduced overall host exploitation by the virus and virus exploitation by the virophage and are predicted to facilitate persistence.
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Affiliation(s)
- Ana del Arco
- Aquatic Ecology and Evolution, Limnological Institute, University of Konstanz, Mainaustraße 252, Konstanz/Egg 78464, Germany
| | - Matthias G Fischer
- Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg 69120, Germany
| | - Lutz Becks
- Aquatic Ecology and Evolution, Limnological Institute, University of Konstanz, Mainaustraße 252, Konstanz/Egg 78464, Germany
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37
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Shanmugasundaram S, Nayak N, Puzhankara L, Kedlaya MN, Rajagopal A, Karmakar S. Bacteriophages: the dawn of a new era in periodontal microbiology? Crit Rev Microbiol 2024; 50:212-223. [PMID: 36883683 DOI: 10.1080/1040841x.2023.2182667] [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: 10/31/2022] [Revised: 01/02/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023]
Abstract
The oral microbiome, populated by a diverse range of species, plays a critical role in the initiation and progression of periodontal disease. The most dominant yet little-discussed players in the microbiome, the bacteriophages, influence the health and disease of the host in various ways. They, not only contribute to periodontal health by preventing the colonization of pathogens and disrupting biofilms but also play a role in periodontal disease by upregulating the virulence of periodontal pathogens through the transfer of antibiotic resistance and virulence factors. Since bacteriophages selectively infect only bacterial cells, they have an enormous scope to be used as a therapeutic strategy; recently, phage therapy has been successfully used to treat antibiotic-resistant systemic infections. Their ability to disrupt biofilms widens the scope against periodontal pathogens and dental plaque biofilms in periodontitis. Future research focussing on the oral phageome and phage therapy's effectiveness and safety could pave way for new avenues in periodontal therapy. This review explores our current understanding of bacteriophages, their interactions in the oral microbiome, and their therapeutic potential in periodontal disease.
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Affiliation(s)
- Shashikiran Shanmugasundaram
- Department of Periodontology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Namratha Nayak
- Department of Periodontology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Lakshmi Puzhankara
- Department of Periodontology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Madhurya N Kedlaya
- Department of Periodontology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Anjale Rajagopal
- Department of Periodontology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Shaswata Karmakar
- Department of Periodontology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
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38
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Zhang C, Li X, Li S, Yin H, Zhao Z. Characterization and genomic analysis of a broad-spectrum lytic phage PG288: A potential natural therapy candidate for Vibrio infections. Virus Res 2024; 341:199320. [PMID: 38224841 PMCID: PMC10835289 DOI: 10.1016/j.virusres.2024.199320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/03/2024] [Accepted: 01/12/2024] [Indexed: 01/17/2024]
Abstract
Vibrio parahaemolyticus, an important zoonotic pathogen, can cause severe diseases and even death in aquatic animals and humans. As the widespread use of antibiotics gradually diminishes their effectiveness, phages, which can selectively lyse bacteria, are garnering increased attention as a valuable alternative antibacterial strategy. This study characterized PG288, a lytic phage utilizing V. parahaemolyticus strain G855 as its host. Morphologically, the phage features a polyhedral head and a long, non-retractable tail. Bactericidal assays revealed that phage PG288 exhibited a strong lytic ability against V. parahaemolyticus strain G855 and demonstrated a broad host range, as evidenced by the ability to infect several distinct Vibrio species. The one-step growth curve indicated a latent period of approximately 50 min for phage PG288, with a burst size of roughly 92 PFU per cell. Additionally, phage PG288 exhibited remarkable stability within a temperature range of 20-50°C and a pH range of 4-10. Genomic analysis unveiled 105 ORFs within phage PG288, notably devoid of genes associated with antibiotic resistance, virulence, and lysogenic activity. Phylogenetic analysis conclusively identified it as a new member of the genus Mardecavirus within the class Caudoviricetes. In summary, this study contributes valuable insights to the phage database, presenting phage PG288 as a promising candidate for phage therapies against Vibrio infections.
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Affiliation(s)
- Chen Zhang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, Hohai University, Nanjing 210098, China; Department of Marine Biology, College of Oceanography, Hohai University, Nanjing 210098, China
| | - Xixi Li
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, Hohai University, Nanjing 210098, China; Department of Marine Biology, College of Oceanography, Hohai University, Nanjing 210098, China
| | - Shen'ao Li
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, Hohai University, Nanjing 210098, China; Department of Marine Biology, College of Oceanography, Hohai University, Nanjing 210098, China
| | - Han Yin
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, Hohai University, Nanjing 210098, China; Department of Marine Biology, College of Oceanography, Hohai University, Nanjing 210098, China
| | - Zhe Zhao
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, Hohai University, Nanjing 210098, China; Department of Marine Biology, College of Oceanography, Hohai University, Nanjing 210098, China.
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Périat C, Kuhn T, Buffi M, Corona-Ramirez A, Fatton M, Cailleau G, Chain PS, Stanley CE, Wick LY, Bindschedler S, Gonzalez D, Li Richter XY, Junier P. Host and nonhost bacteria support bacteriophage dissemination along mycelia and abiotic dispersal networks. MICROLIFE 2024; 5:uqae004. [PMID: 38463165 PMCID: PMC10924533 DOI: 10.1093/femsml/uqae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/01/2024] [Accepted: 02/19/2024] [Indexed: 03/12/2024]
Abstract
Bacteriophages play a crucial role in shaping bacterial communities, yet the mechanisms by which nonmotile bacteriophages interact with their hosts remain poorly understood. This knowledge gap is especially pronounced in structured environments like soil, where spatial constraints and air-filled zones hinder aqueous diffusion. In soil, hyphae of filamentous microorganisms form a network of 'fungal highways' (FHs) that facilitate the dispersal of other microorganisms. We propose that FHs also promote bacteriophage dissemination. Viral particles can diffuse in liquid films surrounding hyphae or be transported by infectable (host) or uninfectable (nonhost) bacterial carriers coexisting on FH networks. To test this, two bacteriophages that infect Pseudomonas putida DSM291 (host) but not KT2440 (nonhost) were used. In the absence of carriers, bacteriophages showed limited diffusion on 3D-printed abiotic networks, but diffusion was significantly improved in Pythium ultimum-formed FHs when the number of connecting hyphae exceeded 20. Transport by both host and nonhost carriers enhanced bacteriophage dissemination. Host carriers were five times more effective in transporting bacteriophages, particularly in FHs with over 30 connecting hyphae. This study enhances our understanding of bacteriophage dissemination in nonsaturated environments like soils, highlighting the importance of biotic networks and bacterial hosts in facilitating this process.
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Affiliation(s)
- Claire Périat
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Thierry Kuhn
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
- Laboratory of Eco-Ethology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Matteo Buffi
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Andrea Corona-Ramirez
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Mathilda Fatton
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Guillaume Cailleau
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Patrick S Chain
- Los Alamos National Laboratory, Bioscience Division, P.O. Box 1663, NM 87545, Los Alamos, United States
| | - Claire E Stanley
- Department of Bioengineering, Imperial College London, B304, Bessemer Building, South Kensington Campus, SW7 2AZ, London, United Kingdom
| | - Lukas Y Wick
- Helmholtz Centre for Environmental Research UFZ, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Saskia Bindschedler
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Diego Gonzalez
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Xiang-Yi Li Richter
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
- Laboratory of Eco-Ethology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
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He M, Wei W, Zhang Y, Xiang Z, Peng D, Kasimumali A, Rong S. Gut microbial metabolites SCFAs and chronic kidney disease. J Transl Med 2024; 22:172. [PMID: 38369469 PMCID: PMC10874542 DOI: 10.1186/s12967-024-04974-6] [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: 11/18/2023] [Accepted: 02/11/2024] [Indexed: 02/20/2024] Open
Abstract
The global incidence of Chronic Kidney Disease (CKD) is steadily escalating, with discernible linkage to the intricate terrain of intestinal microecology. The intestinal microbiota orchestrates a dynamic equilibrium in the organism, metabolizing dietary-derived compounds, a process which profoundly impacts human health. Among these compounds, short-chain fatty acids (SCFAs), which result from microbial metabolic processes, play a versatile role in influencing host energy homeostasis, immune function, and intermicrobial signaling, etc. SCFAs emerge as pivotal risk factors influencing CKD's development and prognosis. This paper review elucidates the impact of gut microbial metabolites, specifically SCFAs, on CKD, highlighting their role in modulating host inflammatory responses, oxidative stress, cellular autophagy, the immune milieu, and signaling cascades. An in-depth comprehension of the interplay between SCFAs and kidney disease pathogenesis may pave the way for their utilization as biomarkers for CKD progression and prognosis or as novel adjunctive therapeutic strategies.
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Affiliation(s)
- Meng He
- Department of Nephrology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Wenqian Wei
- Department of Nephrology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Yichen Zhang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Zhouxia Xiang
- Department of Nephrology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Dan Peng
- Department of Nephrology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Ayijiaken Kasimumali
- Department of Nephrology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Shu Rong
- Department of Nephrology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China.
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41
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Brás A, Braz M, Martinho I, Duarte J, Pereira C, Almeida A. Effect of Bacteriophages against Biofilms of Escherichia coli on Food Processing Surfaces. Microorganisms 2024; 12:366. [PMID: 38399770 PMCID: PMC10892694 DOI: 10.3390/microorganisms12020366] [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: 12/31/2023] [Revised: 02/04/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
The bacterial adhesion to food processing surfaces is a threat to human health, as these surfaces can serve as reservoirs of pathogenic bacteria. Escherichia coli is an easily biofilm-forming bacterium involved in surface contamination that can lead to the cross-contamination of food. Despite the application of disinfection protocols, contamination through food processing surfaces continues to occur. Hence, new, effective, and sustainable alternative approaches are needed. Bacteriophages (or simply phages), viruses that only infect bacteria, have proven to be effective in reducing biofilms. Here, phage phT4A was applied to prevent and reduce E. coli biofilm on plastic and stainless steel surfaces at 25 °C. The biofilm formation capacity of phage-resistant and sensitive bacteria, after treatment, was also evaluated. The inactivation effectiveness of phage phT4A was surface-dependent, showing higher inactivation on plastic surfaces. Maximum reductions in E. coli biofilm of 5.5 and 4.0 log colony-forming units (CFU)/cm2 after 6 h of incubation on plastic and stainless steel, respectively, were observed. In the prevention assays, phage prevented biofilm formation in 3.2 log CFU/cm2 after 12 h. Although the emergence of phage-resistant bacteria has been observed during phage treatment, phage-resistant bacteria had a lower biofilm formation capacity compared to phage-sensitive bacteria. Overall, the results suggest that phages may have applicability as surface disinfectants against pathogenic bacteria, but further studies are needed to validate these findings using phT4A under different environmental conditions and on different materials.
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Affiliation(s)
| | | | | | | | - Carla Pereira
- Department of Biology, CESAM, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal; (A.B.); (M.B.); (I.M.); (J.D.)
| | - Adelaide Almeida
- Department of Biology, CESAM, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal; (A.B.); (M.B.); (I.M.); (J.D.)
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Wang H, Zheng K, Wang M, Ma K, Ren L, Guo R, Ma L, Zhang H, Liu Y, Xiong Y, Wu M, Shao H, Sung YY, Mok WJ, Wong LL, McMinn A, Liang Y. Shewanella phage encoding a putative anti-CRISPR-like gene represents a novel potential viral family. Microbiol Spectr 2024; 12:e0336723. [PMID: 38214523 PMCID: PMC10846135 DOI: 10.1128/spectrum.03367-23] [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: 09/17/2023] [Accepted: 12/15/2023] [Indexed: 01/13/2024] Open
Abstract
Shewanella is a prevalent bacterial genus in deep-sea environments including marine sediments, exhibiting diverse metabolic capabilities that indicate its significant contributions to the marine biogeochemical cycles. However, only a few Shewanella phages were isolated and deposited in the NCBI database. In this study, we report the isolation and characterization of a novel Shewanella phage, vB_SbaS_Y11, that infects Shewanella KR11 and was isolated from the sewage in Qingdao, China. Transmission electron microscopy revealed that vB_SbaS_Y11 has an icosahedral head and a long tail. The genome of vB_SbaS_Y11 is a linear, double-stranded DNA with a length of 62,799 bp and a G+C content of 46.9%, encoding 71 putative open reading frames. No tRNA genes or integrase-related feature genes were identified. An uncharacterized anti-CRISPR AcrVA2 gene was detected in its genome. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analyses indicate that vB_SbaS_Y11 has a novel genomic architecture and shares low similarity to Pseudomonas virus H66 and Pseudomonas phage F116. vB_SbaS_Y11 represents a potential new family-level virus cluster with eight metagenomic assembled viral genomes named Ranviridae.IMPORTANCEThe Gram-negative Shewanella bacterial genus currently includes about 80 species of mostly aquatic Gammaproteobacteria, which were isolated around the globe in a multitude of environments, such as freshwater, seawater, coastal sediments, and the deepest trenches. Here, we present a Shewanella phage vB_SbaS_Y11 that contains an uncharacterized anti-CRISPR AcrVA2 gene and belongs to a potential virus family, Ranviridae. This study will enhance the knowledge about the genome, diversity, taxonomic classification, and global distribution of Shewanella phage populations.
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Affiliation(s)
- Hongmin Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Kaiyang Zheng
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- Haide College, Ocean University of China, Qingdao, China
- Universiti Malaysia Terengganu-Ocean Unversity of China Joint Centre for Marine Studies, Qingdao, China
- The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Keran Ma
- Haide College, Ocean University of China, Qingdao, China
| | - Linyi Ren
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Ruizhe Guo
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Lina Ma
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hong Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yundan Liu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yao Xiong
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Miaolan Wu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- Universiti Malaysia Terengganu-Ocean Unversity of China Joint Centre for Marine Studies, Qingdao, China
| | - Yeong Yik Sung
- Universiti Malaysia Terengganu-Ocean Unversity of China Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Wen Jye Mok
- Universiti Malaysia Terengganu-Ocean Unversity of China Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Li Lian Wong
- Universiti Malaysia Terengganu-Ocean Unversity of China Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- Universiti Malaysia Terengganu-Ocean Unversity of China Joint Centre for Marine Studies, Qingdao, China
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Backman T, Latorre SM, Symeonidi E, Muszyński A, Bleak E, Eads L, Martinez-Koury PI, Som S, Hawks A, Gloss AD, Belnap DM, Manuel AM, Deutschbauer AM, Bergelson J, Azadi P, Burbano HA, Karasov TL. A weaponized phage suppresses competitors in historical and modern metapopulations of pathogenic bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.17.536465. [PMID: 38352526 PMCID: PMC10862724 DOI: 10.1101/2023.04.17.536465] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Bacteriophages, the viruses of bacteria, are proposed to drive bacterial population dynamics, yet direct evidence of their impact on natural populations is limited. Here we identified viral sequences in a metapopulation of wild plant-associated Pseudomonas spp. genomes. We discovered that the most abundant viral cluster does not encode an intact phage but instead encodes a tailocin - a phage-derived element that bacteria use to kill competitors for interbacterial warfare. Each pathogenic Pseudomonas sp. strain carries one of a few distinct tailocin variants, which target variable polysaccharides in the outer membrane of co-occurring pathogenic strains. Analysis of historic herbarium samples from the last 170 years revealed that the same tailocin and receptor variants have persisted in the Pseudomonas populations for at least two centuries, suggesting the continued use of a defined set of tailocin haplotypes and receptors. These results indicate that tailocin genetic diversity can be mined to develop targeted "tailocin cocktails" for microbial control. One-Sentence Summary Bacterial pathogens in a host-associated metapopulation use a repurposed prophage to kill their competitors.
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Narayanan KB, Bhaskar R, Choi SM, Han SS. Development of carrageenan-immobilized lytic coliphage vB_Eco2571-YU1 hydrogel for topical delivery of bacteriophages in wound dressing applications. Int J Biol Macromol 2024; 259:129349. [PMID: 38219934 DOI: 10.1016/j.ijbiomac.2024.129349] [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: 08/08/2023] [Revised: 12/31/2023] [Accepted: 01/07/2024] [Indexed: 01/16/2024]
Abstract
Bacteriophages are employed as cost-effective and efficient antibacterial agents to counter the emergence of antibiotic-resistant bacteria and other host bacteria in phage therapy. The increasing incidence of skin wounds is a significant concern in clinical practice, especially considering the limitations of antibiotic therapy. Furthermore, the lack of an effective delivery system that preserves the stability of bacteriophages hampers their clinical implementation. In recent years, there has been a growing amount of research on bacteriophage applications in veterinary and biomedical sciences. In our study, lytic coliphage vB_Eco2571-YU1 was isolated against pathogenic Escherichia coli host bacteria, and hydrogel wound dressing materials were fabricated with marine polysaccharide carrageenan (carr-vB_Eco2571-YU1) for their antibacterial activity. Transmission electron microscopy (TEM) morphology identified it as a Myoviridae coliphage with an icosahedral head length and width of approximately 60 and 56.8 nm, respectively, and a tail length of 119.7 nm. The one-step growth curve of coliphage revealed a latent period of 10 min, a rise period of 15 min, and a burst size of 120 virions per cell. The bacteriolytic activity of unimmobilized coliphages was observed within 2 h; however, strain-specific phage resistance was acquired after 9 h. In contrast, carr-vB_Eco2571-YU1 showed a sharp decline in the growth of bacteria in the log phase after 2 h and did not allow for the acquisition of phage resistance by the E. coli strain. The stability of coliphage under different pH, temperature, osmolarity, detergents, and organic solvents was evaluated. We also studied the long-term storage of carr-vB_Eco2571-YU1 hydrogels at 4 °C and found that the titer value decreased during a time-dependent period of 28 days. These hydrogels were also found to be hemocompatible using a hemolysis assay. The addition of plasticizer (0.6 % (w/v)) to the carrageenan (2 % (w/v)) to prepare carr-vB_Eco2571-YU1 hydrogels showed a decrease in compressive strength with enhanced elasticity. This phage therapy using polymeric immobilization of bacteriophages is a promising next-generation wound dressing biomaterial alternative to conventional wound and skin care management.
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Affiliation(s)
- Kannan Badri Narayanan
- School of Chemical Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, South Korea; Research Institute of Cell Culture, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, South Korea.
| | - Rakesh Bhaskar
- School of Chemical Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, South Korea; Research Institute of Cell Culture, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, South Korea
| | - Soon Mo Choi
- School of Chemical Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, South Korea; Research Institute of Cell Culture, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, South Korea
| | - Sung Soo Han
- School of Chemical Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, South Korea; Research Institute of Cell Culture, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, South Korea.
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Romeyer Dherbey J, Bertels F. The untapped potential of phage model systems as therapeutic agents. Virus Evol 2024; 10:veae007. [PMID: 38361821 PMCID: PMC10868562 DOI: 10.1093/ve/veae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/18/2023] [Accepted: 01/12/2024] [Indexed: 02/17/2024] Open
Abstract
With the emergence of widespread antibiotic resistance, phages are an appealing alternative to antibiotics in the fight against multidrug-resistant bacteria. Over the past few years, many phages have been isolated from various environments to treat bacterial pathogens. While isolating novel phages for treatment has had some success for compassionate use, developing novel phages into a general therapeutic will require considerable time and financial resource investments. These investments may be less significant for well-established phage model systems. The knowledge acquired from decades of research on their structure, life cycle, and evolution ensures safe application and efficient handling. However, one major downside of the established phage model systems is their inability to infect pathogenic bacteria. This problem is not insurmountable; phage host range can be extended through genetic engineering or evolution experiments. In the future, breeding model phages to infect pathogens could provide a new avenue to develop phage therapeutic agents.
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Affiliation(s)
- Jordan Romeyer Dherbey
- Microbial Population Biology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, Plön, Schleswig-Holstein 24306, Germany
| | - Frederic Bertels
- Microbial Population Biology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, Plön, Schleswig-Holstein 24306, Germany
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46
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Zhang H, Zhang H, Du H, Yu X, Xu Y. The insights into the phage communities of fermented foods in the age of viral metagenomics. Crit Rev Food Sci Nutr 2024:1-13. [PMID: 38214674 DOI: 10.1080/10408398.2023.2299323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Phages play a critical role in the assembly and regulation of fermented food microbiome through lysis and lysogenic lifestyle, which in turn affects the yield and quality of fermented foods. Therefore, it is important to investigate and characterize the diversity and function of phages under complex microbial communities and nutrient substrate conditions to provide novel insights into the regulation of traditional spontaneous fermentation. Viral metagenomics has gradually garnered increasing attention in fermented food research to elucidate phage functions and characterize the interactions between phages and the microbial community. Advances in this technology have uncovered a wide range of phages associated with the production of traditional fermented foods and beverages. This paper reviews the common methods of viral metagenomics applied in fermented food research, and summarizes the ecological functions of phages in traditional fermented foods. In the future, combining viral metagenomics with culturable methods and metagenomics will broaden the scope of research on fermented food systems, revealing the complex role of phages and intricate phage-bacterium interactions.
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Affiliation(s)
- Huadong Zhang
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hongxia Zhang
- College of Life Sciences, Shanxi Normal University, Taiyuan, Shanxi, China
| | - Hai Du
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiaowei Yu
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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Somé BM, Guissou E, Da DF, Richard Q, Choisy M, Yameogo KB, Hien DF, Yerbanga RS, Ouedraogo GA, Dabiré KR, Djidjou-Demasse R, Cohuet A, Lefèvre T. Mosquito ageing modulates the development, virulence and transmission potential of pathogens. Proc Biol Sci 2024; 291:20232097. [PMID: 38166422 PMCID: PMC10762442 DOI: 10.1098/rspb.2023.2097] [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: 09/15/2023] [Accepted: 11/27/2023] [Indexed: 01/04/2024] Open
Abstract
Host age variation is a striking source of heterogeneity that can shape the evolution and transmission dynamic of pathogens. Compared with vertebrate systems, our understanding of the impact of host age on invertebrate-pathogen interactions remains limited. We examined the influence of mosquito age on key life-history traits driving human malaria transmission. Females of Anopheles coluzzii, a major malaria vector, belonging to three age classes (4-, 8- and 12-day-old), were experimentally infected with Plasmodium falciparum field isolates. Our findings revealed reduced competence in 12-day-old mosquitoes, characterized by lower oocyst/sporozoite rates and intensities compared with younger mosquitoes. Despite shorter median longevities in older age classes, infected 12-day-old mosquitoes exhibited improved survival, suggesting that the infection might act as a fountain of youth for older mosquitoes specifically. The timing of sporozoite appearance in the salivary glands remained consistent across mosquito age classes, with an extrinsic incubation period of approximately 13 days. Integrating these results into an epidemiological model revealed a lower vectorial capacity for older mosquitoes compared with younger ones, albeit still substantial owing to extended longevity in the presence of infection. Considering age heterogeneity provides valuable insights for ecological and epidemiological studies, informing targeted control strategies to mitigate pathogen transmission.
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Affiliation(s)
- Bernard M. Somé
- Unité Paludisme et Maladies Tropicales Négligées, Institut de Recherche en Sciences de la Santé (IRSS), 01 BP 545 Bobo Dioulasso, Burkina Faso
- Laboratoire Mixte International sur les Vecteurs (LAMIVECT), Bobo Dioulasso, Burkina Faso
- Département de Biochimie, Université Nazi Boni, 01 BP 1091 Bobo Dioulasso, Burkina Faso
| | - Edwige Guissou
- Unité Paludisme et Maladies Tropicales Négligées, Institut de Recherche en Sciences de la Santé (IRSS), 01 BP 545 Bobo Dioulasso, Burkina Faso
- Laboratoire Mixte International sur les Vecteurs (LAMIVECT), Bobo Dioulasso, Burkina Faso
- Département de Biochimie, Université Nazi Boni, 01 BP 1091 Bobo Dioulasso, Burkina Faso
- MIVEGEC, IRD, CNRS, University of Montpellier, 34090 Montpellier cedex 5, France
- Ecole Normale Supérieure, BP 376 Koudougou, Burkina Faso
| | - Dari F. Da
- Unité Paludisme et Maladies Tropicales Négligées, Institut de Recherche en Sciences de la Santé (IRSS), 01 BP 545 Bobo Dioulasso, Burkina Faso
| | - Quentin Richard
- IMAG, Université de Montpellier, CNRS, 34090 Montpellier, France
| | - Marc Choisy
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 700000, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Koudraogo B. Yameogo
- Unité Paludisme et Maladies Tropicales Négligées, Institut de Recherche en Sciences de la Santé (IRSS), 01 BP 545 Bobo Dioulasso, Burkina Faso
- Laboratoire Mixte International sur les Vecteurs (LAMIVECT), Bobo Dioulasso, Burkina Faso
| | - Domombabele FdS. Hien
- Unité Paludisme et Maladies Tropicales Négligées, Institut de Recherche en Sciences de la Santé (IRSS), 01 BP 545 Bobo Dioulasso, Burkina Faso
- Laboratoire Mixte International sur les Vecteurs (LAMIVECT), Bobo Dioulasso, Burkina Faso
| | - Rakiswende S. Yerbanga
- Unité Paludisme et Maladies Tropicales Négligées, Institut de Recherche en Sciences de la Santé (IRSS), 01 BP 545 Bobo Dioulasso, Burkina Faso
- Laboratoire Mixte International sur les Vecteurs (LAMIVECT), Bobo Dioulasso, Burkina Faso
| | - Georges A. Ouedraogo
- Département de Biochimie, Université Nazi Boni, 01 BP 1091 Bobo Dioulasso, Burkina Faso
| | - Kounbobr R. Dabiré
- Unité Paludisme et Maladies Tropicales Négligées, Institut de Recherche en Sciences de la Santé (IRSS), 01 BP 545 Bobo Dioulasso, Burkina Faso
- Laboratoire Mixte International sur les Vecteurs (LAMIVECT), Bobo Dioulasso, Burkina Faso
| | | | - Anna Cohuet
- Laboratoire Mixte International sur les Vecteurs (LAMIVECT), Bobo Dioulasso, Burkina Faso
- MIVEGEC, IRD, CNRS, University of Montpellier, 34090 Montpellier cedex 5, France
| | - Thierry Lefèvre
- Unité Paludisme et Maladies Tropicales Négligées, Institut de Recherche en Sciences de la Santé (IRSS), 01 BP 545 Bobo Dioulasso, Burkina Faso
- Laboratoire Mixte International sur les Vecteurs (LAMIVECT), Bobo Dioulasso, Burkina Faso
- MIVEGEC, IRD, CNRS, University of Montpellier, 34090 Montpellier cedex 5, France
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48
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Lucia-Sanz A, Peng S, Leung CY(J, Gupta A, Meyer JR, Weitz JS. Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574707. [PMID: 38260415 PMCID: PMC10802490 DOI: 10.1101/2024.01.08.574707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The enormous diversity of bacteriophages and their bacterial hosts presents a significant challenge to predict which phages infect a focal set of bacteria. Infection is largely determined by complementary -and largely uncharacterized- genetics of adsorption, injection, and cell take-over. Here we present a machine learning (ML) approach to predict phage-bacteria interactions trained on genome sequences of and phenotypic interactions amongst 51 Escherichia coli strains and 45 phage λ strains that coevolved in laboratory conditions for 37 days. Leveraging multiple inference strategies and without a priori knowledge of driver mutations, this framework predicts both who infects whom and the quantitative levels of infections across a suite of 2,295 potential interactions. The most effective ML approach inferred interaction phenotypes from independent contributions from phage and bacteria mutations, predicting phage host range with 86% mean classification accuracy while reducing the relative error in the estimated strength of the infection phenotype by 40%. Further, transparent feature selection in the predictive model revealed 18 of 176 phage λ and 6 of 18 E. coli mutations that have a significant influence on the outcome of phage-bacteria interactions, corroborating sites previously known to affect phage λ infections, as well as identifying mutations in genes of unknown function not previously shown to influence bacterial resistance. While the genetic variation studied was limited to a focal, coevolved phage-bacteria system, the method's success at recapitulating strain-level infection outcomes provides a path forward towards developing strategies for inferring interactions in non-model systems, including those of therapeutic significance.
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Affiliation(s)
- Adriana Lucia-Sanz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | | | | | - Animesh Gupta
- Department of Physics, University of California San Diego, La Jolla, California, USA
| | - Justin R. Meyer
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, California, USA
| | - Joshua S. Weitz
- Department of Biology, University of Maryland, College Park, MD, USA
- Department of Physics, University of Maryland, College Park, MD, USA
- Institut d’Biologie, École Normale Supérieure, Paris, France
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49
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Rubio-Portillo E, Robertson S, Antón J. Coral mucus as a reservoir of bacteriophages targeting Vibrio pathogens. THE ISME JOURNAL 2024; 18:wrae017. [PMID: 38366190 PMCID: PMC10945359 DOI: 10.1093/ismejo/wrae017] [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: 10/20/2023] [Revised: 12/18/2023] [Accepted: 01/29/2024] [Indexed: 02/18/2024]
Abstract
The increasing trend in sea surface temperature promotes the spread of Vibrio species, which are known to cause diseases in a wide range of marine organisms. Among these pathogens, Vibrio mediterranei has emerged as a significant threat, leading to bleaching in the coral species Oculina patagonica. Bacteriophages, or phages, are viruses that infect bacteria, thereby regulating microbial communities and playing a crucial role in the coral's defense against pathogens. However, our understanding of phages that infect V. mediterranei is limited. In this study, we identified two phage species capable of infecting V. mediterranei by utilizing a combination of cultivation and metagenomic approaches. These phages are low-abundance specialists within the coral mucus layer that exhibit rapid proliferation in the presence of their hosts, suggesting a potential role in coral defense. Additionally, one of these phages possesses a conserved domain of a leucine-rich repeat protein, similar to those harbored in the coral genome, that plays a key role in pathogen recognition, hinting at potential coral-phage coevolution. Furthermore, our research suggests that lytic Vibrio infections could trigger prophage induction, which may disseminate genetic elements, including virulence factors, in the coral mucus layer. Overall, our findings underscore the importance of historical coral-phage interactions as a form of coral immunity against invasive Vibrio pathogens.
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Affiliation(s)
- Esther Rubio-Portillo
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante 03690, Spain
| | - Sophia Robertson
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante 03690, Spain
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, United States
| | - Josefa Antón
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante 03690, Spain
- Multidisciplinary Institute of Environmental Studies Ramon Margalef, Alicante 03690, Spain
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50
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López-Beltrán A, Botelho J, Iranzo J. Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome. THE ISME JOURNAL 2024; 18:wrae134. [PMID: 39023219 PMCID: PMC11307328 DOI: 10.1093/ismejo/wrae134] [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: 01/23/2024] [Revised: 06/07/2024] [Accepted: 07/17/2024] [Indexed: 07/20/2024]
Abstract
Arms races between mobile genetic elements and prokaryotic hosts are major drivers of ecological and evolutionary change in microbial communities. Prokaryotic defense systems such as CRISPR-Cas have the potential to regulate microbiome composition by modifying the interactions among bacteria, plasmids, and phages. Here, we used longitudinal metagenomic data from 130 healthy and diseased individuals to study how the interplay of genetic parasites and CRISPR-Cas immunity reflects on the dynamics and composition of the human gut microbiome. Based on the coordinated study of 80 000 CRISPR-Cas loci and their targets, we show that CRISPR-Cas immunity effectively modulates bacteriophage abundances in the gut. Acquisition of CRISPR-Cas immunity typically leads to a decrease in the abundance of lytic phages but does not necessarily cause their complete disappearance. Much smaller effects are observed for lysogenic phages and plasmids. Conversely, phage-CRISPR interactions shape bacterial microdiversity by producing weak selective sweeps that benefit immune host lineages. We also show that distal (and chronologically older) regions of CRISPR arrays are enriched in spacers that are potentially functional and target crass-like phages and local prophages. This suggests that exposure to reactivated prophages and other endemic viruses is a major selective pressure in the gut microbiome that drives the maintenance of long-lasting immune memory.
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Affiliation(s)
- Adrián López-Beltrán
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Parque Científico y Tecnológico UPM, Campus de Montegancedo, 28223, Madrid, Spain
| | - João Botelho
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Parque Científico y Tecnológico UPM, Campus de Montegancedo, 28223, Madrid, Spain
| | - Jaime Iranzo
- Centro de Astrobiología (CAB), CSIC-INTA, Ctra. de Torrejón a Ajalvir Km 4, 28850, Torrejón de Ardoz, Madrid, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Campus Río Ebro, 50018, Zaragoza, Spain
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