1
|
Dieppa-Colón E, Martin C, Anantharaman K. Prophage-DB: A comprehensive database to explore diversity, distribution, and ecology of prophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.603044. [PMID: 39071402 PMCID: PMC11275716 DOI: 10.1101/2024.07.11.603044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Background Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact microbial community dynamics, microbial ecology, and evolution. Efforts to document the diversity, host range, infection dynamics, and effects of bacteriophage infection on host cell metabolism are extremely underexplored. Phages are classified as virulent or temperate based on their life cycles. Temperate phages adopt the lysogenic mode of infection, where the genome integrates into the host cell genome forming a prophage. Prophages enable viral genome replication without host cell lysis, and often contribute novel and beneficial traits to the host genome. Current phage research predominantly focuses on lytic phages, leaving a significant gap in knowledge regarding prophages, including their biology, diversity, and ecological roles. Results Here we develop and describe Prophage-DB, a database of prophages, their proteins, and associated metadata that will serve as a resource for viral genomics and microbial ecology. To create the database, we identified and characterized prophages from genomes in three of the largest publicly available databases. We applied several state-of-the-art tools in our pipeline to annotate these viruses, cluster and taxonomically classify them, and detect their respective auxiliary metabolic genes. In total, we identify and characterize over 350,000 prophages and 35,000 auxiliary metabolic genes. Our prophage database is highly representative based on statistical results and contains prophages from a diverse set of archaeal and bacterial hosts which show a wide environmental distribution. Conclusion Prophages are particularly overlooked in viral ecology and merit increased attention due to their vital implications for microbiomes and their hosts. Here, we created Prophage-DB to advance our comprehension of prophages in microbiomes through a comprehensive characterization of prophages in publicly available genomes. We propose that Prophage-DB will serve as a valuable resource for advancing phage research, offering insights into viral taxonomy, host relationships, auxiliary metabolic genes, and environmental distribution.
Collapse
Affiliation(s)
- Etan Dieppa-Colón
- Department of Bacteriology, University of Wisconsin-Madison
- Microbiology Doctoral Training Program, University of Wisconsin-Madison
| | - Cody Martin
- Department of Bacteriology, University of Wisconsin-Madison
- Microbiology Doctoral Training Program, University of Wisconsin-Madison
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison
- Department of Integrative Biology, University of Wisconsin-Madison
| |
Collapse
|
2
|
Al-Anany AM, Fatima R, Nair G, Mayol JT, Hynes AP. Temperate phage-antibiotic synergy across antibiotic classes reveals new mechanism for preventing lysogeny. mBio 2024; 15:e0050424. [PMID: 38757974 PMCID: PMC11237771 DOI: 10.1128/mbio.00504-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
A recent demonstration of synergy between a temperate phage and the antibiotic ciprofloxacin suggested a scalable approach to exploiting temperate phages in therapy, termed temperate phage-antibiotic synergy, which specifically interacted with the lysis-lysogeny decision. To determine whether this would hold true across antibiotics, we challenged Escherichia coli with the phage HK97 and a set of 13 antibiotics spanning seven classes. As expected, given the conserved induction pathway, we observed synergy with classes of drugs known to induce an SOS response: a sulfa drug, other quinolones, and mitomycin C. While some β-lactams exhibited synergy, this appeared to be traditional phage-antibiotic synergy, with no effect on the lysis-lysogeny decision. Curiously, we observed a potent synergy with antibiotics not known to induce the SOS response: protein synthesis inhibitors gentamicin, kanamycin, tetracycline, and azithromycin. The synergy results in an eightfold reduction in the effective minimum inhibitory concentration of gentamicin, complete eradication of the bacteria, and, when administered at sub-optimal doses, drastically decreases the frequency of lysogens emerging from the combined challenge. However, lysogens exhibit no increased sensitivity to the antibiotic; synergy was maintained in the absence of RecA; and the antibiotic reduced the initial frequency of lysogeny rather than selecting against formed lysogens. Our results confirm that SOS-inducing antibiotics broadly result in temperate-phage-specific synergy, but that other antibiotics can interact with temperate phages specifically and result in synergy. This is the first report of a means of chemically blocking entry into lysogeny, providing a new means for manipulating the key lysis-lysogeny decision.IMPORTANCEThe lysis-lysogeny decision is made by most bacterial viruses (bacteriophages, phages), determining whether to kill their host or go dormant within it. With over half of the bacteria containing phages waiting to wake, this is one of the most important behaviors in all of biology. These phages are also considered unusable for therapy because of this behavior. In this paper, we show that many antibiotics bias this behavior to "wake" the dormant phages, forcing them to kill their host, but some also prevent dormancy in the first place. These will be important tools to study this critical decision point and may enable the therapeutic use of these phages.
Collapse
Affiliation(s)
- Amany M Al-Anany
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Rabia Fatima
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Gayatri Nair
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jordan T Mayol
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Alexander P Hynes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| |
Collapse
|
3
|
Shepherd MJ, Fu T, Harrington NE, Kottara A, Cagney K, Chalmers JD, Paterson S, Fothergill JL, Brockhurst MA. Ecological and evolutionary mechanisms driving within-patient emergence of antimicrobial resistance. Nat Rev Microbiol 2024:10.1038/s41579-024-01041-1. [PMID: 38689039 DOI: 10.1038/s41579-024-01041-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2024] [Indexed: 05/02/2024]
Abstract
The ecological and evolutionary mechanisms of antimicrobial resistance (AMR) emergence within patients and how these vary across bacterial infections are poorly understood. Increasingly widespread use of pathogen genome sequencing in the clinic enables a deeper understanding of these processes. In this Review, we explore the clinical evidence to support four major mechanisms of within-patient AMR emergence in bacteria: spontaneous resistance mutations; in situ horizontal gene transfer of resistance genes; selection of pre-existing resistance; and immigration of resistant lineages. Within-patient AMR emergence occurs across a wide range of host niches and bacterial species, but the importance of each mechanism varies between bacterial species and infection sites within the body. We identify potential drivers of such differences and discuss how ecological and evolutionary analysis could be embedded within clinical trials of antimicrobials, which are powerful but underused tools for understanding why these mechanisms vary between pathogens, infections and individuals. Ultimately, improving understanding of how host niche, bacterial species and antibiotic mode of action combine to govern the ecological and evolutionary mechanism of AMR emergence in patients will enable more predictive and personalized diagnosis and antimicrobial therapies.
Collapse
Affiliation(s)
- Matthew J Shepherd
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK.
| | - Taoran Fu
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Niamh E Harrington
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Anastasia Kottara
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Kendall Cagney
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Steve Paterson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Joanne L Fothergill
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Michael A Brockhurst
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK.
| |
Collapse
|
4
|
Stanton IC, Tipper HJ, Chau K, Klümper U, Subirats J, Murray AK. Does Environmental Exposure to Pharmaceutical and Personal Care Product Residues Result in the Selection of Antimicrobial-Resistant Microorganisms, and is this Important in Terms of Human Health Outcomes? ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024; 43:623-636. [PMID: 36416260 DOI: 10.1002/etc.5498] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/14/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
The environment plays a critical role in the development, dissemination, and transmission of antimicrobial resistance (AMR). Pharmaceuticals and personal care products (PPCPs) enter the environment through direct application to the environment and through anthropogenic pollution. Although there is a growing body of evidence defining minimal selective concentrations (MSCs) of antibiotics and the role antibiotics play in horizontal gene transfer (HGT), there is limited evidence on the role of non-antibiotic PPCPs. Existing data show associations with the development of resistance or effects on bacterial growth rather than calculating selective endpoints. Research has focused on laboratory-based systems rather than in situ experiments, although PPCP concentrations found throughout wastewater, natural water, and soil environments are often within the range of laboratory-derived MSCs and at concentrations shown to promote HGT. Increased selection and HGT of AMR by PPCPs will result in an increase in total AMR abundance in the environment, increasing the risk of exposure and potential transmission of environmental AMR to humans. There is some evidence to suggest that humans can acquire resistance from environmental settings, with water environments being the most frequently studied. However, because this is currently limited, we recommend that more evidence be gathered to understand the risk the environment plays in regard to human health. In addition, we recommend that future research efforts focus on MSC-based experiments for non-antibiotic PPCPS, particularly in situ, and investigate the effect of PPCP mixtures on AMR. Environ Toxicol Chem 2024;43:623-636. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
Collapse
Affiliation(s)
| | | | - Kevin Chau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Uli Klümper
- Institute of Hydrobiology, Technische Universitӓt Dresden, Dresden, Germany
| | - Jessica Subirats
- Institute of Environmental Assessment and Water Research, Spanish Council for Scientific Research (IDAEA-CSIC), Barcelona, Spain
| | - Aimee K Murray
- College of Medicine and Health, University of Exeter, Cornwall, UK
| |
Collapse
|
5
|
Leal Rodríguez C, Shah SA, Rasmussen MA, Thorsen J, Boulund U, Pedersen CET, Castro-Mejía JL, Poulsen CE, Poulsen CS, Deng L, Larsen FAN, Widdowson M, Zhang Y, Sørensen SJ, Moineau S, Petit MA, Chawes B, Bønnelykke K, Nielsen DS, Stokholm J. The infant gut virome is associated with preschool asthma risk independently of bacteria. Nat Med 2024; 30:138-148. [PMID: 38102298 DOI: 10.1038/s41591-023-02685-x] [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: 06/14/2023] [Accepted: 11/07/2023] [Indexed: 12/17/2023]
Abstract
Bacteriophage (also known as phage) communities that inhabit the gut have a major effect on the structure and functioning of bacterial populations, but their roles and association with health and disease in early life remain unknown. Here, we analyze the gut virome of 647 children aged 1 year from the Copenhagen Prospective Studies on Asthma in Childhood2010 (COPSAC2010) mother-child cohort, all deeply phenotyped from birth and with longitudinally assessed asthma diagnoses. Specific temperate gut phage taxa were found to be associated with later development of asthma. In particular, the joint abundances of 19 caudoviral families were found to significantly contribute to this association. Combining the asthma-associated virome and bacteriome signatures had additive effects on asthma risk, implying an independent virome-asthma association. Moreover, the virome-associated asthma risk was modulated by the host TLR9 rs187084 gene variant, suggesting a direct interaction between phages and the host immune system. Further studies will elucidate whether phages, alongside bacteria and host genetics, can be used as preclinical biomarkers for asthma.
Collapse
Affiliation(s)
- Cristina Leal Rodríguez
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Gentofte, Denmark
| | - Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Gentofte, Denmark
| | - Morten Arendt Rasmussen
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Gentofte, Denmark
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan Thorsen
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Gentofte, Denmark
| | - Ulrika Boulund
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Gentofte, Denmark
| | - Casper-Emil Tingskov Pedersen
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Gentofte, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Christina Egeø Poulsen
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Gentofte, Denmark
| | - Casper Sahl Poulsen
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Gentofte, Denmark
| | - Ling Deng
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | | | - Michael Widdowson
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Gentofte, Denmark
| | - Yichang Zhang
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sylvain Moineau
- Département de Biochimie, de Microbiologie, et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC, Canada
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec City, QC, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, QC, Canada
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, Agroparistech, Micalis Institute, Jouy-en-Josas, France
| | - Bo Chawes
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Gentofte, Denmark
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Gentofte, Denmark
| | - Dennis S Nielsen
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Gentofte, Denmark.
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
6
|
Li S, Li X, Chang H, Zhong N, Ren N, Ho SH. Comprehensive insights into antibiotic resistance gene migration in microalgal-bacterial consortia: Mechanisms, factors, and perspectives. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:166029. [PMID: 37541493 DOI: 10.1016/j.scitotenv.2023.166029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/06/2023]
Abstract
With the overuse of antibiotics, antibiotic resistance gene (ARG) prevalence is gradually increasing. ARGs are considered emerging contaminants that are broadly concentrated and dispersed in most aquatic environments. Recently, interest in microalgal-bacterial biotreatment of antibiotics has increased, as eukaryotes are not the primary target of antimicrobial drugs. Moreover, research has shown that microalgal-bacterial consortia can minimize the transmission of antibiotic resistance in the environment. Unfortunately, reviews surrounding the ARG migration mechanism in microalgal-bacterial consortia have not yet been performed. This review briefly introduces the migration of ARGs in aquatic environments. Additionally, an in-depth summary of horizontal gene transfer (HGT) between cyanobacteria and bacteria and from bacteria to eukaryotic microalgae is presented. Factors influencing gene transfer in microalgal-bacterial consortia are discussed systematically, including bacteriophage abundance, environmental conditions (temperature, pH, and nutrient availability), and other selective pressure conditions including nanomaterials, heavy metals, and pharmaceuticals and personal care products. Furthermore, considering that quorum sensing could be involved in DNA transformation by affecting secondary metabolites, current knowledge surrounding quorum sensing regulation of HGT of ARGs is summarized. In summary, this review gives valuable information to promote the development of practical and innovative techniques for ARG removal by microalgal-bacterial consortia.
Collapse
Affiliation(s)
- Shengnan Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Xue Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Haixing Chang
- College of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China
| | - Nianbing Zhong
- Liangjiang International College, Chongqing University of Technology, Chongqing 401135, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Shih-Hsin Ho
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China.
| |
Collapse
|
7
|
Avellaneda-Franco L, Dahlman S, Barr JJ. The gut virome and the relevance of temperate phages in human health. Front Cell Infect Microbiol 2023; 13:1241058. [PMID: 37577374 PMCID: PMC10413269 DOI: 10.3389/fcimb.2023.1241058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 06/29/2023] [Indexed: 08/15/2023] Open
Abstract
Alterations in the gut virome impact human health. Bacteriophages, viruses that infect bacteria, dominate the gut virome and are mainly composed by virulent and temperate phages. While virulent phages exclusively replicate within and lyse their bacterial host's cell, temperate phages switch from an integrated state residing within their bacterial host's chromosome to an induced free virion state via an induction event. How often do these induction events occur and what are their implications on gut homeostasis? Here, we summarize the current knowledge of the gut virome based on metagenomics and present how the proportion of induced temperate phages varies amongst individuals, age, and disease states. Finally, we highlight the importance of building upon classical culture-dependent techniques and sequencing approaches to improve our understanding of temperate phages to enable their potential therapeutic use.
Collapse
Affiliation(s)
| | | | - Jeremy J. Barr
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| |
Collapse
|
8
|
Takeuchi N, Hamada-Zhu S, Suzuki H. Prophages and plasmids can display opposite trends in the types of accessory genes they carry. Proc Biol Sci 2023; 290:20231088. [PMID: 37339743 DOI: 10.1098/rspb.2023.1088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 06/01/2023] [Indexed: 06/22/2023] Open
Abstract
Mobile genetic elements (MGEs), such as phages and plasmids, often possess accessory genes encoding bacterial functions, facilitating bacterial evolution. Are there rules governing the arsenal of accessory genes MGEs carry? If such rules exist, they might be reflected in the types of accessory genes different MGEs carry. To test this hypothesis, we compare prophages and plasmids with respect to the frequencies at which they carry antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in the genomes of 21 pathogenic bacterial species using public databases. Our results indicate that prophages tend to carry VFGs more frequently than ARGs in three species, whereas plasmids tend to carry ARGs more frequently than VFGs in nine species, relative to genomic backgrounds. In Escherichia coli, where this prophage-plasmid disparity is detected, prophage-borne VFGs encode a much narrower range of functions than do plasmid-borne VFGs, typically involved in damaging host cells or modulating host immunity. In the species where the above disparity is not detected, ARGs and VFGs are barely found in prophages and plasmids. These results indicate that MGEs can differentiate in the types of accessory genes they carry depending on their infection strategies, suggesting a rule governing horizontal gene transfer mediated by MGEs.
Collapse
Affiliation(s)
- Nobuto Takeuchi
- School of Biological Sciences, the University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- Universal Biology Institute, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Sophia Hamada-Zhu
- School of Biological Sciences, the University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Haruo Suzuki
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| |
Collapse
|
9
|
Pargin E, Roach MJ, Skye A, Papudeshi B, Inglis LK, Mallawaarachchi V, Grigson SR, Harker C, Edwards RA, Giles SK. The human gut virome: composition, colonization, interactions, and impacts on human health. Front Microbiol 2023; 14:963173. [PMID: 37293229 PMCID: PMC10244655 DOI: 10.3389/fmicb.2023.963173] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 05/08/2023] [Indexed: 06/10/2023] Open
Abstract
The gut virome is an incredibly complex part of the gut ecosystem. Gut viruses play a role in many disease states, but it is unknown to what extent the gut virome impacts everyday human health. New experimental and bioinformatic approaches are required to address this knowledge gap. Gut virome colonization begins at birth and is considered unique and stable in adulthood. The stable virome is highly specific to each individual and is modulated by varying factors such as age, diet, disease state, and use of antibiotics. The gut virome primarily comprises bacteriophages, predominantly order Crassvirales, also referred to as crAss-like phages, in industrialized populations and other Caudoviricetes (formerly Caudovirales). The stability of the virome's regular constituents is disrupted by disease. Transferring the fecal microbiome, including its viruses, from a healthy individual can restore the functionality of the gut. It can alleviate symptoms of chronic illnesses such as colitis caused by Clostridiodes difficile. Investigation of the virome is a relatively novel field, with new genetic sequences being published at an increasing rate. A large percentage of unknown sequences, termed 'viral dark matter', is one of the significant challenges facing virologists and bioinformaticians. To address this challenge, strategies include mining publicly available viral datasets, untargeted metagenomic approaches, and utilizing cutting-edge bioinformatic tools to quantify and classify viral species. Here, we review the literature surrounding the gut virome, its establishment, its impact on human health, the methods used to investigate it, and the viral dark matter veiling our understanding of the gut virome.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Sarah K. Giles
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| |
Collapse
|
10
|
Burgold-Voigt S, Monecke S, Busch A, Bocklisch H, Braun SD, Diezel C, Hotzel H, Liebler-Tenorio EM, Müller E, Reinicke M, Reissig A, Ruppelt-Lorz A, Ehricht R. Characterisation of a Staphylococcus aureus Isolate Carrying Phage-Borne Enterotoxin E from a European Badger ( Meles meles). Pathogens 2023; 12:pathogens12050704. [PMID: 37242375 DOI: 10.3390/pathogens12050704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Staphylococcus (S.) aureus colonizes up to 30% of all humans and can occasionally cause serious infections. It is not restricted to humans as it can also often be found in livestock and wildlife. Recent studies have shown that wildlife strains of S. aureus usually belong to other clonal complexes than human strains and that they might differ significantly with regard to the prevalence of genes encoding antimicrobial resistance properties and virulence factors. Here, we describe a strain of S. aureus isolated from a European badger (Meles meles). For molecular characterisation, DNA microarray-based technology was combined with various next-generation sequencing (NGS) methods. Bacteriophages from this isolate were induced with Mitomycin C and characterized in detail by transmission electron microscopy (TEM) and NGS. The S. aureus isolate belonged to ST425 and had a novel spa repeat sequence (t20845). It did not carry any resistance genes. The uncommon enterotoxin gene see was detected in one of its three temperate bacteriophages. It was possible to demonstrate the induction of all three prophages, although only one of them was expected to be capable of excision based on its carriage of the excisionase gene xis. All three bacteriophages belonged to the family Siphoviridae. Minor differences in size and shape of their heads were noted in TEM images. The results highlight the ability of S. aureus to colonize or infect different host species successfully, which can be attributed to a variety of virulence factors on mobile genetic elements, such as bacteriophages. As shown in the strain described herein, temperate bacteriophages not only contribute to the fitness of their staphylococcal host by transferring virulence factors, but also increase mobility among themselves by sharing genes for excision and mobilization with other prophages.
Collapse
Affiliation(s)
- Sindy Burgold-Voigt
- Leibniz-Institute of Photonic Technology (Leibniz-IPHT), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Stefan Monecke
- Leibniz-Institute of Photonic Technology (Leibniz-IPHT), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institute for Medical Microbiology and Virology, Dresden University Hospital, 01307 Dresden, Germany
| | - Anne Busch
- Department of Anaesthesiology and Intensive Care Medicine, University Hospital, 07747 Jena, Germany
| | - Herbert Bocklisch
- Thuringian State Authority for Food-Safety and Consumer Protection (TLLV), 99947 Bad Langensalza, Germany
| | - Sascha D Braun
- Leibniz-Institute of Photonic Technology (Leibniz-IPHT), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Celia Diezel
- Leibniz-Institute of Photonic Technology (Leibniz-IPHT), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Institute of Bacterial Infections and Zoonoses, 07751 Jena, Germany
| | | | - Elke Müller
- Leibniz-Institute of Photonic Technology (Leibniz-IPHT), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Martin Reinicke
- Leibniz-Institute of Photonic Technology (Leibniz-IPHT), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Annett Reissig
- Leibniz-Institute of Photonic Technology (Leibniz-IPHT), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Antje Ruppelt-Lorz
- Institute for Medical Microbiology and Virology, Dresden University Hospital, 01307 Dresden, Germany
| | - Ralf Ehricht
- Leibniz-Institute of Photonic Technology (Leibniz-IPHT), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institute of Physical Chemistry, Friedrich Schiller University, 07743 Jena, Germany
| |
Collapse
|
11
|
Moura de Sousa J, Lourenço M, Gordo I. Horizontal gene transfer among host-associated microbes. Cell Host Microbe 2023; 31:513-527. [PMID: 37054673 DOI: 10.1016/j.chom.2023.03.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Horizontal gene transfer is an important evolutionary force, facilitating bacterial diversity. It is thought to be pervasive in host-associated microbiomes, where bacterial densities are high and mobile elements are frequent. These genetic exchanges are also key for the rapid dissemination of antibiotic resistance. Here, we review recent studies that have greatly extended our knowledge of the mechanisms underlying horizontal gene transfer, the ecological complexities of a network of interactions involving bacteria and their mobile elements, and the effect of host physiology on the rates of genetic exchanges. Furthermore, we discuss other, fundamental challenges in detecting and quantifying genetic exchanges in vivo, and how studies have contributed to start overcoming these challenges. We highlight the importance of integrating novel computational approaches and theoretical models with experimental methods where multiple strains and transfer elements are studied, both in vivo and in controlled conditions that mimic the intricacies of host-associated environments.
Collapse
Affiliation(s)
- Jorge Moura de Sousa
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, 75015 Paris, France
| | - Marta Lourenço
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, F-75015 Paris, France
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande,6, Oeiras, Portugal.
| |
Collapse
|
12
|
Braga LPP, Schumacher RI. Awaking the dormant virome in the rhizosphere. Mol Ecol 2023; 32:2985-2999. [PMID: 36807953 DOI: 10.1111/mec.16893] [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: 11/18/2022] [Revised: 01/16/2023] [Accepted: 02/06/2023] [Indexed: 02/22/2023]
Abstract
The rhizosphere is a vital soil compartment providing key plant-beneficial functions. However, little is known about the mechanisms driving viral diversity in the rhizosphere. Viruses can establish lytic or lysogenic interactions with their bacterial hosts. In the latter, they assume a dormant state integrated in the host genome and can be awakened by different perturbations that impact host cell physiology, triggering a viral bloom, which is potentially a fundamental mechanism driving soil viral diversity, as 22%-68% of soil bacteria are predicted to harbour dormant viruses. Here we assessed the viral bloom response in rhizospheric viromes by exposing them to three contrasting soil perturbation agents: earthworms, herbicide and antibiotic pollutant. The viromes were next screened for rhizosphere-relevant genes and also used as inoculant on microcosms incubations to test their impacts on pristine microbiomes. Our results show that while post-perturbation viromes diverged from control conditions, viral communities exposed to both herbicide and antibiotic pollutant were more similar to each other than those influenced by earthworms. The latter also favoured an increase in viral populations harbouring genes involved in plant-beneficial functions. Post-perturbation viromes inoculated on soil microcosms changed the diversity of pristine microbiomes, suggesting that viromes are important components of the soil ecological memory driving eco-evolutionary processes that determine future microbiome trajectories according to past events. Our findings demonstrate that viromes are active players in the rhizosphere and need to be considered in efforts to understand and control the microbial processes towards sustainable crop production.
Collapse
Affiliation(s)
- Lucas P P Braga
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, Brazil.,Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Robert I Schumacher
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, Brazil
| |
Collapse
|
13
|
Sutcliffe SG, Reyes A, Maurice CF. Bacteriophages playing nice: Lysogenic bacteriophage replication stable in the human gut microbiota. iScience 2023; 26:106007. [PMID: 36798434 PMCID: PMC9926308 DOI: 10.1016/j.isci.2023.106007] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 10/28/2022] [Accepted: 01/13/2023] [Indexed: 01/19/2023] Open
Abstract
Bacteriophages, viruses specific to bacteria, coexist with their bacterial hosts with limited diversity fluctuations in the guts of healthy individuals where they replicate mostly via lysogenic replication. This favors 'piggy-back-the-winner' over 'kill-the-winner' dynamics which are driven by lytic bacteriophage replication. Revisiting the deep-viral sequencing data of a healthy individual sampled over 2.4 years, we explore how these dynamics occur. Prophages found in assembled bacterial metagenomes were also found extra-cellularly, as induced phage particles (iPPs), likely derived from prophage activation. These iPPs were diverse and continually present in low abundance, relative to the highly abundant but less diverse lytic phage population. The continuous detection of low levels of iPPs suggests that spontaneous induction regularly occurs in this healthy individual, possibly allowing prophages to maintain their ability to replicate and avoiding degradation and loss from the gut microbiota.
Collapse
Affiliation(s)
- Steven G. Sutcliffe
- McGill Centre for Microbiome Research, McGill University, Montreal, QC, Canada,Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA,Corresponding author
| | - Corinne F. Maurice
- McGill Centre for Microbiome Research, McGill University, Montreal, QC, Canada,Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada,Corresponding author
| |
Collapse
|
14
|
Jansen D, Matthijnssens J. The Emerging Role of the Gut Virome in Health and Inflammatory Bowel Disease: Challenges, Covariates and a Viral Imbalance. Viruses 2023; 15:173. [PMID: 36680214 PMCID: PMC9861652 DOI: 10.3390/v15010173] [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: 12/02/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Virome research is a rapidly growing area in the microbiome field that is increasingly associated with human diseases, such as inflammatory bowel disease (IBD). Although substantial progress has been made, major methodological challenges limit our understanding of the virota. In this review, we describe challenges that must be considered to accurately report the virome composition and the current knowledge on the virome in health and IBD. First, the description of the virome shows strong methodological biases related to wetlab (e.g., VLP enrichment) and bioinformatics approaches (viral identification and classification). Second, IBD patients show consistent viral imbalances characterized by a high relative abundance of phages belonging to the Caudovirales and a low relative abundance of phages belonging to the Microviridae. Simultaneously, a sporadic contraction of CrAss-like phages and a potential expansion of the lysogenic potential of the intestinal virome are observed. Finally, despite numerous studies that have conducted diversity analysis, it is difficult to draw firm conclusions due to methodological biases. Overall, we present the many methodological and environmental factors that influence the virome, its current consensus in health and IBD, and a contributing hypothesis called the "positive inflammatory feedback loop" that may play a role in the pathophysiology of IBD.
Collapse
Affiliation(s)
| | - Jelle Matthijnssens
- Laboratory of Viral Metagenomics, Rega Institute, Department of Microbiology, Immunology and Transplantation, University of Leuven, B-3000 Leuven, Belgium
| |
Collapse
|
15
|
Strathdee SA, Hatfull GF, Mutalik VK, Schooley RT. Phage therapy: From biological mechanisms to future directions. Cell 2023; 186:17-31. [PMID: 36608652 PMCID: PMC9827498 DOI: 10.1016/j.cell.2022.11.017] [Citation(s) in RCA: 140] [Impact Index Per Article: 140.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/01/2022] [Accepted: 11/16/2022] [Indexed: 01/07/2023]
Abstract
Increasing antimicrobial resistance rates have revitalized bacteriophage (phage) research, the natural predators of bacteria discovered over 100 years ago. In order to use phages therapeutically, they should (1) preferably be lytic, (2) kill the bacterial host efficiently, and (3) be fully characterized to exclude side effects. Developing therapeutic phages takes a coordinated effort of multiple stakeholders. Herein, we review the state of the art in phage therapy, covering biological mechanisms, clinical applications, remaining challenges, and future directions involving naturally occurring and genetically modified or synthetic phages.
Collapse
Affiliation(s)
- Steffanie A Strathdee
- Center for Innovative Phage Applications and Therapeutics, Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA 92093-0507, USA.
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Vivek K Mutalik
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert T Schooley
- Center for Innovative Phage Applications and Therapeutics, Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA 92093-0507, USA
| |
Collapse
|
16
|
Correction: Sutcliffe et al. Common Oral Medications Lead to Prophage Induction in Bacterial Isolates from the Human Gut. Viruses 2021, 13, 455. Viruses 2022; 15:v15010025. [PMID: 36680300 PMCID: PMC9865624 DOI: 10.3390/v15010025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 12/24/2022] Open
Abstract
In the original publication [...].
Collapse
|
17
|
Abstract
PURPOSE OF REVIEW Recent years have seen great strides made in the field of viral metagenomics. Many studies have reported alterations in the virome in different disease states. The vast majority of the human intestinal virome consists of bacteriophages, viruses that infect bacteria. The dynamic relationship between gut bacterial populations and bacteriophages is influenced by environmental factors that also impact host health and disease. In this review, we focus on studies highlighting the dynamics of the gut virome and fluctuations associated with disease states. RECENT FINDINGS Novel correlations have been identified between the human gut virome and diseases such as obesity, necrotizing enterocolitis and severe acute respiratory syndrome coronavirus 2 infection. Further associations between the virome and cognition, diet and geography highlight the complexity of factors that can influence the dynamic relationship between gut bacteria, bacteriophages and health. SUMMARY Here, we highlight some novel associations between the virome and health that will be the foundation for future studies in this field. The future development of microbiome-based interventions, identification of biomarkers, and novel therapeutics will require a thorough understanding of the gut virome and its dynamics.
Collapse
Affiliation(s)
- Hiba Shareefdeen
- APC Microbiome Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| |
Collapse
|
18
|
Henrot C, Petit M. Signals triggering prophage induction in the gut microbiota. Mol Microbiol 2022; 118:494-502. [PMID: 36164818 PMCID: PMC9827884 DOI: 10.1111/mmi.14983] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/15/2022] [Accepted: 09/18/2022] [Indexed: 01/12/2023]
Abstract
Compared to bacteria of the gut microbiota, bacteriophages are still poorly characterised, and their physiological importance is far less known. Temperate phages are probably a major actor in the gut, as it is estimated that 80% of intestinal bacteria are lysogens, meaning that they are carrying prophages. In addition, prophage induction rates are higher in the gut than in vitro. However, studies on the signals leading to prophage induction have essentially focused on genotoxic agents with poor relevance for this environment. In this review, we sum up recent findings about signals able to trigger prophage induction in the gut. Three categories of signals are at play: those originating from interactions between intestinal microbes, those from the human or animal host physiology and those from external intakes. These recent results highlight the diversity of factors influencing prophage induction in the gut, and start to unveil ways by which microbiota composition may be modulated.
Collapse
Affiliation(s)
- Caroline Henrot
- Université Paris‐Saclay, INRAEAgroParisTech, Micalis InstituteJouy‐en‐JosasFrance,Master de Biologie, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1Université de LyonLyonFrance
| | - Marie‐Agnès Petit
- Université Paris‐Saclay, INRAEAgroParisTech, Micalis InstituteJouy‐en‐JosasFrance
| |
Collapse
|
19
|
Mining of Thousands of Prokaryotic Genomes Reveals High Abundance of Prophages with a Strictly Narrow Host Range. mSystems 2022; 7:e0032622. [PMID: 35880895 PMCID: PMC9426530 DOI: 10.1128/msystems.00326-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Phages and prophages are one of the principal modulators of microbial populations. However, much of their diversity is still poorly understood. Here, we extracted 33,624 prophages from 13,713 complete prokaryotic genomes to explore the prophage diversity and their relationships with their host. Our results reveal that prophages were present in 75% of the genomes studied. In addition, Enterobacterales were significantly enriched in prophages. We also found that pathogens are a significant reservoir of prophages. Finally, we determined that the prophage relatedness and the range of genomic hosts were delimited by the evolutionary relationships of their hosts. On a broader level, we got insights into the prophage population, identified in thousands of publicly available prokaryotic genomes, by comparing the prophage distribution and relatedness between them and their hosts. IMPORTANCE Phages and prophages play an essential role in controlling their host populations either by modulating the host abundance or providing them with genes that benefit the host. The constant growth in next-generation sequencing technology has caused the development of powerful computational tools to identify phages and prophages with high precision. Making it possible to explore the prophage populations integrated into host genomes on a large scale. However, it is still a new and under-explored area, and efforts are still required to identify prophage populations to understand their dynamics with their hosts.
Collapse
|
20
|
Sinha A, Li Y, Mirzaei MK, Shamash M, Samadfam R, King IL, Maurice CF. Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates the severity of DSS colitis. MICROBIOME 2022; 10:105. [PMID: 35799219 PMCID: PMC9264660 DOI: 10.1186/s40168-022-01275-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/13/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND Inflammatory bowel diseases (IBDs) including Crohn's disease (CD) and ulcerative colitis (UC) are characterized by chronic and debilitating gut inflammation. Altered bacterial communities of the intestine are strongly associated with IBD initiation and progression. The gut virome, which is primarily composed of bacterial viruses (bacteriophages, phages), is thought to be an important factor regulating and shaping microbial communities in the gut. While alterations in the gut virome have been observed in IBD patients, the contribution of these viruses to alterations in the bacterial community and heightened inflammatory responses associated with IBD patients remains largely unknown. RESULTS Here, we performed in vivo microbial cross-infection experiments to follow the effects of fecal virus-like particles (VLPs) isolated from UC patients and healthy controls on bacterial diversity and severity of experimental colitis in human microbiota-associated (HMA) mice. Shotgun metagenomics confirmed that several phages were transferred to HMA mice, resulting in treatment-specific alterations in the gut virome. VLPs from healthy and UC patients also shifted gut bacterial diversity of these mice, an effect that was amplified during experimental colitis. VLPs isolated from UC patients specifically altered the relative abundance of several bacterial taxa previously implicated in IBD progression. Additionally, UC VLP administration heightened colitis severity in HMA mice, as indicated by shortened colon length and increased pro-inflammatory cytokine production. Importantly, this effect was dependent on intact VLPs. CONCLUSIONS Our findings build on recent literature indicating that phages are dynamic regulators of bacterial communities in the gut and implicate the intestinal virome in modulating intestinal inflammation and disease. Video Abstract.
Collapse
Affiliation(s)
- Anshul Sinha
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Yue Li
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, Guangdong, China
| | - Mohammadali Khan Mirzaei
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
- Institute of Virology, Helmholtz Center Munich and Technical University of Munich, 85764, Neuherberg, Bavaria, Germany
| | - Michael Shamash
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Rana Samadfam
- Charles River Laboratories, 22022 Transcanadienne, Senneville, QC, H9X 3R3, Canada
| | - Irah L King
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada.
- McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, QC, Canada.
| | - Corinne F Maurice
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada.
- McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, QC, Canada.
| |
Collapse
|
21
|
Cao Z, Sugimura N, Burgermeister E, Ebert MP, Zuo T, Lan P. The gut virome: A new microbiome component in health and disease. EBioMedicine 2022; 81:104113. [PMID: 35753153 PMCID: PMC9240800 DOI: 10.1016/j.ebiom.2022.104113] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/14/2022] [Accepted: 05/30/2022] [Indexed: 12/19/2022] Open
Abstract
The human gastrointestinal tract harbours an abundance of viruses, collectively known as the gut virome. The gut virome is highly heterogeneous across populations and is linked to geography, ethnicity, diet, lifestyle, and urbanisation. The currently known function of the gut virome varies greatly across human populations, and much remains unknown. We review current literature on the human gut virome, and the intricate trans-kingdom interplay among gut viruses, bacteria, and the mammalian host underlying health and diseases. We summarise evidence on the use of the gut virome as diagnostic markers and a therapeutic target. We shed light on novel avenues of microbiome-inspired diagnosis and therapies. We also review pre-clinical and clinical studies on gut virome-rectification-based therapies, including faecal microbiota transplantation, faecal virome transplantation, and refined phage therapy. Our review suggests that future research effort should focus on unravelling the mechanisms exerted by gut viruses/phages in human pathophysiology, and on developing phage-prompted precision therapies.
Collapse
Affiliation(s)
- Zhirui Cao
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, China; Centre for Faecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Naoki Sugimura
- Department of Gastroenterology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Elke Burgermeister
- Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Matthias P Ebert
- Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany; DKFZ-Hector Cancer Institute, Mannheim, Germany; Mannheim Cancer Centre (MCC), University Medical Centre Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Tao Zuo
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, China; Centre for Faecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
| | - Ping Lan
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, China; Centre for Faecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
| |
Collapse
|
22
|
Lindell AE, Zimmermann-Kogadeeva M, Patil KR. Multimodal interactions of drugs, natural compounds and pollutants with the gut microbiota. Nat Rev Microbiol 2022; 20:431-443. [PMID: 35102308 PMCID: PMC7615390 DOI: 10.1038/s41579-022-00681-5] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2022] [Indexed: 02/08/2023]
Abstract
The gut microbiota contributes to diverse aspects of host physiology, ranging from immunomodulation to drug metabolism. Changes in the gut microbiota composition are associated with various diseases as well as with the response to medications. It is therefore important to understand how different lifestyle and environmental factors shape gut microbiota composition. Beyond the commonly considered factor of diet, small-molecule drugs have recently been identified as major effectors of the microbiota composition. Other xenobiotics, such as environmental or chemical pollutants, can also impact gut bacterial communities. Here, we review the mechanisms of interactions between gut bacteria and antibiotics, host-targeted drugs, natural food compounds, food additives and environmental pollutants. While xenobiotics can impact bacterial growth and metabolism, bacteria in turn can bioaccumulate or chemically modify these compounds. These reciprocal interactions can manifest in complex xenobiotic-microbiota-host relationships. Our Review highlights the need to study mechanisms underlying interactions with pollutants and food additives towards deciphering the dynamics and evolution of the gut microbiota.
Collapse
Affiliation(s)
- Anna E Lindell
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | | | - Kiran R Patil
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK.
| |
Collapse
|
23
|
Shkoporov AN, Turkington CJ, Hill C. Mutualistic interplay between bacteriophages and bacteria in the human gut. Nat Rev Microbiol 2022; 20:737-749. [PMID: 35773472 DOI: 10.1038/s41579-022-00755-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 12/12/2022]
Abstract
Bacteriophages (phages) are often described as obligate predators of their bacterial hosts, and phage predation is one of the leading forces controlling the density and distribution of bacterial populations. Every 48 h half of all bacteria on Earth are killed by phages. Efficient killing also forms the basis of phage therapy in humans and animals and the use of phages as food preservatives. In turn, bacteria have a plethora of resistance systems against phage attack, but very few bacterial species, if any, have entirely escaped phage predation. However, in complex communities and environments such as the human gut, this antagonistic model of attack and counter-defence does not fully describe the scope of phage-bacterium interactions. In this Review, we explore some of the more mutualistic aspects of phage-bacterium interactions in the human gut, and we suggest that the relationship between phages and their bacterial hosts in the gut is best characterized not as a fight to the death between enemies but rather as a mutualistic relationship between partners.
Collapse
Affiliation(s)
- Andrey N Shkoporov
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland. .,Department of Medicine, University College Cork, Cork, Ireland.
| | | | - Colin Hill
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland.
| |
Collapse
|
24
|
Tiamani K, Luo S, Schulz S, Xue J, Costa R, Khan Mirzaei M, Deng L. The role of virome in the gastrointestinal tract and beyond. FEMS Microbiol Rev 2022; 46:6608358. [PMID: 35700129 PMCID: PMC9629487 DOI: 10.1093/femsre/fuac027] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 01/11/2023] Open
Abstract
The human gut virome is comprised of diverse commensal and pathogenic viruses. The colonization by these viruses begins right after birth through vaginal delivery, then continues through breastfeeding, and broader environmental exposure. Their constant interaction with their bacterial hosts in the body shapes not only our microbiomes but us. In addition, these viruses interact with the immune cells, trigger a broad range of immune responses, and influence different metabolic pathways. Besides its key role in regulating the human gut homeostasis, the intestinal virome contributes to disease development in distant organs, both directly and indirectly. In this review, we will describe the changes in the gut virome through life, health, and disease, followed by discussing the interactions between the virome, the microbiome, and the human host as well as providing an overview of their contribution to gut disease and disease of distant organs.
Collapse
Affiliation(s)
| | | | - Sarah Schulz
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany,Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Jinling Xue
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany,Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Rita Costa
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany,Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Mohammadali Khan Mirzaei
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany,Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Li Deng
- Corresponding author: Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany; Chair of Prevention of Microbial Diseases, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany. E-mail:
| |
Collapse
|
25
|
Ge Z, Kuang Z, Chen J, Chen J, Liu T, She Z, Lu Y. Comparative genomics analysis of Bacillus velezensis LOH112 isolated from a nonagenarian provides insights into its biocontrol and probiotic traits. Gene 2022; 835:146644. [PMID: 35680027 DOI: 10.1016/j.gene.2022.146644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/28/2022] [Accepted: 06/02/2022] [Indexed: 11/17/2022]
Abstract
Bacillus velezensis has recently received increasing attention as a biological fungicide and a potential probiotic agent because of its broad spectrum of antibacterial and antifungal activities. Here, we evaluated the beneficial traits of a newly isolated B. velezensis strain LOH112 using comprehensive bioinformatics and comparative genomic analyses and in vitro experimental approaches. Whole genome sequencing and assembly results showed that the genome of LOH112 consists of a circular chromosome and a circular plasmid, which encodes proteins involved in important biological processes such as sporulation, quorum sensing, and antibiotic synthesis. LOH112 contains 13 secondary metabolism gene clusters responsible for the production of antimicrobial compounds. In vitro experiments showed that LOH112 effectively inhibits several fungi and Gram-positive pathogenic bacteria, hydrolyzes protein and cellulose, and is capable of forming strong adhesive biofilms. Furthermore, comparative genomics revealed that LOH112 contains 34 strain-specific orthologous gene clusters, including two caseinolytic protease P (clpP) genes responsible for proteomic homeostasis. Selective pressure analysis indicated that the transmembrane transporter and ATP-dependent alanine/valine adenylase genes were strongly positively selected, which may endow LOH112 with better biocontrol ability and potential probiotic properties. Collectively, these results not only provide insights into a deeper understanding of the genomic characterization of LOH112 but also imply the potential application of LOH112 as biocontrol and probiotic agents.
Collapse
Affiliation(s)
- Zhenhuang Ge
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhiqi Kuang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou 510275, China
| | - Jiahao Chen
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou 510275, China
| | - Junyi Chen
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou 510275, China
| | - Tianhao Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhigang She
- School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China
| | - Yongjun Lu
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou 510275, China.
| |
Collapse
|
26
|
Liang G, Gao H, Bushman FD. The pediatric virome in health and disease. Cell Host Microbe 2022; 30:639-649. [PMID: 35550667 DOI: 10.1016/j.chom.2022.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/22/2022] [Accepted: 04/11/2022] [Indexed: 11/03/2022]
Abstract
Associations between the global microbiome and diseases of children have been studied extensively; however, research on the viral component of the microbiome, the "virome," is less advanced. The analysis of disease associations with the virome is often technically challenging, requiring a close examination of the "virome dark matter." The gut is a particularly rich source of viral particles, and now multiple studies have reported intriguing associations of the virome with childhood diseases. For example, virome studies have elucidated new lineages of gut viruses that appear to be tightly associated with childhood diarrhea, and consistent patterns are starting to emerge from virome studies in pediatric IBD. In this review, we summarize the methods for studying the virome and recent research on the nature of the virome during childhood, focusing on specific studies of the intestinal virome in pediatric diseases.
Collapse
Affiliation(s)
- Guanxiang Liang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
| | - Hongyan Gao
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6076, USA.
| |
Collapse
|
27
|
Rehabilitation of a misbehaving microbiome: phages for the remodeling of bacterial composition and function. iScience 2022; 25:104146. [PMID: 35402871 PMCID: PMC8991392 DOI: 10.1016/j.isci.2022.104146] [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] [Indexed: 12/02/2022] Open
Abstract
The human gut microbiota is considered an adjunct metabolic organ owing to its health impact. Recent studies have shown correlations between gut phage composition and host health. Whereas phage therapy has popularized virulent phages as antimicrobials, both virulent and temperate phages have a natural ecological relationship with their cognate bacteria. Characterization of this evolutionary coadaptation has led to other emergent therapeutic phage applications that do not necessarily rely on bacterial eradication or target pathogens. Here, we present an overview of the tripartite relationship between phages, bacteria, and the mammalian host, and highlight applications of the wildtype and genetically engineered phage for gut microbiome remodeling. In light of new and varied strategies, we propose to categorize phage applications aiming to modulate bacterial composition or function as “phage rehabilitation.” By delineating phage rehab from phage therapy, we believe it will enable greater nuance and understanding of these new phage-based technologies.
Collapse
|
28
|
Leigh SJ, Lynch CMK, Bird BRH, Griffin BT, Cryan JF, Clarke G. Gut microbiota-drug interactions in cancer pharmacotherapies: implications for efficacy and adverse effects. Expert Opin Drug Metab Toxicol 2022; 18:5-26. [PMID: 35176217 DOI: 10.1080/17425255.2022.2043849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION The gut microbiota is involved in host physiology and health. Reciprocal microbiota-drug interactions are increasingly recognized as underlying some individual differences in therapy response and adverse events. Cancer pharmacotherapies are characterized by a high degree of interpatient variability in efficacy and side effect profile and recently, the microbiota has emerged as a factor that may underlie these differences. AREAS COVERED The effects of cancer pharmacotherapy on microbiota composition and function are reviewed with consideration of the relationship between baseline microbiota composition, microbiota modification, antibiotics exposure and cancer therapy efficacy. We assess the evidence implicating the microbiota in cancer therapy-related adverse events including impaired gut function, cognition and pain perception. Finally, potential mechanisms underlying microbiota-cancer drug interactions are described, including direct microbial metabolism, and microbial modulation of liver metabolism and immune function. This review focused on preclinical and clinical studies conducted in the last 5 years. EXPERT OPINION Preclinical and clinical research supports a role for baseline microbiota in cancer therapy efficacy, with emerging evidence that the microbiota modification may assist in side effect management. Future efforts should focus on exploiting this knowledge towards the development of microbiota-targeted therapies. Finally, a focus on specific drug-microbiota-cancer interactions is warranted.
Collapse
Affiliation(s)
| | | | | | | | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Gerard Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| |
Collapse
|
29
|
Wang X, Liu Y, Wu Z, Zhang P, Zhang X. Tea Polyphenols: A Natural Antioxidant Regulates Gut Flora to Protect the Intestinal Mucosa and Prevent Chronic Diseases. Antioxidants (Basel) 2022; 11:antiox11020253. [PMID: 35204136 PMCID: PMC8868443 DOI: 10.3390/antiox11020253] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 02/07/2023] Open
Abstract
The intestinal tract of a healthy human body hosts many microorganisms that are closely linked to all aspects of people’s lives. The impact of intestinal flora on host health is no longer limited to the gut but can also affect every organ in the body through various pathways. Studies have found that intestinal flora can be altered by external factors, which provides new ideas for treating some diseases. Tea polyphenols (TP), a general term for polyphenols in tea, are widely used as a natural antioxidant in various bioactive foods. In recent years, with the progress of research, there have been many experiments that provide strong evidence for the ability of TP to regulate intestinal flora. However, there are very few studies on the use of TP to modify the composition of intestinal microorganisms to maintain health or treat related diseases, and this area has not received sufficient attention. In this review, we outline the mechanisms by which TP regulates intestinal flora and the essential role in maintaining suitable health. In addition, we highlighted the protective effects of TP on intestinal mucosa by regulating intestinal flora and the preventive and therapeutic effects on certain chronic diseases, which will help further explore measures to prevent related chronic diseases.
Collapse
Affiliation(s)
- Xinzhou Wang
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, China; (X.W.); (Y.L.); (Z.W.)
| | - Yanan Liu
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, China; (X.W.); (Y.L.); (Z.W.)
| | - Zufang Wu
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, China; (X.W.); (Y.L.); (Z.W.)
| | - Peng Zhang
- Department of Student Affairs, Xinyang Normal University, Xinyang 464000, China
- Correspondence: (P.Z.); (X.Z.)
| | - Xin Zhang
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, China; (X.W.); (Y.L.); (Z.W.)
- Correspondence: (P.Z.); (X.Z.)
| |
Collapse
|
30
|
Cieślik M, Bagińska N, Jończyk-Matysiak E, Węgrzyn A, Węgrzyn G, Górski A. Temperate Bacteriophages-The Powerful Indirect Modulators of Eukaryotic Cells and Immune Functions. Viruses 2021; 13:v13061013. [PMID: 34071422 PMCID: PMC8228536 DOI: 10.3390/v13061013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/22/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022] Open
Abstract
Bacteriophages are natural biological entities that limit the growth and amplification of bacteria. They are important stimulators of evolutionary variability in bacteria, and currently are considered a weapon against antibiotic resistance of bacteria. Nevertheless, apart from their antibacterial activity, phages may act as modulators of mammalian immune responses. In this paper, we focus on temperate phages able to execute the lysogenic development, which may shape animal or human immune response by influencing various processes, including phagocytosis of bacterial invaders and immune modulation of mammalian host cells.
Collapse
Affiliation(s)
- Martyna Cieślik
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.C.); (N.B.); (E.J.-M.)
| | - Natalia Bagińska
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.C.); (N.B.); (E.J.-M.)
| | - Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.C.); (N.B.); (E.J.-M.)
| | - Alicja Węgrzyn
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdańsk, Poland;
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland;
| | - Andrzej Górski
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.C.); (N.B.); (E.J.-M.)
- Phage Therapy Unit, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland
- Infant Jesus Hospital, The Medical University of Warsaw, 02-006 Warsaw, Poland
- Correspondence:
| |
Collapse
|
31
|
Temperate phage-antibiotic synergy eradicates bacteria through depletion of lysogens. Cell Rep 2021; 35:109172. [PMID: 34038739 DOI: 10.1016/j.celrep.2021.109172] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 03/13/2021] [Accepted: 05/04/2021] [Indexed: 01/02/2023] Open
Abstract
There is renewed interest in bacterial viruses (phages) as alternatives to antibiotics. All phage treatments to date have used virulent phages rather than temperate ones, as these can integrate into the genome of the bacterial host and lie dormant. However, temperate phages are abundant and easier to isolate. To make use of these entities, we leverage stressors known to awaken these dormant, integrated phages. Co-administration of the temperate phage HK97 with sub-inhibitory concentrations of the antibiotic ciprofloxacin results in bacterial eradication (≥8 log reduction) in vitro. This synergy is mechanistically distinct from phage-antibiotic-synergy described for virulent phages. Instead, the antibiotic specifically selects against bacteria in which the phage has integrated. As the interaction between temperate phages and stressors such as ciprofloxacin are known to be widespread, this approach may be broadly applicable and enable the use of temperate phages to combat bacterial infections.
Collapse
|