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Feltin C, Garneau JR, Morris CE, Bérard A, Torres-Barceló C. Novel phages of Pseudomonas syringae unveil numerous potential auxiliary metabolic genes. J Gen Virol 2024; 105. [PMID: 38833289 DOI: 10.1099/jgv.0.001990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024] Open
Abstract
Relatively few phages that infect plant pathogens have been isolated and investigated. The Pseudomonas syringae species complex is present in various environments, including plants. It can cause major crop diseases, such as bacterial canker on apricot trees. This study presents a collection of 25 unique phage genomes that infect P. syringae. These phages were isolated from apricot orchards with bacterial canker symptoms after enrichment with 21 strains of P. syringae. This collection comprises mostly virulent phages, with only three being temperate. They belong to 14 genera, 11 of which are newly discovered, and 18 new species, revealing great genetic diversity within this collection. Novel DNA packaging systems have been identified bioinformatically in one of the new phage species, but experimental confirmation is required to define the precise mechanism. Additionally, many phage genomes contain numerous potential auxiliary metabolic genes with diversified putative functions. At least three phages encode genes involved in bacterial tellurite resistance, a toxic metalloid. This suggests that viruses could play a role in bacterial stress tolerance. This research emphasizes the significance of continuing the search for new phages in the agricultural ecosystem to unravel novel ecological diversity and new gene functions. This work contributes to the foundation for future fundamental and applied research on phages infecting phytopathogenic bacteria.
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Affiliation(s)
- Chloé Feltin
- INRAE, Pathologie Végétale, F-84140, Montfavet, France
| | - Julian R Garneau
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
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2
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Abs E, Chase AB, Manzoni S, Ciais P, Allison SD. Microbial evolution-An under-appreciated driver of soil carbon cycling. GLOBAL CHANGE BIOLOGY 2024; 30:e17268. [PMID: 38562029 DOI: 10.1111/gcb.17268] [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: 12/20/2023] [Revised: 03/18/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Although substantial advances in predicting the ecological impacts of global change have been made, predictions of the evolutionary impacts have lagged behind. In soil ecosystems, microbes act as the primary energetic drivers of carbon cycling; however, microbes are also capable of evolving on timescales comparable to rates of global change. Given the importance of soil ecosystems in global carbon cycling, we assess the potential impact of microbial evolution on carbon-climate feedbacks in this system. We begin by reviewing the current state of knowledge concerning microbial evolution in response to global change and its specific effect on soil carbon dynamics. Through this integration, we synthesize a roadmap detailing how to integrate microbial evolution into ecosystem biogeochemical models. Specifically, we highlight the importance of microscale mechanistic soil carbon models, including choosing an appropriate evolutionary model (e.g., adaptive dynamics, quantitative genetics), validating model predictions with 'omics' and experimental data, scaling microbial adaptations to ecosystem level processes, and validating with ecosystem-scale measurements. The proposed steps will require significant investment of scientific resources and might require 10-20 years to be fully implemented. However, through the application of multi-scale integrated approaches, we will advance the integration of microbial evolution into predictive understanding of ecosystems, providing clarity on its role and impact within the broader context of environmental change.
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Affiliation(s)
- Elsa Abs
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California, USA
- Laboratoire Des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Alexander B Chase
- Department of Earth Sciences, Southern Methodist University, Dallas, Texas, USA
| | - Stefano Manzoni
- Department of Physical Geography and Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - Philippe Ciais
- Laboratoire Des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Steven D Allison
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California, USA
- Department of Earth System Science, University of California, Irvine, Irvine, California, USA
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3
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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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4
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Würstle S, Lee A, Kortright KE, Winzig F, An W, Stanley GL, Rajagopalan G, Harris Z, Sun Y, Hu B, Blazanin M, Hajfathalian M, Bollyky PL, Turner PE, Koff JL, Chan BK. Optimized preparation pipeline for emergency phage therapy against Pseudomonas aeruginosa at Yale University. Sci Rep 2024; 14:2657. [PMID: 38302552 PMCID: PMC10834462 DOI: 10.1038/s41598-024-52192-3] [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: 09/25/2023] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Bacteriophage therapy is one potential strategy to treat antimicrobial resistant or persistent bacterial infections, and the year 2021 marked the centennial of Felix d'Hérelle's first publication on the clinical applications of phages. At the Center for Phage Biology & Therapy at Yale University, a preparatory modular approach has been established to offer safe and potent phages for single-patient investigational new drug applications while recognizing the time constraints imposed by infection(s). This study provides a practical walkthrough of the pipeline with an Autographiviridae phage targeting Pseudomonas aeruginosa (phage vB_PaeA_SB, abbreviated to ΦSB). Notably, a thorough phage characterization and the evolutionary selection pressure exerted on bacteria by phages, analogous to antibiotics, are incorporated into the pipeline.
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Affiliation(s)
- Silvia Würstle
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
- Technical University of Munich, 81675, Munich, Germany
| | - Alina Lee
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Kaitlyn E Kortright
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Franziska Winzig
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
- Technical University of Munich, 81675, Munich, Germany
| | - William An
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Gail L Stanley
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Govindarajan Rajagopalan
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Zach Harris
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Ying Sun
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Buqu Hu
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Michael Blazanin
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Maryam Hajfathalian
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Paul L Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Paul E Turner
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
- Program in Microbiology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Jonathan L Koff
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA.
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA.
| | - Benjamin K Chan
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA.
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA.
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Miao Y, Sun Z, Ma C, Lin C, Wang G, Yang C. VirGrapher: a graph-based viral identifier for long sequences from metagenomes. Brief Bioinform 2024; 25:bbae036. [PMID: 38343326 PMCID: PMC10859693 DOI: 10.1093/bib/bbae036] [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: 12/13/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 02/15/2024] Open
Abstract
Viruses are the most abundant biological entities on earth and are important components of microbial communities. A metagenome contains all microorganisms from an environmental sample. Correctly identifying viruses from these mixed sequences is critical in viral analyses. It is common to identify long viral sequences, which has already been passed thought pipelines of assembly and binning. Existing deep learning-based methods divide these long sequences into short subsequences and identify them separately. This makes the relationships between them be omitted, leading to poor performance on identifying long viral sequences. In this paper, VirGrapher is proposed to improve the identification performance of long viral sequences by constructing relationships among short subsequences from long ones. VirGrapher see a long sequence as a graph and uses a Graph Convolutional Network (GCN) model to learn multilayer connections between nodes from sequences after a GCN-based node embedding model. VirGrapher achieves a better AUC value and accuracy on validation set, which is better than three benchmark methods.
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Affiliation(s)
- Yan Miao
- College of Computer and Control Engineering, Northeast Forestry University, Hexing Road, 150040, Heilongjiang Province, China
| | - Zhenyuan Sun
- College of Computer and Control Engineering, Northeast Forestry University, Hexing Road, 150040, Heilongjiang Province, China
| | - Chenjing Ma
- College of Computer and Control Engineering, Northeast Forestry University, Hexing Road, 150040, Heilongjiang Province, China
| | - Chen Lin
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiangannan Road, 361104, Fujian Province, China
| | - Guohua Wang
- College of Computer and Control Engineering, Northeast Forestry University, Hexing Road, 150040, Heilongjiang Province, China
| | - Chunxue Yang
- College of Landscape Architecture, Northeast Forestry University, Hexing Road, 150040, Heilongjiang Province, China
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6
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Rossi FPN, Flores VS, Uceda-Campos G, Amgarten DE, Setubal JC, da Silva AM. Comparative Analyses of Bacteriophage Genomes. Methods Mol Biol 2024; 2802:427-453. [PMID: 38819567 DOI: 10.1007/978-1-0716-3838-5_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Bacterial viruses (bacteriophages or phages) are the most abundant and diverse biological entities on Earth. There is a renewed worldwide interest in phage-centered research motivated by their enormous potential as antimicrobials to cope with multidrug-resistant pathogens. An ever-growing number of complete phage genomes are becoming available, derived either from newly isolated phages (cultivated phages) or recovered from metagenomic sequencing data (uncultivated phages). Robust comparative analysis is crucial for a comprehensive understanding of genotypic variations of phages and their related evolutionary processes, and to investigate the interaction mechanisms between phages and their hosts. In this chapter, we present a protocol for phage comparative genomics employing tools selected out of the many currently available, focusing on complete genomes of phages classified in the class Caudoviricetes. This protocol provides accurate identification of similarities, differences, and patterns among new and previously known complete phage genomes as well as phage clustering and taxonomic classification.
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Affiliation(s)
| | - Vinicius Sousa Flores
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil
| | - Guillermo Uceda-Campos
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil
| | | | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil
| | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil.
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7
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Xu Z, Ding Z, Shi L, Xie Y, Zhang Y, Wang Z, Liu Q. Coevolution between marine Aeromonas and phages reveals temporal trade-off patterns of phage resistance and host population fitness. THE ISME JOURNAL 2023; 17:2200-2209. [PMID: 37814126 PMCID: PMC10689771 DOI: 10.1038/s41396-023-01529-3] [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: 07/13/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/11/2023]
Abstract
Coevolution of bacteria and phages is an important host and parasite dynamic in marine ecosystems, contributing to the understanding of bacterial community diversity. On the time scale, questions remain concerning what is the difference between phage resistance patterns in marine bacteria and how advantageous mutations gradually accumulate during coevolution. In this study, marine Aeromonas was co-cultured with its phage for 180 days and their genetic and phenotypic dynamics were measured every 30 days. We identified 11 phage resistance genes and classified them into three categories: lipopolysaccharide (LPS), outer membrane protein (OMP), and two-component system (TCS). LPS shortening and OMP mutations are two distinct modes of complete phage resistance, while TCS mutants mediate incomplete resistance by repressing the transcription of phage genes. The co-mutation of LPS and OMP was a major mode for bacterial resistance at a low cost. The mutations led to significant reductions in the growth and virulence of bacterial populations during the first 60 days of coevolution, with subsequent leveling off. Our findings reveal the marine bacterial community dynamics and evolutionary trade-offs of phage resistance during coevolution, thus granting further understanding of the interaction of marine microbes.
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Affiliation(s)
- Zhenhe Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China
| | - Zihan Ding
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China
| | - Lijia Shi
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuzhen Xie
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuanxing Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), 519000, Zhuhai, China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, 200237, China
| | - Zhuang Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China.
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, 200237, China.
| | - Qin Liu
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China.
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, 200237, China.
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8
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Van Cauwenberghe J, Simms EL. How might bacteriophages shape biological invasions? mBio 2023; 14:e0188623. [PMID: 37812005 PMCID: PMC10653932 DOI: 10.1128/mbio.01886-23] [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] [Indexed: 10/10/2023] Open
Abstract
Invasions by eukaryotes dependent on environmentally acquired bacterial mutualists are often limited by the ability of bacterial partners to survive and establish free-living populations. Focusing on the model legume-rhizobium mutualism, we apply invasion biology hypotheses to explain how bacteriophages can impact the competitiveness of introduced bacterial mutualists. Predicting how phage-bacteria interactions affect invading eukaryotic hosts requires knowing the eco-evolutionary constraints of introduced and native microbial communities, as well as their differences in abundance and diversity. By synthesizing research from invasion biology, as well as bacterial, viral, and community ecology, we create a conceptual framework for understanding and predicting how phages can affect biological invasions through their effects on bacterial mutualists.
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Affiliation(s)
- Jannick Van Cauwenberghe
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Ellen L. Simms
- Department of Integrative Biology, University of California, Berkeley, California, USA
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9
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Wodarz D, Komarova NL. Mutant fixation in the presence of a natural enemy. Nat Commun 2023; 14:6642. [PMID: 37863909 PMCID: PMC10589345 DOI: 10.1038/s41467-023-41787-5] [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: 03/02/2023] [Accepted: 09/19/2023] [Indexed: 10/22/2023] Open
Abstract
The literature about mutant invasion and fixation typically assumes populations to exist in isolation from their ecosystem. Yet, populations are part of ecological communities, and enemy-victim (e.g. predator-prey or pathogen-host) interactions are particularly common. We use spatially explicit, computational pathogen-host models (with wild-type and mutant hosts) to re-visit the established theory about mutant fixation, where the pathogen equally attacks both wild-type and mutant individuals. Mutant fitness is assumed to be unrelated to infection. We find that pathogen presence substantially weakens selection, increasing the fixation probability of disadvantageous mutants and decreasing it for advantageous mutants. The magnitude of the effect rises with the infection rate. This occurs because infection induces spatial structures, where mutant and wild-type individuals are mostly spatially separated. Thus, instead of mutant and wild-type individuals competing with each other, it is mutant and wild-type "patches" that compete, resulting in smaller fitness differences and weakened selection. This implies that the deleterious mutant burden in natural populations might be higher than expected from traditional theory.
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Affiliation(s)
- Dominik Wodarz
- Department of Population Health and Disease Prevention, University of California, Irvine, CA, 92697, US.
- Department of Mathematics, University of California, Irvine, CA, 92697, US.
- School of Biological Sciences, Ecology, Behavior & Evolution Department, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
| | - Natalia L Komarova
- Department of Mathematics, University of California, Irvine, CA, 92697, US
- Department of Mathematics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
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10
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Alseth EO, Custodio R, Sundius SA, Kuske RA, Brown SP, Westra ER. The impact of phage and phage resistance on microbial community dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559468. [PMID: 37808693 PMCID: PMC10557685 DOI: 10.1101/2023.09.26.559468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Where there are bacteria, there will be bacteriophages. These viruses are known to be important players in shaping the wider microbial community in which they are embedded, with potential implications for human health. On the other hand, bacteria possess a range of distinct immune mechanisms that provide protection against bacteriophages, including the mutation or complete loss of the phage receptor, and CRISPR-Cas adaptive immunity. Yet little is known about how interactions between phages and these different phage resistance mechanisms affect the wider microbial community in which they are embedded. Here, we conducted a 10-day, fully factorial evolution experiment to examine how phage impact the structure and dynamics of an artificial four-species bacterial community that includes either Pseudomonas aeruginosa wild type or an isogenic mutant unable to evolve phage resistance through CRISPR-Cas. Our results show that the microbial community structure is drastically altered by the addition of phage, with Acinetobacter baumannii becoming the dominant species and P. aeruginosa being driven nearly extinct, whereas P. aeruginosa outcompetes the other species in the absence of phage. Moreover, we find that a P. aeruginosa strain with the ability to evolve CRISPR-based resistance generally does better when in the presence of A. baumannii, but that this benefit is largely lost over time as phage is driven extinct. Combined, our data highlight how phage-targeting a dominant species allows for the competitive release of the strongest competitor whilst also contributing to community diversity maintenance and potentially preventing the reinvasion of the target species, and underline the importance of mapping community composition before therapeutically applying phage.
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Affiliation(s)
- Ellinor O Alseth
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Rafael Custodio
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK
| | - Sarah A Sundius
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Math, Georgia Institute of Technology, Atlanta, Georgia, USA
- Interdisciplinary Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Rachel A Kuske
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Math, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Sam P. Brown
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Edze R Westra
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK
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11
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Aghdam SA, Lahowetz RM, Brown AMV. Divergent endophytic viromes and phage genome repertoires among banana ( Musa) species. Front Microbiol 2023; 14:1127606. [PMID: 37362937 PMCID: PMC10288200 DOI: 10.3389/fmicb.2023.1127606] [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: 12/19/2022] [Accepted: 05/02/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction Viruses generally cause disease, but some viruses may be beneficial as resident regulators of their hosts or host microbiomes. Plant-associated viruses can help plants survive by increasing stress tolerance or regulating endophytic communities. The goal of this study was to characterize endophytic virus communities in banana and plantain (Musa spp.) genotypes, including cultivated and wild species, to assess virome repertoires and detect novel viruses. Methods DNA viral communities were characterized by shotgun sequencing of an enriched endosphere extract from leaves and roots or corm of 7 distinct Musa genotypes (M. balbisiana, Thai Black, M. textilis, M. sikkimensis, Dwarf Cavendish, Williams Hybrid, and FHIA-25 Hybrid). Results Results showed abundant virus-like contigs up to 108,191 bp long with higher relative abundance in leaves than roots. Analyses predicted 733 phage species in 51 families, with little overlap in phage communities among plants. Phage diversity was higher in roots and in diploid wild hosts. Ackermanniviridae and Rhizobium phage were generally the most abundant taxa. A Rhizobium RR1-like phage related to a phage of an endophytic tumor-causing rhizobium was found, bearing a holin gene and a partial Shiga-like toxin gene, raising interest in its potential to regulate endophytic Rhizobiaceae. Klebsiella phages were of interest for possible protection against Fusarium wilt, and other phages were predicted with potential to regulate Erwinia, Pectobacterium, and Ralstonia-associated diseases. Although abundant phage-containing contigs were functionally annotated, revealing 1,038 predicted viral protein domains, gene repertoires showed high divergence from database sequences, suggesting novel phages in these banana cultivars. Plant DNA viruses included 56 species of Badnavirus and 26 additional non-Musa plant viruses with distributions that suggested a mixture of resident and transient plant DNA viruses in these samples. Discussion Together, the disparate viral communities in these plants from a shared environment suggest hosts drive the composition of these virus communities. This study forms a first step in understanding the endophytic virome in this globally important food crop, which is currently threatened by fungal, bacterial, and viral diseases.
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12
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Lu H, Zhu X, Wu L, Lou X, Pan X, Liu B, Zhang H, Zhu L, Li L, Wu Z. Alterations in the intestinal microbiome and metabolic profile of patients with cirrhosis supplemented with lactulose, Clostridium butyricum, and Bifidobacterium longum infantis: a randomized placebo-controlled trial. Front Microbiol 2023; 14:1169811. [PMID: 37180228 PMCID: PMC10170289 DOI: 10.3389/fmicb.2023.1169811] [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: 02/20/2023] [Accepted: 03/27/2023] [Indexed: 05/16/2023] Open
Abstract
Background Liver cirrhosis is commonly accompanied by intestinal dysbiosis and metabolic defects. Many clinical trials have shown microbiota-targeting strategies represent promising interventions for managing cirrhosis and its complications. However, the influences of the intestinal metagenomes and metabolic profiles of patients have not been fully elucidated. Methods We administered lactulose, Clostridium butyricum, and Bifidobacterium longum infantis as a synbiotic and used shotgun metagenomics and non-targeted metabolomics to characterize the results. Results Patients treated with the synbiotic for 12 weeks had lower dysbiosis index (DI) scores than placebo-treated patients and patients at baseline (NIP group). We identified 48 bacterial taxa enriched in the various groups, 66 differentially expressed genes, 18 differentially expressed virulence factor genes, 10 differentially expressed carbohydrate-active enzyme genes, and 173 metabolites present at differing concentrations in the Synbiotic versus Placebo group, and the Synbiotic versus NIP group. And Bifidobacteria species, especially B. longum, showed positive associations with many differentially expressed genes in synbiotic-treated patients. Metabolites pathway enrichment analysis showed that synbiotic significantly affected purine metabolism and aminoacyl-tRNA biosynthesis. And the purine metabolism and aminoacyl-tRNA biosynthesis were no longer significant differences in the Synbiotic group versus the healthy controls group. In conclusion, although littles influence on clinical parameters in the early intervention, the synbiotic showed a potential benefit to patients by ameliorating intestinal dysbiosis and metabolic defects; and the DI of intestinal microbiota is useful for the evaluation of the effect of clinical microbiota-targeting strategies on cirrhotic patients. Clinical Trial Registration https://www.clinicaltrials.gov, identifiers NCT05687409.
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Affiliation(s)
- Haifeng Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaofei Zhu
- Department of Infectious DiseasesHangzhou Ninth People's Hospital, Hangzhou, Zhejiang, China
| | - Lingyun Wu
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaobin Lou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaxia Pan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Bowen Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Hua Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lingxiao Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shangdong, China
- Research Units of Infectious Disease and Microecology, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhongwen Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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13
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Pilosof S. Conceptualizing microbe-plasmid communities as complex adaptive systems. Trends Microbiol 2023:S0966-842X(23)00025-2. [PMID: 36822952 DOI: 10.1016/j.tim.2023.01.007] [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: 10/14/2022] [Revised: 12/29/2022] [Accepted: 01/23/2023] [Indexed: 02/24/2023]
Abstract
Plasmids shape microbial communities' diversity, structure, and function. Nevertheless, we lack a mechanistic understanding of how community structure and dynamics emerge from local microbe-plasmid interactions and coevolution. Addressing this gap is challenging because multiple processes operate simultaneously at multiple levels of organization. For example, immunity operates between a plasmid and a cell, but incompatibility mechanisms regulate coexistence between plasmids. Conceptualizing microbe-plasmid communities as complex adaptive systems is a promising approach to overcoming these challenges. I illustrate how agent-based evolutionary modeling, extended by network analysis, can be used to quantify the relative importance of local processes governing community dynamics. These theoretical developments can advance our understanding of plasmid ecology and evolution, especially when combined with empirical data.
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Affiliation(s)
- Shai Pilosof
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er-Sheva, Israel.
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14
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Schackart KE, Graham JB, Ponsero AJ, Hurwitz BL. Evaluation of computational phage detection tools for metagenomic datasets. Front Microbiol 2023; 14:1078760. [PMID: 36760501 PMCID: PMC9902911 DOI: 10.3389/fmicb.2023.1078760] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/09/2023] [Indexed: 01/25/2023] Open
Abstract
Introduction As new computational tools for detecting phage in metagenomes are being rapidly developed, a critical need has emerged to develop systematic benchmarks. Methods In this study, we surveyed 19 metagenomic phage detection tools, 9 of which could be installed and run at scale. Those 9 tools were assessed on several benchmark challenges. Fragmented reference genomes are used to assess the effects of fragment length, low viral content, phage taxonomy, robustness to eukaryotic contamination, and computational resource usage. Simulated metagenomes are used to assess the effects of sequencing and assembly quality on the tool performances. Finally, real human gut metagenomes and viromes are used to assess the differences and similarities in the phage communities predicted by the tools. Results We find that the various tools yield strikingly different results. Generally, tools that use a homology approach (VirSorter, MARVEL, viralVerify, VIBRANT, and VirSorter2) demonstrate low false positive rates and robustness to eukaryotic contamination. Conversely, tools that use a sequence composition approach (VirFinder, DeepVirFinder, Seeker), and MetaPhinder, have higher sensitivity, including to phages with less representation in reference databases. These differences led to widely differing predicted phage communities in human gut metagenomes, with nearly 80% of contigs being marked as phage by at least one tool and a maximum overlap of 38.8% between any two tools. While the results were more consistent among the tools on viromes, the differences in results were still significant, with a maximum overlap of 60.65%. Discussion: Importantly, the benchmark datasets developed in this study are publicly available and reusable to enable the future comparability of new tools developed.
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Affiliation(s)
- Kenneth E. Schackart
- Department of Biosystems Engineering, The University of Arizona, Tucson, AZ, United States
| | - Jessica B. Graham
- BIO5 Institute, The University of Arizona, Tucson, AZ, United States
| | - Alise J. Ponsero
- Department of Biosystems Engineering, The University of Arizona, Tucson, AZ, United States
- BIO5 Institute, The University of Arizona, Tucson, AZ, United States
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Bonnie L. Hurwitz
- Department of Biosystems Engineering, The University of Arizona, Tucson, AZ, United States
- BIO5 Institute, The University of Arizona, Tucson, AZ, United States
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15
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Ulrich L, Giez C, Steiner LX, Hentschel U, Lachnit T. Adaptive lifestyle of bacteria determines phage-bacteria interaction. Front Microbiol 2022; 13:1056388. [PMID: 36560945 PMCID: PMC9763317 DOI: 10.3389/fmicb.2022.1056388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
Bacteriophages and their interactions with microbes are not well understood. As a first step toward achieving a better understanding, we isolated and sequenced the Curvibacter phage PCA1 for the purpose of eliminating Curvibacter sp. AEP1.3, the main colonizer of Hydra vulgaris AEP. Our experiments showed that PCA1 phage caused a strong, virulent infection only in sessile Curvibacter sp. AEP1.3 but was unable to infect planktonic and host-associated bacterial cells of the same strain. In an effort to investigate this phenomenon, we compared sessile, planktonic, and host-associated bacteria via RNA sequencing and found that all three states differed significantly in their expression patterns. This finding led us to propose that the adaptive lifestyle of Curvibacter sp. AEP1.3 results in varying degrees of susceptibility to bacteriophage infection. This concept could be relevant for phage research and phage therapy in particular. Finally, we were able to induce phage infection in planktonic cells and pinpoint the infection process to a membrane protein. We further identified potential phage-binding protein candidates based on expression pattern analysis.
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Affiliation(s)
- Laura Ulrich
- Zoological Institute, Christian-Albrechts-Universität, Kiel, Germany
| | - Christoph Giez
- Zoological Institute, Christian-Albrechts-Universität, Kiel, Germany
| | - Leon X. Steiner
- RD3 Marine Ecology, RU Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Ute Hentschel
- RD3 Marine Ecology, RU Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Tim Lachnit
- Zoological Institute, Christian-Albrechts-Universität, Kiel, Germany,*Correspondence: Tim Lachnit,
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16
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Taylor M, Janasky L, Vega N. Convergent structure with divergent adaptations in combinatorial microbiome communities. FEMS Microbiol Ecol 2022; 98:6726631. [PMID: 36170949 DOI: 10.1093/femsec/fiac115] [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: 06/13/2022] [Revised: 09/13/2022] [Accepted: 09/26/2022] [Indexed: 01/21/2023] Open
Abstract
Adaptation of replicate microbial communities frequently produces shared trajectories of community composition and structure. However, divergent adaptation of individual community members can occur and is associated with community-level divergence. The extent to which community-based adaptation of microbes should be convergent when community members are similar but not identical is, therefore, not well-understood. In these experiments, adaptation of combinatorial minimal communities of bacteria with the model host Caenorhabditis elegans produces structurally similar communities over time, but with divergent adaptation of member taxa and differences in community-level resistance to invasion. These results indicate that community-based adaptation from taxonomically similar starting points can produce compositionally similar communities that differ in traits of member taxa and in ecological properties.
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Affiliation(s)
- Megan Taylor
- Biology Department, Emory University, Atlanta, GA, 30322, United States
| | - Lili Janasky
- Biology Department, Emory University, Atlanta, GA, 30322, United States
| | - Nic Vega
- Biology Department, Emory University, Atlanta, GA, 30322, United States.,Physics Department, Emory University, Atlanta, GA, 30322, United States
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17
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Li J, Yang F, Xiao M, Li A. Advances and challenges in cataloging the human gut virome. Cell Host Microbe 2022; 30:908-916. [PMID: 35834962 DOI: 10.1016/j.chom.2022.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 06/02/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022]
Abstract
The human gut virome, which is often referred to as the "dark matter" of the gut microbiome, remains understudied. A better understanding of the composition and variations of the gut virome across populations is critical for exploring its impact on diseases and health. A series of advances in the characterization of human gut virome have unveiled high genetic diversity and various functional potentials of gut viruses. Here, we summarize the recently available human gut virome databases and discuss their features, procedures, and challenges with the intention to provide a reference to researchers to use while choosing a profiling database. We also propose a "best practice" for cataloging the viral population.
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Affiliation(s)
- Junhua Li
- BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China.
| | | | - Minfeng Xiao
- BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China.
| | - Aixin Li
- BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
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18
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Abstract
The majority of viruses within the gut are obligate bacterial viruses known as bacteriophages (phages). Their bacteriotropism underscores the study of phage ecology in the gut, where they modulate and coevolve with gut bacterial communities. Traditionally, these ecological and evolutionary questions were investigated empirically via in vitro experimental evolution and, more recently, in vivo models were adopted to account for physiologically relevant conditions of the gut. Here, we probed beyond conventional phage-bacteria coevolution to investigate potential tripartite evolutionary interactions between phages, their bacterial hosts, and the mammalian gut mucosa. To capture the role of the mammalian gut, we recapitulated a life-like gut mucosal layer using in vitro lab-on-a-chip devices (to wit, the gut-on-a-chip) and showed that the mucosal environment supports stable phage-bacteria coexistence. Next, we experimentally coevolved lytic phage populations within the gut-on-a-chip devices alongside their bacterial hosts. We found that while phages adapt to the mucosal environment via de novo mutations, genetic recombination was the key evolutionary force in driving mutational fitness. A single mutation in the phage capsid protein Hoc-known to facilitate phage adherence to mucus-caused altered phage binding to fucosylated mucin glycans. We demonstrated that the altered glycan-binding phenotype provided the evolved mutant phage a competitive fitness advantage over its ancestral wild-type phage in the gut-on-a-chip mucosal environment. Collectively, our findings revealed that phages-in addition to their evolutionary relationship with bacteria-are able to evolve in response to a mammalian-derived mucosal environment.
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19
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Sadiq FA, Hansen MF, Burmølle M, Heyndrickx M, Flint S, Lu W, Chen W, Zhang H. Towards understanding mechanisms and functional consequences of bacterial interactions with members of various kingdoms in complex biofilms that abound in nature. FEMS Microbiol Rev 2022; 46:6595875. [PMID: 35640890 DOI: 10.1093/femsre/fuac024] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/11/2022] [Accepted: 05/27/2022] [Indexed: 11/12/2022] Open
Abstract
The microbial world represents a phenomenal diversity of microorganisms from different kingdoms of life which occupy an impressive set of ecological niches. Most, if not all, microorganisms once colonise a surface develop architecturally complex surface-adhered communities which we refer to as biofilms. They are embedded in polymeric structural scaffolds serve as a dynamic milieu for intercellular communication through physical and chemical signalling. Deciphering microbial ecology of biofilms in various natural or engineered settings has revealed co-existence of microorganisms from all domains of life, including Bacteria, Archaea and Eukarya. The coexistence of these dynamic microbes is not arbitrary, as a highly coordinated architectural setup and physiological complexity show ecological interdependence and myriads of underlying interactions. In this review, we describe how species from different kingdoms interact in biofilms and discuss the functional consequences of such interactions. We highlight metabolic advances of collaboration among species from different kingdoms, and advocate that these interactions are of great importance and need to be addressed in future research. Since trans-kingdom biofilms impact diverse contexts, ranging from complicated infections to efficient growth of plants, future knowledge within this field will be beneficial for medical microbiology, biotechnology, and our general understanding of microbial life in nature.
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Affiliation(s)
- Faizan Ahmed Sadiq
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology & Food Sciences Unit, Melle, Belgium
| | - Mads Frederik Hansen
- Section of Microbiology, Department of Biology, University of Copenhagen, Denmark
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Denmark
| | - Marc Heyndrickx
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology & Food Sciences Unit, Melle, Belgium.,Department of Pathology, Bacteriology and Poultry Diseases, Ghent University, Merelbeke, Belgium
| | - Steve Flint
- School of Food and Advanced Technology, Massey University, Private Bag, 11222, Palmerston North, New Zealand
| | - Wenwei Lu
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
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20
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Chen J, Gissendanner CR, Tikhe CV, Li HF, Sun Q, Husseneder C. Genomics and Geographic Diversity of Bacteriophages Associated With Endosymbionts in the Guts of Workers and Alates of Coptotermes Species (Blattodea: Rhinotermitidae). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.881538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Subterranean termites depend nutritionally on their gut microbiota, which includes protozoa as well as taxonomically and functionally diverse bacteria. Our previous metavirome study revealed a high diversity and novel families of bacteriophages in the guts of Coptotermes formosanus workers from New Orleans, Louisiana, United States. Two assembled bacteriophage genomes (Phages TG-crAlp-04 and 06, family Podoviridae) existed in all colonies and showed similarity to a prophage (ProJPt-Bp1) previously sequenced from a bacterial endosymbiont (Candidatus Azobacteroides pseudotrichonymphae, CAP) of protozoa in the gut of a termite species of the genus Prorhinotermes from Taiwan. In this study the genomes of Phage TG-crAlp-04 and 06 were subjected to detailed functional annotation. Both phage genomes contained conserved genes for DNA packaging, head and tail morphogenesis, and phage replication. Approximately 30% of the amino acid sequences derived from genes in both genomes matched to those of ProJPt-Bp1 phage or other phages from the crAss-like phage group. No integrase was identified; the lack of a lysogeny module is a characteristic of crAss-like phages. Primers were designed to sequence conserved genes of the two phages and their putative host bacterium (CAP) to detect their presence in different termite species from native and introduced distribution ranges. Related strains of the host bacterium were found across different termite genera and geographic regions. Different termite species had separate CAP strains, but intraspecific geographical variation was low. These results together with the fact that CAP is an important intracellular symbiont of obligate cellulose-digesting protozoa, suggest that CAP is a core gut bacterium and co-evolved across several subterranean termite species. Variants of both crAss-like phages were detected in different Coptotermes species from the native and introduced range, but they did not differentiate by species or geographic region. Since similar phages were detected in different termite species, we propose the existence of a core virome associated with core bacterial endosymbionts of protozoa in the guts of subterranean termites. This work provides a strong basis for further study of the quadripartite relationship of termites, protozoa, bacteria, and bacteriophages.
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21
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Venturini C, Petrovic Fabijan A, Fajardo Lubian A, Barbirz S, Iredell J. Biological foundations of successful bacteriophage therapy. EMBO Mol Med 2022; 14:e12435. [PMID: 35620963 PMCID: PMC9260219 DOI: 10.15252/emmm.202012435] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 12/20/2022] Open
Abstract
Bacteriophages (phages) are selective viral predators of bacteria. Abundant and ubiquitous in nature, phages can be used to treat bacterial infections (phage therapy), including refractory infections and those resistant to antibiotics. However, despite an abundance of anecdotal evidence of efficacy, significant hurdles remain before routine implementation of phage therapy into medical practice, including a dearth of robust clinical trial data. Phage-bacterium interactions are complex and diverse, characterized by co-evolution trajectories that are significantly influenced by the environments in which they occur (mammalian body sites, water, soil, etc.). An understanding of the molecular mechanisms underpinning these dynamics is essential for successful clinical translation. This review aims to cover key aspects of bacterium-phage interactions that affect bacterial killing by describing the most relevant published literature and detailing the current knowledge gaps most likely to influence therapeutic success.
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Affiliation(s)
- Carola Venturini
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
| | - Aleksandra Petrovic Fabijan
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Faculty of Health and Medicine, School of Medicine, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Alicia Fajardo Lubian
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Faculty of Health and Medicine, School of Medicine, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Stefanie Barbirz
- Department of Medicine, Science Faculty, MSB Medical School Berlin, Berlin, Germany
| | - Jonathan Iredell
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Faculty of Health and Medicine, School of Medicine, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,Westmead Hospital, Western Sydney Local Health District, Westmead, NSW, Australia
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22
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Koskella B, Hernandez CA, Wheatley RM. Understanding the Impacts of Bacteriophage Viruses: From Laboratory Evolution to Natural Ecosystems. Annu Rev Virol 2022; 9:57-78. [PMID: 35584889 DOI: 10.1146/annurev-virology-091919-075914] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viruses of bacteriophages (phages) have broad effects on bacterial ecology and evolution in nature that mediate microbial interactions, shape bacterial diversity, and influence nutrient cycling and ecosystem function. The unrelenting impact of phages within the microbial realm is the result, in large part, of their ability to rapidly evolve in response to bacterial host dynamics. The knowledge gained from laboratory systems, typically using pairwise interactions between single-host and single-phage systems, has made clear that phages coevolve with their bacterial hosts rapidly, somewhat predictably, and primarily by counteradapting to host resistance. Recent advancement in metagenomics approaches, as well as a shifting focus toward natural microbial communities and host-associated microbiomes, is beginning to uncover the full picture of phage evolution and ecology within more complex settings. As these data reach their full potential, it will be critical to ask when and how insights gained from studies of phage evolution in vitro can be meaningfully applied to understanding bacteria-phage interactions in nature. In this review, we explore the myriad ways that phages shape and are themselves shaped by bacterial host populations and communities, with a particular focus on observed and predicted differences between the laboratory and complex microbial communities. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, California, USA;
| | - Catherine A Hernandez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
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23
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Nadar S, Khan T, Patching SG, Omri A. Development of Antibiofilm Therapeutics Strategies to Overcome Antimicrobial Drug Resistance. Microorganisms 2022; 10:microorganisms10020303. [PMID: 35208758 PMCID: PMC8879831 DOI: 10.3390/microorganisms10020303] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/19/2022] [Accepted: 01/25/2022] [Indexed: 02/04/2023] Open
Abstract
A biofilm is a community of stable microorganisms encapsulated in an extracellular matrix produced by themselves. Many types of microorganisms that are found on living hosts or in the environment can form biofilms. These include pathogenic bacteria that can serve as a reservoir for persistent infections, and are culpable for leading to a broad spectrum of chronic illnesses and emergence of antibiotic resistance making them difficult to be treated. The absence of biofilm-targeting antibiotics in the drug discovery pipeline indicates an unmet opportunity for designing new biofilm inhibitors as antimicrobial agents using various strategies and targeting distinct stages of biofilm formation. The strategies available to control biofilm formation include targeting the enzymes and proteins specific to the microorganism and those involved in the adhesion pathways leading to formation of resistant biofilms. This review primarily focuses on the recent strategies and advances responsible for identifying a myriad of antibiofilm agents and their mechanism of biofilm inhibition, including extracellular polymeric substance synthesis inhibitors, adhesion inhibitors, quorum sensing inhibitors, efflux pump inhibitors, and cyclic diguanylate inhibitors. Furthermore, we present the structure–activity relationships (SAR) of these agents, including recently discovered biofilm inhibitors, nature-derived bioactive scaffolds, synthetic small molecules, antimicrobial peptides, bioactive compounds isolated from fungi, non-proteinogenic amino acids and antibiotics. We hope to fuel interest and focus research efforts on the development of agents targeting the uniquely complex, physical and chemical heterogeneous biofilms through a multipronged approach and combinatorial therapeutics for a more effective control and management of biofilms across diseases.
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Affiliation(s)
- Sahaya Nadar
- Department of Pharmaceutical Chemistry, St. John Institute of Pharmacy and Research, Mumbai 400056, India;
| | - Tabassum Khan
- Department of Pharmaceutical Chemistry & Quality Assurance, SVKM’s Dr. Bhanuben Nanavati College of Pharmacy, Mumbai 400056, India;
| | - Simon G. Patching
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- Correspondence: or (S.G.P.); (A.O.)
| | - Abdelwahab Omri
- The Novel Drug & Vaccine Delivery Systems Facility, Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON P3E 2C6, Canada
- Correspondence: or (S.G.P.); (A.O.)
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24
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Mycelia-Assisted Isolation of Non-Host Bacteria Able to Co-Transport Phages. Viruses 2022; 14:v14020195. [PMID: 35215789 PMCID: PMC8877629 DOI: 10.3390/v14020195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 11/27/2022] Open
Abstract
Recent studies have demonstrated that phages can be co-transported with motile non-host bacteria, thereby enabling their invasion of biofilms and control of biofilm composition. Here, we developed a novel approach to isolate non-host bacteria able to co-transport phages from soil. It is based on the capability of phage-carrying non-host bacteria to move along mycelia out of soil and form colonies in plaques of their co-transported phages. The approach was tested using two model phages of differing surface hydrophobicity, i.e., hydrophobic Escherichia virus T4 (T4) and hydrophilic Pseudoalteromonas phage HS2 (HS2). The phages were mixed into soil and allowed to be transported by soil bacteria along the mycelia of Pythium ultimum. Five phage-carrying bacterial species were isolated (Viridibacillus sp., Enterobacter sp., Serratia sp., Bacillus sp., Janthinobacterium sp.). These bacteria exhibited phage adsorption efficiencies of ≈90–95% for hydrophobic T4 and 30–95% for hydrophilic HS2. The phage adsorption efficiency of Viridibacillus sp. was ≈95% for both phages and twofold higher than T4-or HS2-adsorption to their respective hosts, qualifying Viridibacillus sp. as a potential super carrier for phages. Our approach offers an effective and target-specific way to identify and isolate phage-carrying bacteria in natural and man-made environments.
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25
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Chaffringeon L, Lamy-Besnier Q, Debarbieux L, De Sordi L. The intestinal virome: lessons from animal models. Curr Opin Virol 2021; 51:141-148. [PMID: 34700287 DOI: 10.1016/j.coviro.2021.09.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/21/2021] [Accepted: 09/29/2021] [Indexed: 12/28/2022]
Abstract
Mucosal surfaces in contact with the environment host specific microbiota. The intestinal tract harbours the most abundant and diverse bacterial and viral populations interacting with each other as well as with the host. Viruses of the microbiota are important components of this ecosystem, as shown by viral alterations associated with various pathologies. However, practical and ethical constraints limit functional studies of the virome in humans, making animal models invaluable experimental tools to understand its impact on intestinal physiology. In this review, we present the recent advances in the study of virome in animal models. We focus on the strategies used to characterise viral changes in disease models and approaches to modulate the microbiota using viruses. In reviewing the interplay between viruses, bacteria, and the animal host, we highlight the potential and limitations of these models in elucidating the role of the virome in determining human health and disease.
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Affiliation(s)
- Lorenzo Chaffringeon
- Sorbonne Université, INSERM, Centre de Recherche St Antoine, UMRS_938, Paris, France; Department of Microbiology, Institut Pasteur, Paris, F-75015, France; Paris Center for Microbiome Medicine (PaCeMM) FHU, AP-HP, Paris, France
| | - Quentin Lamy-Besnier
- Department of Microbiology, Institut Pasteur, Paris, F-75015, France; Université de Paris, Paris, France
| | | | - Luisa De Sordi
- Sorbonne Université, INSERM, Centre de Recherche St Antoine, UMRS_938, Paris, France; Paris Center for Microbiome Medicine (PaCeMM) FHU, AP-HP, Paris, France.
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26
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Bono LM, Mao S, Done RE, Okamoto KW, Chan BK, Turner PE. Advancing phage therapy through the lens of virus host-breadth and emergence potential. Adv Virus Res 2021; 111:63-110. [PMID: 34663499 DOI: 10.1016/bs.aivir.2021.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Phages are viruses that specifically infect bacteria, and their biodiversity contributes to historical and current development of phage therapy to treat myriad bacterial infections. Phage therapy holds promise as an alternative to failing chemical antibiotics, but there are benefits and costs of this technology. Here, we review the rich history of phage therapy, highlighting reasons (often political) why it was widely rejected by Western medicine until recently. One longstanding idea involves mixing different phages together in cocktails, to increase the probability of killing target pathogenic bacteria without pre-screening for phage susceptibility. By challenging 30 lytic phages to infect 14 strains of the bacteria Pseudomonas aeruginosa, we showed that some phages were "generalists" with broad host-ranges, emphasizing that extreme host-specificity of phages was not necessarily a liability. Using a "greedy algorithm" analysis, we identified the best cocktail mixture of phages to achieve broad bacteria killing. Additionally, we review how virus host-range can evolve and connect lessons learned from virus emergence-including contributions of elevated virus mutation rates in promoting emergence and virus evolutionary transitions from specialized to generalized host-use-as cautionary tales for avoiding risk of "off-target" phage emergence on commensal bacteria in microbiomes. Throughout, we highlight how fundamental understanding of virus ecology and evolution is vital for developing phage therapy; heeding these principles should help in designing therapeutic strategies that do not recapitulate consequences of virus selection to emerge on novel hosts.
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Affiliation(s)
- Lisa M Bono
- Department of Biology, Emory University, Atlanta, GA, United States.
| | - Stephanie Mao
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Rachel E Done
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, GA, United States; Division of Pulmonary, Allergy and Immunology, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
| | - Kenichi W Okamoto
- Department of Biology, University of St. Thomas, St. Paul, MN, United States
| | - Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States; Microbiology Program, Yale School of Medicine, New Haven, CT, United States
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The Characterization of a Novel Phage, pPa_SNUABM_DT01, Infecting Pseudomonas aeruginosa. Microorganisms 2021; 9:microorganisms9102040. [PMID: 34683360 PMCID: PMC8541153 DOI: 10.3390/microorganisms9102040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/15/2021] [Accepted: 09/24/2021] [Indexed: 12/25/2022] Open
Abstract
The bacterial genus Pseudomonas is a common causative agent of infections in veterinary medicine. In this study, we focused on Pseudomonas aeruginosa canine otitis externa isolates. Due to prolonged antibiotic treatment of otitis externa, antibiotic resistance is common and has become a major complication. Many alternatives to antibiotics have been studied, with bacteriophages emerging as the most promising alternatives. Here, we isolated and characterized a novel phage, pPa_SNUABM_DT01, by investigating its morphology, growth, lysis kinetics, and genomic characteristics. Phages have a vigorous capacity to eliminate bacterial cells through bacterial lysis. This capacity is dependent on the multiplicity of infection (MOI), but even at low MOIs, the phage successfully inhibited bacterial regrowth. The phage genome was 265,520 bp in size and comprised 312 putative open reading frames (ORFs). Comparative genome analysis demonstrated that the phage is a novel species in Myoviridae. The nucleotide similarity was moderately high compared with the Pseudomonas virus, Noxifer. However, a phylogenetic analysis and a dot plot indicated that pPa_SNUABM_DT01 is not closely related to the Phikzvirus or Noxifervirus genus but, instead, belongs to a novel one. The genome comparisons also indicate that the phage, pPa_SNUABM_DT01, could be a novel genus.
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28
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Evolution in a Community Context: towards Understanding the Causes and Consequences of Adaptive Evolution in the Human Gut Microbiota over Short Time Scales. mSystems 2021; 6:e0083221. [PMID: 34427532 PMCID: PMC8407120 DOI: 10.1128/msystems.00832-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
How important is adaptive evolution to the unique diversity that we can observe for each individual human gut microbiome? How do gut microbes evolve in response to changes in their environment, and how does evolution in real time impact microbial functionality in the context of host health? My interdisciplinary research uses in vitro microcosm models to test how different abiotic and biotic factors impact microbial evolution in a community context. We complement this approach by tracking focal species as they evolve in real time and in their natural environment of the human gut. Our aim is to provide a better understanding of how the dynamics and outcomes of microbial evolution differ between individual gut environments, and in response to different selection pressures, so that we can move closer to rational gut microbiome treatments that promote host health and prevent and treat human disease.
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29
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Bond MC, Vidakovic L, Singh PK, Drescher K, Nadell CD. Matrix-trapped viruses can prevent invasion of bacterial biofilms by colonizing cells. eLife 2021; 10:65355. [PMID: 34240700 PMCID: PMC8346279 DOI: 10.7554/elife.65355] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 07/08/2021] [Indexed: 12/19/2022] Open
Abstract
Bacteriophages can be trapped in the matrix of bacterial biofilms, such that the cells inside them are protected. It is not known whether these phages are still infectious and whether they pose a threat to newly arriving bacteria. Here, we address these questions using Escherichia coli and its lytic phage T7. Prior work has demonstrated that T7 phages are bound in the outermost curli polymer layers of the E. coli biofilm matrix. We show that these phages do remain viable and can kill colonizing cells that are T7-susceptible. If cells colonize a resident biofilm before phages do, we find that they can still be killed by phage exposure if it occurs soon thereafter. However, if colonizing cells are present on the biofilm long enough before phage exposure, they gain phage protection via envelopment within curli-producing clusters of the resident biofilm cells.
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Affiliation(s)
- Matthew C Bond
- Department of Biological Sciences, Dartmouth College, Hanover, United States
| | - Lucia Vidakovic
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Praveen K Singh
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Department of Physics, Philipps University Marburg, Marburg, Germany.,Biozentrum, University of Basel, Basel, Switzerland
| | - Carey D Nadell
- Department of Biological Sciences, Dartmouth College, Hanover, United States
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