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Baquero DP, Medvedeva S, Martin-Gallausiaux C, Pende N, Sartori-Rupp A, Tachon S, Pedron T, Debarbieux L, Borrel G, Gribaldo S, Krupovic M. Stable coexistence between an archaeal virus and the dominant methanogen of the human gut. Nat Commun 2024; 15:7702. [PMID: 39231967 PMCID: PMC11375127 DOI: 10.1038/s41467-024-51946-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: 04/18/2024] [Accepted: 08/21/2024] [Indexed: 09/06/2024] Open
Abstract
The human gut virome, which is mainly composed of bacteriophages, also includes viruses infecting archaea, yet their role remains poorly understood due to lack of isolates. Here, we characterize a temperate archaeal virus (MSTV1) infecting Methanobrevibacter smithii, the dominant methanogenic archaeon of the human gut. The MSTV1 genome is integrated in the host chromosome as a provirus which is sporadically induced, resulting in virion release. Using cryo-electron tomography, we capture several intracellular virion assembly intermediates and confirm that only a small fraction of the host population actively produces virions in vitro. Similar low frequency of induction is observed in a mouse colonization model, using mice harboring a stable consortium of 12 bacterial species (OMM12). Transcriptomic analysis suggests a regulatory lysogeny-lysis switch involving an interplay between viral proteins to maintain virus-host equilibrium, ensuring host survival and viral persistence. Thus, our study sheds light on archaeal virus-host interactions and highlights similarities with bacteriophages in establishing stable coexistence with their hosts in the gut.
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Affiliation(s)
- Diana P Baquero
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Sofia Medvedeva
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Camille Martin-Gallausiaux
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Nika Pende
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit Evolutionary Biology of the Microbial Cell, Paris, France
- University of Vienna, Archaea Physiology and Biotechnology Group, Vienna, Austria
| | - Anna Sartori-Rupp
- Institut Pasteur, NanoImaging Core Facility, Centre de Ressources et Recherches Technologiques (C2RT), Paris, France
| | - Stéphane Tachon
- Institut Pasteur, NanoImaging Core Facility, Centre de Ressources et Recherches Technologiques (C2RT), Paris, France
| | - Thierry Pedron
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, Paris, France
| | - Laurent Debarbieux
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, Paris, France
| | - Guillaume Borrel
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Simonetta Gribaldo
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit Evolutionary Biology of the Microbial Cell, Paris, France.
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France.
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2
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Zhu Y, Li R, Yan S, Chen X, Cen S, Xie S. Habitat- and lifestyle-dependent structural and functional characteristics of viruses in mangrove wetlands of different functional zonings. ENVIRONMENTAL RESEARCH 2024; 252:119070. [PMID: 38710431 DOI: 10.1016/j.envres.2024.119070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/24/2024] [Accepted: 04/30/2024] [Indexed: 05/08/2024]
Abstract
Mangrove wetlands, as one of the natural ecosystems with the most ecological services, have garnered widespread attention about their microbial driven biogeochemical cycling. Urbanization have led to different spatial patterns of environmental conditions and microbial communities in mangroves. However, viruses, as the pivotal drivers of biogeochemical cycling in mangroves, remain inadequately explored in terms of how their ecological potential and complex interactions with host respond to functional zonings. To address this knowledge gap, we conducted a comprehensive investigation on the structural and functional properties of temperate and lytic viruses in mangrove wetlands from different functional zonings by jointly using high-throughput sequencing, prokaryotic and viral metagenomics. Multiple environmental factors were found to significantly influence the taxonomic and functional composition, as well as lysogen-lysis decision-making of mangrove viruses. Furthermore, enriched auxiliary metabolic genes (AMGs) involved in methane, nitrogen and sulfur metabolism, and heavy metal resistance were unveiled in mangrove viruses, whose community composition was closely related to lifestyle and host. The virus-host pairs with different lifestyles were also discovered to react to environmental changes in different ways, which provided an empirical evidence for how virus and bacteria dynamics were specific to viral lifestyles in nature. This study expands our comprehension of the intricate interactions among virus, prokaryotic host and the environment in mangrove wetlands from multiple perspectives, including viral lifestyles, virus-host interactions, and habitat dependence. Importantly, it provides a new ecological perspective on how mangrove viruses are adapted to the stress posed by urbanization.
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Affiliation(s)
- Ying Zhu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Ruili Li
- School of Environment and Energy, Peking University, Shenzhen, 518055, China; Guangdong Mangrove Engineering Technology Research Center, Peking University, Shenzhen, 518055, China.
| | - Shuang Yan
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Xiuli Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Shipeng Cen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
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3
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Bai S, Huang Z, Li XG. Genome analysis of Rossellomorea sp. y25, a deep sea bacterium isolated from the sediments of South China Sea. Mar Genomics 2024; 75:101110. [PMID: 38735673 DOI: 10.1016/j.margen.2024.101110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/19/2024] [Accepted: 04/19/2024] [Indexed: 05/14/2024]
Abstract
Rossellomorea sp. y25, a putative new species of yellow pigment-producing, aerobic and chemoheterotrophic bacterium belonging to the family Bacillaceae, was isolated from the sediments at the depth of 1829 m in the South China Sea. In this study, we present the complete genome sequences of strain y25, which consisted of only one circular chromosome with 4,633,006 bp and the content of G + C was 41.76%. A total of 4466 CDSs, 106 tRNA, 33 rRNA, and 101 sRNA genes were obtained. Genomic analysis of strain y25 showed that it has the ability to produce antioxidant carotenoids and a large number of heavy metal resistance genes, such as arsenic, cadmium and zinc. In addition, strain y25 contains a prophage that may contribute to host protection against lysis by related Bacillus-like phages. This is the first report of genome-wide information on a bacterium of the genus Rossellomorea isolated from the deep sea, providing insights into how microorganisms of this genus adapt to deep-sea environments.
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Affiliation(s)
- Shijie Bai
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Zhaosong Huang
- School of Biological Science and Technology, University of Jinan, Jinan 250024, China
| | - Xue-Gong Li
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China.
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4
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Zhang Y, Zhang X, Liao J, Wei Z, Zhang Z, Liang T. Organoselenium-Catalyzed C2,3-Diarylation of N-H Indoles. J Org Chem 2024; 89:7216-7224. [PMID: 38693864 DOI: 10.1021/acs.joc.4c00622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
An organoselenium-catalyzed C2,3-diarylation of unprotected N-H indoles with electron-rich aromatics has been developed. This one-pot multicomponent tandem cross-dehydrogenation coupling reaction allows for the incorporation of two different aromatic groups to indoles. More importantly, this approach offers significant advantages, including a high atom and step economy, eliminating the need for prepreparation of the reaction substrates, streamlining the synthetic process and enhancing its practicality. Overall, this organoselenium-catalyzed C2,3-diarylation reaction presents an efficient and versatile strategy for the functionalization of indole derivatives.
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Affiliation(s)
- Yingying Zhang
- Guangxi Colleges and Universities Key Laboratory of Applied Chemistry Technology and Resource Development, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Xiaoxiang Zhang
- Guangxi Colleges and Universities Key Laboratory of Applied Chemistry Technology and Resource Development, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Junqiu Liao
- Guangxi Colleges and Universities Key Laboratory of Applied Chemistry Technology and Resource Development, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Zongwu Wei
- School of Resources, Environment and Materials, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Zhuan Zhang
- Guangxi Colleges and Universities Key Laboratory of Applied Chemistry Technology and Resource Development, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Taoyuan Liang
- Guangxi Colleges and Universities Key Laboratory of Applied Chemistry Technology and Resource Development, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
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5
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Dion MB, Shah SA, Deng L, Thorsen J, Stokholm J, Krogfelt KA, Schjørring S, Horvath P, Allard A, Nielsen DS, Petit MA, Moineau S. Escherichia coli CRISPR arrays from early life fecal samples preferentially target prophages. THE ISME JOURNAL 2024; 18:wrae005. [PMID: 38366192 PMCID: PMC10910852 DOI: 10.1093/ismejo/wrae005] [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: 12/26/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/18/2024]
Abstract
CRISPR-Cas systems are defense mechanisms against phages and other nucleic acids that invade bacteria and archaea. In Escherichia coli, it is generally accepted that CRISPR-Cas systems are inactive in laboratory conditions due to a transcriptional repressor. In natural isolates, it has been shown that CRISPR arrays remain stable over the years and that most spacer targets (protospacers) remain unknown. Here, we re-examine CRISPR arrays in natural E. coli isolates and investigate viral and bacterial genomes for spacer targets using a bioinformatics approach coupled to a unique biological dataset. We first sequenced the CRISPR1 array of 1769 E. coli isolates from the fecal samples of 639 children obtained during their first year of life. We built a network with edges between isolates that reflect the number of shared spacers. The isolates grouped into 34 modules. A search for matching spacers in bacterial genomes showed that E. coli spacers almost exclusively target prophages. While we found instances of self-targeting spacers, those involving a prophage and a spacer within the same bacterial genome were rare. The extensive search for matching spacers also expanded the library of known E. coli protospacers to 60%. Altogether, these results favor the concept that E. coli's CRISPR-Cas is an antiprophage system and highlight the importance of reconsidering the criteria use to deem CRISPR-Cas systems active.
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Affiliation(s)
- Moïra B Dion
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC G1V 0A6, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC G1V 0A6, Canada
| | - Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
| | - Ling Deng
- Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg, Denmark
| | - Jonathan Thorsen
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
- Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg, Denmark
| | - Karen A Krogfelt
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, 2300S Copenhagen, Denmark
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark
| | - Susanne Schjørring
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, 2300S Copenhagen, Denmark
| | - Philippe Horvath
- IFF Danisco, Health & Biosciences, Dangé-Saint-Romain 86220, France
| | - Antoine Allard
- Département de physique, de génie physique et d’optique, Université Laval, Québec, QC G1V 0A6, Canada
- Centre interdisciplinaire en modélisation mathématique, Université Laval, Québec, QC G1V 0A6, Canada
| | - Dennis S Nielsen
- Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg, Denmark
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Micalis, Jouy-en-Josas 78350, France
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC G1V 0A6, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC G1V 0A6, Canada
- Félix d’Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec, QC G1V 0A6, Canada
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6
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Mahmud MR, Tamanna SK, Akter S, Mazumder L, Akter S, Hasan MR, Acharjee M, Esti IZ, Islam MS, Shihab MMR, Nahian M, Gulshan R, Naser S, Pirttilä AM. Role of bacteriophages in shaping gut microbial community. Gut Microbes 2024; 16:2390720. [PMID: 39167701 PMCID: PMC11340752 DOI: 10.1080/19490976.2024.2390720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 08/23/2024] Open
Abstract
Phages are the most diversified and dominant members of the gut virobiota. They play a crucial role in shaping the structure and function of the gut microbial community and consequently the health of humans and animals. Phages are found mainly in the mucus, from where they can translocate to the intestinal organs and act as a modulator of gut microbiota. Understanding the vital role of phages in regulating the composition of intestinal microbiota and influencing human and animal health is an emerging area of research. The relevance of phages in the gut ecosystem is supported by substantial evidence, but the importance of phages in shaping the gut microbiota remains unclear. Although information regarding general phage ecology and development has accumulated, detailed knowledge on phage-gut microbe and phage-human interactions is lacking, and the information on the effects of phage therapy in humans remains ambiguous. In this review, we systematically assess the existing data on the structure and ecology of phages in the human and animal gut environments, their development, possible interaction, and subsequent impact on the gut ecosystem dynamics. We discuss the potential mechanisms of prophage activation and the subsequent modulation of gut bacteria. We also review the link between phages and the immune system to collect evidence on the effect of phages on shaping the gut microbial composition. Our review will improve understanding on the influence of phages in regulating the gut microbiota and the immune system and facilitate the development of phage-based therapies for maintaining a healthy and balanced gut microbiota.
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Affiliation(s)
- Md. Rayhan Mahmud
- Department of Production Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | | | - Sharmin Akter
- Department of Microbiology, Jagannath University, Dhaka, Bangladesh
| | - Lincon Mazumder
- Department of Microbiology, Jagannath University, Dhaka, Bangladesh
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Sumona Akter
- Department of Microbiology, Jagannath University, Dhaka, Bangladesh
| | | | - Mrityunjoy Acharjee
- Department of Microbiology, Stamford University Bangladesh, Dhaka, Bangladesh
| | - Israt Zahan Esti
- Department of Microbiology, Jagannath University, Dhaka, Bangladesh
- Department of Molecular Systems Biology, Faculty of Technology, University of Turku, Turku, Finland
| | - Md. Saidul Islam
- Department of Microbiology, Jagannath University, Dhaka, Bangladesh
| | | | - Md. Nahian
- Department of Microbiology, Jagannath University, Dhaka, Bangladesh
| | - Rubaiya Gulshan
- Department of Microbiology, Jagannath University, Dhaka, Bangladesh
| | - Sadia Naser
- Department of Microbiology, Jagannath University, Dhaka, Bangladesh
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7
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Luo S, Ru J, Mirzaei MK, Xue J, Peng X, Ralser A, Mejías-Luque R, Gerhard M, Deng L. Gut virome profiling identifies an association between temperate phages and colorectal cancer promoted by Helicobacter pylori infection. Gut Microbes 2023; 15:2257291. [PMID: 37747149 PMCID: PMC10578192 DOI: 10.1080/19490976.2023.2257291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/06/2023] [Indexed: 09/26/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide. While a close correlation between chronic Helicobacter pylori infection and CRC has been reported, the role of the virome has been overlooked. Here, we infected Apc-mutant mouse models and C57BL/6 mice with H. pylori and conducted a comprehensive metagenomics analysis of H. pylori-induced changes in lower gastrointestinal tract bacterial and viral communities. We observed an expansion of temperate phages in H. pylori infected Apc+/1638N mice at the early stage of carcinogenesis. Some of the temperate phages were predicted to infect bacteria associated with CRC, including Enterococcus faecalis. We also observed a high prevalence of virulent genes, such as flgJ, cwlJ, and sleB, encoded by temperate phages. In addition, we identified phages associated with pre-onset and onset of H. pylori-promoted carcinogenesis. Through co-occurrence network analysis, we found strong associations between the viral and bacterial communities in infected mice before the onset of carcinogenesis. These findings suggest that the expansion of temperate phages, possibly caused by prophage induction triggered by H. pylori infection, may have contributed to the development of CRC in mice by interacting with the bacterial community.
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Affiliation(s)
- Shiqi Luo
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, Neuherberg, Germany
- Chair for Preventions of Microbial Diseases, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Jinlong Ru
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, Neuherberg, Germany
- Chair for Preventions of Microbial Diseases, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mohammadali Khan Mirzaei
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, Neuherberg, Germany
- Chair for Preventions of Microbial Diseases, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Jinling Xue
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, Neuherberg, Germany
- Chair for Preventions of Microbial Diseases, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Xue Peng
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, Neuherberg, Germany
- Faculty of Biology, Biocenter, Ludwig Maximilian University of Munich, Munich, Germany
| | - Anna Ralser
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
| | - Raquel Mejías-Luque
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
| | - Markus Gerhard
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
| | - Li Deng
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, Neuherberg, Germany
- Chair for Preventions of Microbial Diseases, School of Life Sciences, Technical University of Munich, Freising, Germany
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8
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Ragunathan PT, Ng Kwan Lim E, Ma X, Massé E, Vanderpool CK. Mechanisms of Regulation of Cryptic Prophage-Encoded Gene Products in Escherichia coli. J Bacteriol 2023; 205:e0012923. [PMID: 37439671 PMCID: PMC10448788 DOI: 10.1128/jb.00129-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/12/2023] [Indexed: 07/14/2023] Open
Abstract
The dicBF operon of Qin cryptic prophage in Escherichia coli K-12 encodes the small RNA (sRNA) DicF and small protein DicB, which regulate host cell division and are toxic when overexpressed. While new functions of DicB and DicF have been identified in recent years, the mechanisms controlling the expression of the dicBF operon have remained unclear. Transcription from dicBp, the major promoter of the dicBF operon, is repressed by DicA. In this study, we discovered that transcription of the dicBF operon and processing of the polycistronic mRNA is regulated by multiple mechanisms. DicF sRNA accumulates during stationary phase and is processed from the polycistronic dicBF mRNA by the action of both RNase III and RNase E. DicA-mediated transcriptional repression of dicBp can be relieved by an antirepressor protein, Rem, encoded on the Qin prophage. Ectopic production of Rem results in cell filamentation due to strong induction of the dicBF operon, and filamentation is mediated by DicF and DicB. Spontaneous derepression of dicBp occurs in a subpopulation of cells independent of the antirepressor. This phenomenon is reminiscent of the bistable switch of λ phage with DicA and DicC performing functions similar to those of CI and Cro, respectively. Additional experiments demonstrate stress-dependent induction of the dicBF operon. Collectively, our results illustrate that toxic genes carried on cryptic prophages are subject to layered mechanisms of control, some that are derived from the ancestral phage and some that are likely later adaptations. IMPORTANCE Cryptic or defective prophages have lost genes necessary to excise from the bacterial chromosome and produce phage progeny. In recent years, studies have found that cryptic prophage gene products influence diverse aspects of bacterial host cell physiology. However, to obtain a complete understanding of the relationship between cryptic prophages and the host bacterium, identification of the environmental, host, or prophage-encoded factors that induce the expression of cryptic prophage genes is crucial. In this study, we examined the regulation of a cryptic prophage operon in Escherichia coli encoding a small RNA and a small protein that are involved in inhibiting bacterial cell division, altering host metabolism, and protecting the host bacterium from phage infections.
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Affiliation(s)
- Preethi T. Ragunathan
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Evelyne Ng Kwan Lim
- Department of Biochemistry and Functional Genomics, University of Sherbrooke, Sherbrooke, Québec, Canada
| | - Xiangqian Ma
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Eric Massé
- Department of Biochemistry and Functional Genomics, University of Sherbrooke, Sherbrooke, Québec, Canada
| | - Carin K. Vanderpool
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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9
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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.
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Affiliation(s)
| | | | - Jeremy J. Barr
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
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10
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Zhang Y, Wang R. The human gut phageome: composition, development, and alterations in disease. Front Microbiol 2023; 14:1213625. [PMID: 37476672 PMCID: PMC10354272 DOI: 10.3389/fmicb.2023.1213625] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/15/2023] [Indexed: 07/22/2023] Open
Abstract
The human gastrointestinal tract is colonized by a large number of microorganisms, including bacteria, archaea, viruses, and eukaryotes. The bacterial community has been widely confirmed to have a significant impact on human health, while viruses, particularly phages, have received less attention. Phages are viruses that specifically infect bacteria. They are abundant in the biosphere and exist in a symbiotic relationship with their host bacteria. Although the application of high-throughput sequencing and bioinformatics technology has greatly improved our understanding of the genomic diversity, taxonomic composition, and spatio-temporal dynamics of the human gut phageome, there is still a large portion of sequencing data that is uncharacterized. Preliminary studies have predicted that the phages play a crucial role in driving microbial ecology and evolution. Prior to exploring the function of phages, it is necessary to address the obstacles that hinder establishing a comprehensive sequencing database with sufficient biological properties and understanding the impact of phage-bacteria interactions on human health. In this study, we provide an overview of the human gut phageome, including its composition, structure, and development. We also explore the various factors that may influence the phageome based on current research, including age, diet, ethnicity, and geographical location. Additionally, we summarize the relationship between the phageome and human diseases, such as IBD, IBS, obesity, diabetes, and metabolic syndrome.
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11
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Zou G, He L, Rao J, Song Z, Du H, Li R, Wang W, Zhou Y, Liang L, Chen H, Li J. Improving the safety and efficacy of phage therapy from the perspective of phage-mammal interactions. FEMS Microbiol Rev 2023; 47:fuad042. [PMID: 37442611 DOI: 10.1093/femsre/fuad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 06/30/2023] [Accepted: 07/12/2023] [Indexed: 07/15/2023] Open
Abstract
Phage therapy has re-emerged as a promising solution for combating antimicrobial-resistant bacterial infections. Increasingly, studies have revealed that phages possess therapeutic potential beyond their antimicrobial properties, including regulating the gut microbiome and maintain intestinal homeostasis, as a novel nanocarrier for targeted drug delivery. However, the complexity and unpredictability of phage behavior during treatment pose a significant challenge in clinical practice. The intricate interactions established between phages, humans, and bacteria throughout their long coexistence in the natural ecosystem contribute to the complexity of phage behavior in therapy, raising concerns about their efficacy and safety as therapeutic agents. Revealing the mechanisms by which phages interact with the human body will provide a theoretical basis for increased application of promising phage therapy. In this review, we provide a comprehensive summary of phage-mammal interactions, including signaling pathways, adaptive immunity responses, and phage-mediated anti-inflammatory responses. Then, from the perspective of phage-mammalian immune system interactions, we present the first systematic overview of the factors affecting phage therapy, such as the mode of administration, the physiological status of the patient, and the biological properties of the phage, to offer new insights into phage therapy for various human diseases.
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Affiliation(s)
- Geng Zou
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, College of Veterinary Medicine, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Lijun He
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, College of Veterinary Medicine, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Rao
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, College of Veterinary Medicine, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhiyong Song
- College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Hu Du
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, College of Veterinary Medicine, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Runze Li
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, College of Veterinary Medicine, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenjing Wang
- College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Zhou
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, College of Veterinary Medicine, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Lu Liang
- School of Bioscience, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom
| | - Huanchun Chen
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, College of Veterinary Medicine, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinquan Li
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, College of Veterinary Medicine, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
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12
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Shah SA, Deng L, Thorsen J, Pedersen AG, Dion MB, Castro-Mejía JL, Silins R, Romme FO, Sausset R, Jessen LE, Ndela EO, Hjelmsø M, Rasmussen MA, Redgwell TA, Leal Rodríguez C, Vestergaard G, Zhang Y, Chawes B, Bønnelykke K, Sørensen SJ, Bisgaard H, Enault F, Stokholm J, Moineau S, Petit MA, Nielsen DS. Expanding known viral diversity in the healthy infant gut. Nat Microbiol 2023; 8:986-998. [PMID: 37037943 PMCID: PMC10159846 DOI: 10.1038/s41564-023-01345-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 02/17/2023] [Indexed: 04/12/2023]
Abstract
The gut microbiome is shaped through infancy and impacts the maturation of the immune system, thus protecting against chronic disease later in life. Phages, or viruses that infect bacteria, modulate bacterial growth by lysis and lysogeny, with the latter being especially prominent in the infant gut. Viral metagenomes (viromes) are difficult to analyse because they span uncharted viral diversity, lacking marker genes and standardized detection methods. Here we systematically resolved the viral diversity in faecal viromes from 647 1-year-olds belonging to Copenhagen Prospective Studies on Asthma in Childhood 2010, an unselected Danish cohort of healthy mother-child pairs. By assembly and curation we uncovered 10,000 viral species from 248 virus family-level clades (VFCs). Most (232 VFCs) were previously unknown, belonging to the Caudoviricetes viral class. Hosts were determined for 79% of phage using clustered regularly interspaced short palindromic repeat spacers within bacterial metagenomes from the same children. Typical Bacteroides-infecting crAssphages were outnumbered by undescribed phage families infecting Clostridiales and Bifidobacterium. Phage lifestyles were conserved at the viral family level, with 33 virulent and 118 temperate phage families. Virulent phages were more abundant, while temperate ones were more prevalent and diverse. Together, the viral families found in this study expand existing phage taxonomy and provide a resource aiding future infant gut virome research.
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Affiliation(s)
- Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark.
| | - Ling Deng
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan Thorsen
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders G Pedersen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Moïra B Dion
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Quebec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Quebec, Canada
| | | | - Ronalds Silins
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Fie O Romme
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Romain Sausset
- Université Paris-Saclay, INRAE, Agroparistech, Micalis institute, Jouy-en-Josas, France
| | - Leon E Jessen
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Eric Olo Ndela
- Lab de Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Mathis Hjelmsø
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Morten A Rasmussen
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Tamsin A Redgwell
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Cristina Leal Rodríguez
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Gisle Vestergaard
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Yichang Zhang
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Bo Chawes
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Francois Enault
- Lab de Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Department of Food Science, 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, Quebec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Quebec, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Quebec, Canada
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, Agroparistech, Micalis institute, Jouy-en-Josas, France
| | - Dennis S Nielsen
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark.
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13
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Yuan L, Ju F. Potential Auxiliary Metabolic Capabilities and Activities Reveal Biochemical Impacts of Viruses in Municipal Wastewater Treatment Plants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:5485-5498. [PMID: 36947091 DOI: 10.1021/acs.est.2c07800] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Viruses influence biogeochemical cycles in oceans, freshwater, soil, and human gut through infection and by modulating virocell metabolism through virus-encoded auxiliary metabolic genes (vAMGs). However, the geographical distribution, potential metabolic function, and engineering significance of vAMGs in wastewater treatment plants (WWTPs) remain to be explored. Here, 752 single-contig viral genomes with high confidence, 510 of which belonged to Caudovirales, were recovered from the activated sludge metagenomes of 32 geographically distributed WWTPs. A total of 101 vAMGs involved in various metabolic pathways were identified, the most common of which were the queuosine biosynthesis genes folE, queD, and queE and the sulfur metabolism gene cysH. Phylogenetic analysis and virus-host relationship prediction revealed the probable evolutionary histories of vAMGs involved in carbon (acpP and prsA), nitrogen (amoC), sulfur (cysH), and phosphate (phoH) metabolism, which potentially mediate microbial carbon and nutrient cycling. Notably, 11 of the 38 (28.3%) vAMGs identified in the metagenomes with corresponding metatranscriptomes were transcriptionally expressed, implying an active functional state. This meta-analysis provides the first broad catalog of vAMGs in municipal WWTPs and how they may assist in the basic physiological reactions of their microbial hosts or nutrient cycling in the WWTPs, and therefore, may have important effects on the engineering of wastewater treatment processes.
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Affiliation(s)
- Ling Yuan
- Environmental Science and Engineering Department, Zhejiang University, Hangzhou 310012, Zhejiang, China
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310030, Zhejiang, China
- Environmental Microbiome and Biotechnology Laboratory (EMBLab), Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou 310030, Zhejiang, China
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310030, Zhejiang, China
- Environmental Microbiome and Biotechnology Laboratory (EMBLab), Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou 310030, Zhejiang, China
- Research Center for Industries of the Future, Westlake University, Hangzhou 310030, Zhejiang, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
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14
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Brüssow H. The human microbiome project at ten years - some critical comments and reflections on "our third genome", the human virome. MICROBIOME RESEARCH REPORTS 2023; 2:7. [PMID: 38045612 PMCID: PMC10688805 DOI: 10.20517/mrr.2022.20] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/02/2023] [Accepted: 03/21/2023] [Indexed: 12/05/2023]
Abstract
The Human Microbiome Project (HMP) has raised great expectations claiming the far-reaching influence of the microbiome on human health and disease ranging from obesity and malnutrition to effects going well beyond the gut. So far, with the notable exception of fecal microbiota transplantation in Clostridioides difficile infection, practical application of microbiome intervention has only achieved modest clinical effects. It is argued here that we need criteria for the link between microbiome and disease modelled on the links between pathogens and infectious disease in Koch's postulates. The most important question is whether the microbiome change is a cause of the given disease or a consequence of a pathology leading to disease where the microbiome change is only a parallel event without a causal connection to the disease - in philosophical parlance, an epiphenomenon. Also discussed here is whether human virome research is a necessary complement to the microbiome project with a high potential for practical applications.
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Affiliation(s)
- Harald Brüssow
- KU Leuven, Department of Biosystems, Laboratory of Gene Technology, Leuven B-3001, Belgium
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15
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Tundra Soil Viruses Mediate Responses of Microbial Communities to Climate Warming. mBio 2023; 14:e0300922. [PMID: 36786571 PMCID: PMC10127799 DOI: 10.1128/mbio.03009-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
The rise of global temperature causes the degradation of the substantial reserves of carbon (C) stored in tundra soils, in which microbial processes play critical roles. Viruses are known to influence the soil C cycle by encoding auxiliary metabolic genes and infecting key microorganisms, but their regulation of microbial communities under climate warming remains unexplored. In this study, we evaluated the responses of viral communities for about 5 years of experimental warming at two depths (15 to 25 cm and 45 to 55 cm) in the Alaskan permafrost region. Our results showed that the viral community and functional gene composition and abundances (including viral functional genes related to replication, structure, infection, and lysis) were significantly influenced by environmental conditions such as total nitrogen (N), total C, and soil thawing duration. Although long-term warming did not impact the viral community composition at the two depths, some glycoside hydrolases encoded by viruses were more abundant at both depths of the warmed plots. With the continuous reduction of total C, viruses may alleviate methane release by altering infection strategies on methanogens. Importantly, viruses can adopt lysogenic and lytic lifestyles to manipulate microbial communities at different soil depths, respectively, which could be one of the major factors causing the differences in microbial responses to warming. This study provides a new ecological perspective on how viruses regulate the responses of microbes to warming at community and functional scales. IMPORTANCE Permafrost thawing causes microbial release of greenhouse gases, exacerbating climate warming. Some previous studies examined the responses of the microbial communities and functions to warming in permafrost region, but the roles of viruses in mediating the responses of microbial communities to warming are poorly understood. This study revealed that warming induced changes in some viral functional classes and in the virus/microbe ratios for specific lineages, which might influence the entire microbial community. Furthermore, differences in viral communities and functions, along with soil depths, are important factors influencing microbial responses to warming. Collectively, our study revealed the regulation of microbial communities by viruses and demonstrated the importance of viruses in the microbial ecology research.
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16
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Misson P, Bruder E, Cornuault JK, De Paepe M, Nicolas P, Demarre G, Lakisic G, Petit MA, Espeli O, Lecointe F. Phage production is blocked in the adherent-invasive Escherichia coli LF82 upon macrophage infection. PLoS Pathog 2023; 19:e1011127. [PMID: 36730457 PMCID: PMC9928086 DOI: 10.1371/journal.ppat.1011127] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 02/14/2023] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) strains are frequently recovered from stools of patients with dysbiotic microbiota. They have remarkable properties of adherence to the intestinal epithelium, and survive better than other E. coli in macrophages. The best studied of these AIEC is probably strain LF82, which was isolated from a Crohn's disease patient. This strain contains five complete prophages, which have not been studied until now. We undertook their analysis, both in vitro and inside macrophages, and show that all of them form virions. The Gally prophage is by far the most active, generating spontaneously over 108 viral particles per mL of culture supernatants in vitro, more than 100-fold higher than the other phages. Gally is also over-induced after a genotoxic stress generated by ciprofloxacin and trimethoprim. However, upon macrophage infection, a genotoxic environment, this over-induction is not observed. Analysis of the transcriptome and key steps of its lytic cycle in macrophages suggests that the excision of the Gally prophage continues to be repressed in macrophages. We conclude that strain LF82 has evolved an efficient way to block the lytic cycle of its most active prophage upon macrophage infection, which may participate to its good survival in macrophages.
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Affiliation(s)
- Pauline Misson
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Emma Bruder
- Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS, INSERM, Université PSL, Paris, France
| | - Jeffrey K. Cornuault
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Marianne De Paepe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pierre Nicolas
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
| | - Gaëlle Demarre
- Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS, INSERM, Université PSL, Paris, France
| | - Goran Lakisic
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Olivier Espeli
- Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS, INSERM, Université PSL, Paris, France
| | - François Lecointe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- * E-mail:
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17
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When bacteria are phage playgrounds: interactions between viruses, cells, and mobile genetic elements. Curr Opin Microbiol 2022; 70:102230. [PMID: 36335712 DOI: 10.1016/j.mib.2022.102230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/23/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
Abstract
Studies of viral adaptation have focused on the selective pressures imposed by hosts. However, there is increasing evidence that interactions between viruses, cells, and other mobile genetic elements are determinant to the success of infections. These interactions are often associated with antagonism and competition, but sometimes involve cooperation or parasitism. We describe two key types of interactions - defense systems and genetic regulation - that allow the partners of the interaction to destroy or control the others. These interactions evolve rapidly by genetic exchanges, including among competing partners. They are sometimes followed by functional diversification. Gene exchanges also facilitate the emergence of cross-talk between elements in the same bacterium. In the end, these processes produce multilayered networks of interactions that shape the outcome of viral infections.
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18
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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.
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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
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19
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Tang X, Fan C, Zeng G, Zhong L, Li C, Ren X, Song B, Liu X. Phage-host interactions: The neglected part of biological wastewater treatment. WATER RESEARCH 2022; 226:119183. [PMID: 36244146 DOI: 10.1016/j.watres.2022.119183] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/29/2022] [Accepted: 09/29/2022] [Indexed: 05/25/2023]
Abstract
In wastewater treatment plants (WWTPs), the stable operation of biological wastewater treatment is strongly dependent on the stability of associated microbiota. Bacteriophages (phages), viruses that specifically infect bacteria and archaea, are highly abundant and diverse in WWTPs. Although phages do not have known metabolic functions for themselves, they can shape functional microbiota via various phage-host interactions to impact biological wastewater treatment. However, the developments of phage-host interaction in WWTPs and their impact on biological wastewater treatment are overlooked. Here, we review the current knowledge regarding the phage-host interactions in biological wastewater treatment, mainly focusing on the characteristics of different phage populations, the phage-driven changes in functional microbiota, and the potential driving factors of phage-host interactions. We also discuss the efforts required further to understand and manipulate the phage-host interactions in biological wastewater treatment. Overall, this review advocates more attention to the phage dynamics in WWTPs.
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Affiliation(s)
- Xiang Tang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Changzheng Fan
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China.
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Linrui Zhong
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Chao Li
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China; Nova Skantek (Hunan) Environ Energy Co., Ltd., Changsha 410100, P.R. China
| | - Xiaoya Ren
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Biao Song
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Xigui Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
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20
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Efimov AD, Golomidova AK, Kulikov EE, Belalov IS, Ivanov PA, Letarov AV. RB49-like Bacteriophages Recognize O Antigens as One of the Alternative Primary Receptors. Int J Mol Sci 2022; 23:ijms231911329. [PMID: 36232640 PMCID: PMC9569957 DOI: 10.3390/ijms231911329] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022] Open
Abstract
The power of most of the enterobacterial O antigen types to provide robust protection against direct recognition of the cell surface by bacteriophage receptor-recognition proteins (RBP) has been recently recognized. The bacteriophages infecting O antigen producing strains of E. coli employ various strategies to tackle this nonspecific protection. T-even related phages, including RB49-like viruses, often have wide host ranges, being considered good candidates for use in phage therapy. However, the mechanisms by which these phages overcome the O antigen barrier remain unknown. We demonstrate here that RB49 and related phages Cognac49 and Whisky49 directly use certain types of O antigen as their primary receptors recognized by the virus long tail fibers (LTF) RBP gp38, so the O antigen becomes an attractant instead of an obstacle. Simultaneously to recognize multiple O antigen types, LTFs of each of these phages can bind to additional receptors, such as OmpA protein, enabling them to infect some rough strains of E. coli. We speculate that the mechanical force of the deployment of the short tail fibers (STF) triggered by the LTF binding to the O antigen or underneath of it, allows the receptor binding domains of STF to break through the O polysaccharide layer.
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Affiliation(s)
- Alexandr D Efimov
- Laboratory of Microbial Viruses, Winogradsky Institute of Microbiology RC Biotechnology RAS, 117312 Moscow, Russia
| | - Alla K Golomidova
- Laboratory of Microbial Viruses, Winogradsky Institute of Microbiology RC Biotechnology RAS, 117312 Moscow, Russia
| | - Eugene E Kulikov
- Laboratory of Microbial Viruses, Winogradsky Institute of Microbiology RC Biotechnology RAS, 117312 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ilya S Belalov
- Laboratory of Microbial Viruses, Winogradsky Institute of Microbiology RC Biotechnology RAS, 117312 Moscow, Russia
| | - Pavel A Ivanov
- Laboratory of Microbial Viruses, Winogradsky Institute of Microbiology RC Biotechnology RAS, 117312 Moscow, Russia
| | - Andrey V Letarov
- Laboratory of Microbial Viruses, Winogradsky Institute of Microbiology RC Biotechnology RAS, 117312 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
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21
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Kennedy EA, Holtz LR. Gut virome in early life: origins and implications. Curr Opin Virol 2022; 55:101233. [PMID: 35690009 PMCID: PMC9575407 DOI: 10.1016/j.coviro.2022.101233] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 12/15/2022]
Abstract
The human body is colonized by a multitude of bacteria, fungi, and viruses, which play important roles in health and disease. Microbial colonization during early life is thought to be a particularly important period with lasting consequences for health. Viral populations in the gut are particularly dynamic in early life before they stabilize in adulthood. The composition of the early-life virome is increasingly recognized as a determinant of disease later in life. Here, we review the development of the virome in healthy infants, as well as the role of the early-life virome in the development of disease states including diarrhea, malnutrition, and autoimmune diseases.
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Affiliation(s)
- Elizabeth A Kennedy
- Washington University School of Medicine, Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, St. Louis, MO 63110, USA
| | - Lori R Holtz
- Washington University School of Medicine, Department of Pediatrics, St. Louis, MO 63110, USA.
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22
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Sprotte S, Rasmussen TS, Cho GS, Brinks E, Lametsch R, Neve H, Vogensen FK, Nielsen DS, Franz CMAP. Morphological and Genetic Characterization of Eggerthella lenta Bacteriophage PMBT5. Viruses 2022; 14:1598. [PMID: 35893664 PMCID: PMC9394477 DOI: 10.3390/v14081598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/01/2022] [Accepted: 07/19/2022] [Indexed: 01/27/2023] Open
Abstract
Eggerthella lenta is a common member of the human gut microbiome. We here describe the isolation and characterization of a putative virulent bacteriophage having E. lenta as host. The double-layer agar method for isolating phages was adapted to anaerobic conditions for isolating bacteriophage PMBT5 from sewage on a strictly anaerobic E. lenta strain of intestinal origin. For this, anaerobically grown E. lenta cells were concentrated by centrifugation and used for a 24 h phage enrichment step. Subsequently, this suspension was added to anaerobically prepared top (soft) agar in Hungate tubes and further used in the double-layer agar method. Based on morphological characteristics observed by transmission electron microscopy, phage PMBT5 could be assigned to the Siphoviridae phage family. It showed an isometric head with a flexible, noncontractile tail and a distinct single 45 nm tail fiber under the baseplate. Genome sequencing and assembly resulted in one contig of 30,930 bp and a mol% GC content of 51.3, consisting of 44 predicted protein-encoding genes. Phage-related proteins could be largely identified based on their amino acid sequence, and a comparison with metagenomes in the human virome database showed that the phage genome exhibits similarity to two distantly related phages.
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Affiliation(s)
- Sabrina Sprotte
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 24103 Kiel, Germany; (G.-S.C.); (E.B.); (H.N.); (C.M.A.P.F.)
| | - Torben S. Rasmussen
- Department of Food Science, Faculty of Science, University of Copenhagen, 1958 Frederiksberg, Denmark; (T.S.R.); (R.L.); (F.K.V.); (D.S.N.)
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 24103 Kiel, Germany; (G.-S.C.); (E.B.); (H.N.); (C.M.A.P.F.)
| | - Erik Brinks
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 24103 Kiel, Germany; (G.-S.C.); (E.B.); (H.N.); (C.M.A.P.F.)
| | - René Lametsch
- Department of Food Science, Faculty of Science, University of Copenhagen, 1958 Frederiksberg, Denmark; (T.S.R.); (R.L.); (F.K.V.); (D.S.N.)
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 24103 Kiel, Germany; (G.-S.C.); (E.B.); (H.N.); (C.M.A.P.F.)
| | - Finn K. Vogensen
- Department of Food Science, Faculty of Science, University of Copenhagen, 1958 Frederiksberg, Denmark; (T.S.R.); (R.L.); (F.K.V.); (D.S.N.)
| | - Dennis S. Nielsen
- Department of Food Science, Faculty of Science, University of Copenhagen, 1958 Frederiksberg, Denmark; (T.S.R.); (R.L.); (F.K.V.); (D.S.N.)
| | - Charles M. A. P. Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 24103 Kiel, Germany; (G.-S.C.); (E.B.); (H.N.); (C.M.A.P.F.)
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23
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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.
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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:
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24
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Díaz-Galián MV, Vega-Rodríguez MA, Molina F. PhageCocktail: An R package to design phage cocktails from experimental phage-bacteria infection networks. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2022; 221:106865. [PMID: 35576688 DOI: 10.1016/j.cmpb.2022.106865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 04/18/2022] [Accepted: 05/07/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND OBJECTIVE Phage therapy is a resurgent strategy used in medicine and the food industry to lyse bacteria that cause damage to health or spoil a food product. Frequently, phage-bacteria infection networks have a large size, making it impossible to manually study all possible phage cocktails. Thus, this article presents an R package called PhageCocktail to automatically design efficient phage cocktails from phage-bacteria infection networks. METHODS This R package includes four different methods for designing phage cocktails: ExhaustiveSearch, ExhaustivePhi, ClusteringSearch, and ClusteringPhi. These four methods are explained in detail and are evaluated using 13 empirical phage-bacteria infection networks. More specifically, runtime and expected success (fraction of lysed bacteria) are analyzed. RESULTS The four methods have variations in terms of runtime and quality of the results. ExhaustiveSearch always provides the best possible phage cocktail, but its runtime could be long. ExhaustivePhi only focuses on one cocktail size, the one estimated as the best; thus, its runtime is less than ExhaustiveSearch, but it can produce cocktails with more phages than necessary. ClusteringSearch and ClusteringPhi are very fast (generally, less than one millisecond), providing always immediate results due to clustering techniques, but their accuracies can be lower, yielding cocktails with lower expected successes. CONCLUSIONS The larger the phage-bacteria infection network is, the more complex its analysis is. Thus, this tool eases this task for scientists and other users while designing phage cocktails of good quality. This R package includes four different methods; therefore, users may choose among them, considering their preferences in speed and accuracy of results.
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Affiliation(s)
- María Victoria Díaz-Galián
- Escuela Politécnica, Universidad de Extremadura (https://ror.org/0174shg90), Avda. de la Universidad s/n, Cáceres, 10003, Spain.
| | - Miguel A Vega-Rodríguez
- Escuela Politécnica, Universidad de Extremadura (https://ror.org/0174shg90), Avda. de la Universidad s/n, Cáceres, 10003, Spain.
| | - Felipe Molina
- Facultad de Ciencias, Universidad de Extremadura (https://ror.org/0174shg90), Avda. de Elvas s/n, Badajoz, 06006, Spain.
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25
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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: 10] [Impact Index Per Article: 5.0] [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.
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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.
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26
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Lourenço M, Chaffringeon L, Lamy-Besnier Q, Titécat M, Pédron T, Sismeiro O, Legendre R, Varet H, Coppée JY, Bérard M, De Sordi L, Debarbieux L. The gut environment regulates bacterial gene expression which modulates susceptibility to bacteriophage infection. Cell Host Microbe 2022; 30:556-569.e5. [PMID: 35421351 DOI: 10.1016/j.chom.2022.03.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 01/14/2022] [Accepted: 03/10/2022] [Indexed: 11/24/2022]
Abstract
Abundance and diversity of bacteria and their viral predators, bacteriophages (phages), in the digestive tract are associated with human health. Particularly intriguing is the long-term coexistence of these two antagonistic populations. We performed genome-wide RNA sequencing on a human enteroaggregative Escherichia coli isolate to identify genes differentially expressed between in vitro conditions and in murine intestines. We experimentally demonstrated that four of these differentially expressed genes modified the interactions between E. coli and three virulent phages by either increasing or decreasing its susceptibility/resistance pattern and also by interfering with biofilm formation. Therefore, the regulation of bacterial genes expression during the colonization of the digestive tract influences the coexistence of phages and bacteria, highlighting the intricacy of tripartite relationships between phages, bacteria, and the animal host in intestinal homeostasis.
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Affiliation(s)
- Marta Lourenço
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Bacteriophage Bacterium Host, 75015 Paris, France; Sorbonne Université, Collège Doctoral, 75005 Paris, France
| | - Lorenzo Chaffringeon
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Bacteriophage Bacterium Host, 75015 Paris, France; Sorbonne Université, INSERM, Centre de Recherche St Antoine, UMRS_938, Paris, France; Paris Center for Microbiome Medicine (PaCeMM) FHU, AP-HP, Paris, Ile-de-France, France
| | - Quentin Lamy-Besnier
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Bacteriophage Bacterium Host, 75015 Paris, France
| | - Marie Titécat
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Bacteriophage Bacterium Host, 75015 Paris, France; Université de Lille, INSERM, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, 59000 Lille, France
| | - Thierry Pédron
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Bacteriophage Bacterium Host, 75015 Paris, France
| | - Odile Sismeiro
- Transcriptome and EpiGenome Platform, Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Université Paris Cité, 75015 Paris, France
| | - Rachel Legendre
- Transcriptome and EpiGenome Platform, Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Université Paris Cité, 75015 Paris, France; Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, Université Paris Cité, 75015 Paris, France
| | - Hugo Varet
- Transcriptome and EpiGenome Platform, Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Université Paris Cité, 75015 Paris, France; Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, Université Paris Cité, 75015 Paris, France
| | - Jean-Yves Coppée
- Transcriptome and EpiGenome Platform, Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Université Paris Cité, 75015 Paris, France
| | - Marion Bérard
- Institut Pasteur, Université Paris Cité, DT, Animalerie Centrale, Centre de Gnotobiologie, 75724 Paris, France
| | - Luisa De Sordi
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Bacteriophage Bacterium Host, 75015 Paris, France; Sorbonne Université, INSERM, Centre de Recherche St Antoine, UMRS_938, Paris, France; Paris Center for Microbiome Medicine (PaCeMM) FHU, AP-HP, Paris, Ile-de-France, France
| | - Laurent Debarbieux
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Bacteriophage Bacterium Host, 75015 Paris, France.
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27
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Kitti T, Kongfak S, Leungtongkam U, Thummeepak R, Tasanapak K, Thanwisai A, Sitthisak S. Comparative genome analysis of Escherichia coli bacteriophages isolated from sewage and chicken meat. Virus Res 2022; 315:198784. [DOI: 10.1016/j.virusres.2022.198784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 11/26/2022]
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28
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Isolation and Characterization of a Novel Temperate Escherichia coli Bacteriophage, Kapi1, Which Modifies the O-Antigen and Contributes to the Competitiveness of Its Host during Colonization of the Murine Gastrointestinal Tract. mBio 2022; 13:e0208521. [PMID: 35073745 PMCID: PMC8787464 DOI: 10.1128/mbio.02085-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In this study, we describe the isolation and characterization of novel bacteriophage vB_EcoP_Kapi1 (Kapi1) isolated from a strain of commensal Escherichia coli inhabiting the gastrointestinal tract of healthy mice. We show that Kapi1 is a temperate phage integrated into tRNA argW of strain MP1 and describe its genome annotation and structure. Kapi1 shows limited homology to other characterized prophages but is most similar to the seroconverting phages of Shigella flexneri and clusters taxonomically with P22-like phages. The receptor for Kapi1 is the lipopolysaccharide O-antigen, and we further show that Kapi1 alters the structure of its host's O-antigen in multiple ways. Kapi1 displays unstable lysogeny, and we find that the lysogenic state is more stable during growth in simulated intestinal fluid. Furthermore, Kapi1 lysogens have a competitive advantage over their nonlysogenic counterparts both in vitro and in vivo, suggesting a role for Kapi1 during colonization. We thus report the use of MP1 and Kapi1 as a model system to explore the molecular mechanisms of mammalian colonization by E. coli to ask what the role(s) of prophages in this context might be. IMPORTANCE Although research exploring the microbiome has exploded in recent years, our understanding of the viral component of the microbiome is lagging far behind our understanding of the bacterial component. The vast majority of intestinal bacteria carry prophages integrated into their chromosomes, but most of these bacteriophages remain uncharacterized and unexplored. Here, we isolate and characterize a novel temperate bacteriophage infecting a commensal strain of Escherichia coli. We aim to explore the interactions between bacteriophages and their hosts in the context of the gastrointestinal tract, asking what role(s) temperate bacteriophages may play in growth and survival of bacteria in the gut. Understanding the fundamental biology of gut commensal bacteria can inform the development of novel antimicrobial or probiotic strategies for intestinal infections.
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29
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Kauffman KM, Chang WK, Brown JM, Hussain FA, Yang J, Polz MF, Kelly L. Resolving the structure of phage-bacteria interactions in the context of natural diversity. Nat Commun 2022; 13:372. [PMID: 35042853 PMCID: PMC8766483 DOI: 10.1038/s41467-021-27583-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/12/2021] [Indexed: 12/12/2022] Open
Abstract
Microbial communities are shaped by viral predators. Yet, resolving which viruses (phages) and bacteria are interacting is a major challenge in the context of natural levels of microbial diversity. Thus, fundamental features of how phage-bacteria interactions are structured and evolve in the wild remain poorly resolved. Here we use large-scale isolation of environmental marine Vibrio bacteria and their phages to obtain estimates of strain-level phage predator loads, and use all-by-all host range assays to discover how phage and host genomic diversity shape interactions. We show that lytic interactions in environmental interaction networks (as observed in agar overlay) are sparse-with phage predator loads being low for most bacterial strains, and phages being host-strain-specific. Paradoxically, we also find that although overlap in killing is generally rare between tailed phages, recombination is common. Together, these results suggest that recombination during cryptic co-infections is an important mode of phage evolution in microbial communities. In the development of phages for bioengineering and therapeutics it is important to consider that nucleic acids of introduced phages may spread into local phage populations through recombination, and that the likelihood of transfer is not predictable based on lytic host range.
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Affiliation(s)
- Kathryn M Kauffman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Oral Biology, The University at Buffalo, Buffalo, NY, 14214, USA
| | - William K Chang
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Julia M Brown
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
| | - Fatima A Hussain
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Joy Yang
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
| | - Libusha Kelly
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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30
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Menor-Flores M, Vega-Rodríguez MA, Molina F. Computational design of phage cocktails based on phage-bacteria infection networks. Comput Biol Med 2022; 142:105186. [PMID: 34998221 DOI: 10.1016/j.compbiomed.2021.105186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/22/2021] [Accepted: 12/26/2021] [Indexed: 01/16/2023]
Abstract
The misuse and overuse of antibiotics have boosted the proliferation of multidrug-resistant (MDR) bacteria, which are considered a major public health issue in the twenty-first century. Phage therapy may be a promising way in the treatment of infections caused by MDR pathogens, without the side effects of the current available antimicrobials. Phage therapy is based on phage cocktails, that is, combinations of phages able to lyse the target bacteria. In this work, we present and explain in detail two innovative computational methods to design phage cocktails taking into account a given phage-bacteria infection network. One of the methods (Exhaustive Search) always generates the best possible phage cocktail, while the other method (Network Metrics) always keeps a very reduced runtime (a few milliseconds). Both methods have been included in a Cytoscape application that is available for any user. A complete experimental study has been performed, evaluating and comparing the biological quality, runtime, and the impact when additional phages are included in the cocktail.
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Affiliation(s)
- Manuel Menor-Flores
- Escuela Politécnica, Universidad de Extremadura(1), Avda. de la Universidad s/n, 10 003, Cáceres, Spain.
| | - Miguel A Vega-Rodríguez
- Escuela Politécnica, Universidad de Extremadura(1), Avda. de la Universidad s/n, 10 003, Cáceres, Spain.
| | - Felipe Molina
- Facultad de Ciencias, Universidad de Extremadura(1), Avda. de Elvas s/n, 06 006, Badajoz, Spain.
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31
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Maffei E, Shaidullina A, Burkolter M, Heyer Y, Estermann F, Druelle V, Sauer P, Willi L, Michaelis S, Hilbi H, Thaler DS, Harms A. Systematic exploration of Escherichia coli phage-host interactions with the BASEL phage collection. PLoS Biol 2021; 19:e3001424. [PMID: 34784345 PMCID: PMC8594841 DOI: 10.1371/journal.pbio.3001424] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 09/27/2021] [Indexed: 01/08/2023] Open
Abstract
Bacteriophages, the viruses infecting bacteria, hold great potential for the treatment of multidrug-resistant bacterial infections and other applications due to their unparalleled diversity and recent breakthroughs in their genetic engineering. However, fundamental knowledge of the molecular mechanisms underlying phage-host interactions is mostly confined to a few traditional model systems and did not keep pace with the recent massive expansion of the field. The true potential of molecular biology encoded by these viruses has therefore remained largely untapped, and phages for therapy or other applications are often still selected empirically. We therefore sought to promote a systematic exploration of phage-host interactions by composing a well-assorted library of 68 newly isolated phages infecting the model organism Escherichia coli that we share with the community as the BASEL (BActeriophage SElection for your Laboratory) collection. This collection is largely representative of natural E. coli phage diversity and was intensively characterized phenotypically and genomically alongside 10 well-studied traditional model phages. We experimentally determined essential host receptors of all phages, quantified their sensitivity to 11 defense systems across different layers of bacterial immunity, and matched these results to the phages' host range across a panel of pathogenic enterobacterial strains. Clear patterns in the distribution of phage phenotypes and genomic features highlighted systematic differences in the potency of different immunity systems and suggested the molecular basis of receptor specificity in several phage groups. Our results also indicate strong trade-offs between fitness traits like broad host recognition and resistance to bacterial immunity that might drive the divergent adaptation of different phage groups to specific ecological niches. We envision that the BASEL collection will inspire future work exploring the biology of bacteriophages and their hosts by facilitating the discovery of underlying molecular mechanisms as the basis for an effective translation into biotechnology or therapeutic applications.
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Affiliation(s)
- Enea Maffei
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | - Yannik Heyer
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | | | - Luc Willi
- Biozentrum, University of Basel, Basel, Switzerland
| | - Sarah Michaelis
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Hubert Hilbi
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - David S. Thaler
- Biozentrum, University of Basel, Basel, Switzerland
- Program for the Human Environment, Rockefeller University, New York City, New York, United States of America
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32
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Billaud M, Lamy-Besnier Q, Lossouarn J, Moncaut E, Dion MB, Moineau S, Traoré F, Le Chatelier E, Denis C, Estelle J, Achard C, Zemb O, Petit MA. Analysis of viromes and microbiomes from pig fecal samples reveals that phages and prophages rarely carry antibiotic resistance genes. ISME COMMUNICATIONS 2021; 1:55. [PMID: 37938642 PMCID: PMC9723715 DOI: 10.1038/s43705-021-00054-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 09/06/2021] [Accepted: 09/13/2021] [Indexed: 05/09/2023]
Abstract
Understanding the transmission of antibiotic resistance genes (ARGs) is critical for human health. For this, it is necessary to identify which type of mobile genetic elements is able to spread them from animal reservoirs into human pathogens. Previous research suggests that in pig feces, ARGs may be encoded by bacteriophages. However, convincing proof for phage-encoded ARGs in pig viromes is still lacking, because of bacterial DNA contaminating issues. We collected 14 pig fecal samples and performed deep sequencing on both highly purified viral fractions and total microbiota, in order to investigate phage and prophage-encoded ARGs. We show that ARGs are absent from the genomes of active, virion-forming phages (below 0.02% of viral contigs from viromes), but present in three prophages, representing 0.02% of the viral contigs identified in the microbial dataset. However, the corresponding phages were not detected in the viromes, and their genetic maps suggest they might be defective. We conclude that among pig fecal samples, phages and prophages rarely carry ARG. Furthermore, our dataset allows for the first time a comprehensive view of the interplay between prophages and viral particles, and uncovers two large clades, inoviruses and Oengus-like phages.
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Affiliation(s)
- Maud Billaud
- Université Paris- Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- Pherecydes Pharma 22 Bd Benoni Goullin, Nantes, France
| | - Quentin Lamy-Besnier
- Université Paris- Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Julien Lossouarn
- Université Paris- Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Elisabeth Moncaut
- Université Paris- Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Moira B Dion
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Quebec City, QC, G1V 0A6, Canada
- Felix D'Hérelle Reference Center for Bacterial Viruses, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | | | | | | | - Jordi Estelle
- Université Paris-Saclay, INRAE, GABI, Jouy-en-Josas, France
| | - Caroline Achard
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet-Tolosan, France
| | - Olivier Zemb
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet-Tolosan, France
| | - Marie-Agnès Petit
- Université Paris- Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.
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Abstract
Several human intestinal microbiota studies suggest that bacteriophages, viruses infecting bacteria, play a role in gut homeostasis. Currently, bacteriophages are considered a tool to precisely engineer the intestinal microbiota, but they have also attracted considerable attention as a possible solution to fight against bacterial pathogens resistant to antibiotics. These two applications necessitate bacteriophages to reach and kill their bacterial target within the gut environment. Unfortunately, exploitable clinical data in this field are scarce. Here, we review the administration of bacteriophages to target intestinal bacteria in mammalian experimental models. While bacteriophage amplification in the gut was often confirmed, we found that in most studies, it had no significant impact on the load of the targeted bacteria. In particular, we observed that the outcome of bacteriophage treatments is linked to the behavior of the target bacteria toward each animal model. Treatment efficacy ranges from poor in asymptomatic intestinal carriage to high in intestinal disease. This broad range of efficacy underlines the difficulties to reach a consensus on the impact of bacteriophages in the gut and calls for deeper investigations of key parameters that influence the success of such interventions before launching clinical trials.
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Equine Intestinal O-Seroconverting Temperate Coliphage Hf4s: Genomic and Biological Characterization. Appl Environ Microbiol 2021; 87:e0112421. [PMID: 34406832 DOI: 10.1128/aem.01124-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Tailed bacteriophages constitute the bulk of the intestinal viromes of vertebrate animals. However, the relationships between lytic and lysogenic lifestyles of phages in these ecosystems are not always clear and may vary between the species or even between the individuals. The human intestinal (fecal) viromes are dominated mostly by temperate phages, while in horse feces virulent phages are more prevalent. To our knowledge, all the previously reported isolates of horse fecal coliphages are virulent. Temperate coliphage Hf4s was isolated from horse feces, from the indigenous equine Escherichia coli 4s strain. It is a podovirus related to the Lederbergvirus genus (including the well-characterized Salmonella bacteriophage P22). Hf4s recognizes the host O antigen as its primary receptor and possesses a functional O antigen seroconversion cluster that renders the lysogens protected from superinfection by the same bacteriophage and also abolishes the adsorption of some indigenous equine virulent coliphages, such as DT57C, while other phages, such as G7C or phiKT, retain the ability to infect E. coli 4s (Hf4s) lysogens. IMPORTANCE The relationships between virulent and temperate bacteriophages and their impact on high-density symbiotic microbial ecosystems of animals are not always clear and may vary between species or even between individuals. The horse intestinal virome is dominated by virulent phages, and Hf4s is the first temperate equine intestinal coliphage characterized. It recognizes the host O antigen as its primary receptor and possesses a functional O antigen seroconversion cluster that renders the lysogens protected from superinfection by some indigenous equine virulent coliphages, such as DT57C, while other phages, such as G7C or phiKT, retain the ability to infect E. coli 4s (Hf4s) lysogens. These findings raise questions on the significance of bacteriophage-bacteriophage interactions within the ecology of microbial viruses in mammal intestinal ecosystems.
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Moura de Sousa JA, Pfeifer E, Touchon M, Rocha EPC. Causes and Consequences of Bacteriophage Diversification via Genetic Exchanges across Lifestyles and Bacterial Taxa. Mol Biol Evol 2021; 38:2497-2512. [PMID: 33570565 PMCID: PMC8136500 DOI: 10.1093/molbev/msab044] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Bacteriophages (phages) evolve rapidly by acquiring genes from other phages. This results in mosaic genomes. Here, we identify numerous genetic transfers between distantly related phages and aim at understanding their frequency, consequences, and the conditions favoring them. Gene flow tends to occur between phages that are enriched for recombinases, transposases, and nonhomologous end joining, suggesting that both homologous and illegitimate recombination contribute to gene flow. Phage family and host phyla are strong barriers to gene exchange, but phage lifestyle is not. Even if we observe four times more recent transfers between temperate phages than between other pairs, there is extensive gene flow between temperate and virulent phages, and between the latter. These predominantly involve virulent phages with large genomes previously classed as low gene flux, and lead to the preferential transfer of genes encoding functions involved in cell energetics, nucleotide metabolism, DNA packaging and injection, and virion assembly. Such exchanges may contribute to the observed twice larger genomes of virulent phages. We used genetic transfers, which occur upon coinfection of a host, to compare phage host range. We found that virulent phages have broader host ranges and can mediate genetic exchanges between narrow host range temperate phages infecting distant bacterial hosts, thus contributing to gene flow between virulent phages, as well as between temperate phages. This gene flow drastically expands the gene repertoires available for phage and bacterial evolution, including the transfer of functional innovations across taxa.
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Affiliation(s)
| | - Eugen Pfeifer
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France
| | - Marie Touchon
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France
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Chevallereau A, Pons BJ, van Houte S, Westra ER. Interactions between bacterial and phage communities in natural environments. Nat Rev Microbiol 2021; 20:49-62. [PMID: 34373631 DOI: 10.1038/s41579-021-00602-y] [Citation(s) in RCA: 176] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 06/28/2021] [Indexed: 12/20/2022]
Abstract
We commonly acknowledge that bacterial viruses (phages) shape the composition and evolution of bacterial communities in nature and therefore have important roles in ecosystem functioning. This view stems from studies in the 1990s to the first decade of the twenty-first century that revealed high viral abundance, high viral diversity and virus-induced microbial death in aquatic ecosystems as well as an association between collapses in bacterial density and peaks in phage abundance. The recent surge in metagenomic analyses has provided deeper insight into the abundance, genomic diversity and spatio-temporal dynamics of phages in a wide variety of ecosystems, ranging from deep oceans to soil and the mammalian digestive tract. However, the causes and consequences of variations in phage community compositions remain poorly understood. In this Review, we explore current knowledge of the composition and evolution of phage communities, as well as their roles in controlling the population and evolutionary dynamics of bacterial communities. We discuss the need for greater ecological realism in laboratory studies to capture the complexity of microbial communities that thrive in natural environments.
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Affiliation(s)
- Anne Chevallereau
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK. .,Department of Infection, Immunity and Inflammation, Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, Paris, France.
| | - Benoît J Pons
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK
| | - Stineke van Houte
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK
| | - Edze R Westra
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, UK.
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Šimoliūnienė M, Kazlauskas D, Zajančkauskaitė A, Meškys R, Truncaitė L. Escherichia coli trxAgene as a molecular marker for genome engineering of felixounoviruses. Biochim Biophys Acta Gen Subj 2021; 1865:129967. [PMID: 34324954 DOI: 10.1016/j.bbagen.2021.129967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/02/2021] [Accepted: 07/24/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Bacterial viruses (bacteriophages or phages) have a lot of uncharacterized genes, which hinders the progress of their applied research. Functional characterization of these genes is often hampered by a lack of suitable methods for engineering of phage genomes. METHODS Phages vB_EcoM_Alf5 (Alf5) and VB_EcoM_VpaE1 (VpaE1) were used as the model phages of Felixounovirus genus. The phage-coded properties were predicted by bioinformatics analysis. The 'pull-down' assay was used for detection of protein-protein interactions. Primer extension analysis was used for the DNA polymerase (DNAP) activity testing. Bacteriophage lambda Redγβα-assisted homologous recombination was used for construction of phage mutants. RESULTS Bioinformatics analysis showed that felixounoviruses encode DNA polymerase, which is homologous to the T7 DNAP. We found that the Escherichia coli thioredoxin A (TrxA) in vitro interacts with the predicted DNAP of Alf5 phage (gp096) and enhances its activity. Phages Alf5 and VpaE1 do not grow on E. coli strains lacking trxA gene unless it is provided in trans. This feature was used for construction of the deletion/insertion mutants of non-essential genes of felixounoviruses. CONCLUSION DNA replication of phages from Felixonuvirus genus depends on the host trxA, which therefore may be used as a molecular marker for their genome engineering. GENERAL SIGNIFICANCE We present a proof-of-principle of a strategy for targeted engineering of bacteriophages of Felixounovirus genus. The method developed here will facilitate the basic and applied research of this unexplored phage group. Furthermore, detected functional interactions between the phage and host proteins will be significant for basic research of DNA replication.
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Affiliation(s)
- Monika Šimoliūnienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 7 Saulėtekio av., LT-10257 Vilnius, Lithuania.
| | - Darius Kazlauskas
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, 7 Saulėtekio av., LT-10257 Vilnius, Lithuania.
| | - Aurelija Zajančkauskaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 7 Saulėtekio av., LT-10257 Vilnius, Lithuania.
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 7 Saulėtekio av., LT-10257 Vilnius, Lithuania.
| | - Lidija Truncaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 7 Saulėtekio av., LT-10257 Vilnius, Lithuania.
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Hibernation-Promoting Factor Sequesters Staphylococcus aureus Ribosomes to Antagonize RNase R-Mediated Nucleolytic Degradation. mBio 2021; 12:e0033421. [PMID: 34253058 PMCID: PMC8406268 DOI: 10.1128/mbio.00334-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Bacterial and eukaryotic hibernation factors prevent translation by physically blocking the decoding center of ribosomes, a phenomenon called ribosome hibernation that often occurs in response to nutrient deprivation. The human pathogen Staphylococcus aureus lacking the sole hibernation factor HPF undergoes massive ribosome degradation via an unknown pathway. Using genetic and biochemical approaches, we find that inactivating the 3′-to-5′ exonuclease RNase R suppresses ribosome degradation in the Δhpf mutant. In vitro cell-free degradation assays confirm that 30S and 70S ribosomes isolated from the Δhpf mutant are extremely susceptible to RNase R, in stark contrast to nucleolytic resistance of the HPF-bound 70S and 100S complexes isolated from the wild type. In the absence of HPF, specific S. aureus 16S rRNA helices are sensitive to nucleolytic cleavage. These RNase hot spots are distinct from that found in the Escherichia coli ribosomes. S. aureus RNase R is associated with ribosomes, but unlike the E. coli counterpart, it is not regulated by general stressors and acetylation. The results not only highlight key differences between the evolutionarily conserved RNase R homologs but also provide direct evidence that HPF preserves ribosome integrity beyond its role in translational avoidance, thereby poising the hibernating ribosomes for rapid resumption of translation.
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Kirsch JM, Brzozowski RS, Faith D, Round JL, Secor PR, Duerkop BA. Bacteriophage-Bacteria Interactions in the Gut: From Invertebrates to Mammals. Annu Rev Virol 2021; 8:95-113. [PMID: 34255542 DOI: 10.1146/annurev-virology-091919-101238] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacteria and their viruses (bacteriophages or phages) interact antagonistically and beneficially in polymicrobial communities such as the guts of animals. These interactions are multifaceted and are influenced by environmental conditions. In this review, we discuss phage-bacteria interactions as they relate to the complex environment of the gut. Within the mammalian and invertebrate guts, phages and bacteria engage in diverse interactions including genetic coexistence through lysogeny, and phages directly modulate microbiota composition and the immune system with consequences that are becoming recognized as potential drivers of health and disease. With greater depth of understanding of phage-bacteria interactions in the gut and the outcomes, future phage therapies become possible. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Joshua M Kirsch
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA;
| | - Robert S Brzozowski
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA;
| | - Dominick Faith
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA;
| | - June L Round
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, Utah 84113, USA;
| | - Patrick R Secor
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA;
| | - Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA;
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Rethinking phage-bacteria-eukaryotic relationships and their influence on human health. Cell Host Microbe 2021; 29:681-688. [PMID: 33735620 DOI: 10.1016/j.chom.2021.02.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/19/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023]
Abstract
There is a rapidly growing body of research demonstrating the unique and often surprising mechanisms by which bacteriophages, specialized viruses of bacteria, can influence human health and disease states. This can occur directly by shaping their bacterial host's ecology through top-down pressure or via more indirect routes, including influencing the human body's metabolism or immune system. These microbial interactions can affect health and disease states in both the local environment or by influencing the body's distal organs or systems. Here we provide an update on the current understanding of bacteriophages' influence on human health within the context of tripartite symbioses with their bacterial and human hosts.
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41
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Abstract
Oral bacteriophages (or phages), especially periodontal ones, constitute a growing area of interest, but research on oral phages is still in its infancy. Phages are bacterial viruses that may persist as intracellular parasitic deoxyribonucleic acid (DNA) or use bacterial metabolism to replicate and cause bacterial lysis. The microbiomes of saliva, oral mucosa, and dental plaque contain active phage virions, bacterial lysogens (ie, carrying dormant prophages), and bacterial strains containing short fragments of phage DNA. In excess of 2000 oral phages have been confirmed or predicted to infect species of the phyla Actinobacteria (>300 phages), Bacteroidetes (>300 phages), Firmicutes (>1000 phages), Fusobacteria (>200 phages), and Proteobacteria (>700 phages) and three additional phyla (few phages only). This article assesses the current knowledge of the diversity of the oral phage population and the mechanisms by which phages may impact the ecology of oral biofilms. The potential use of phage-based therapy to control major periodontal pathogens is also discussed.
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Affiliation(s)
- Szymon P Szafrański
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Hannover, Germany
| | - Jørgen Slots
- Division of Periodontology, Diagnostic Sciences and Dental Hygiene, Ostrow School of Dentistry of USC, University of Southern California, Los Angeles, California, USA
| | - Meike Stiesch
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Hannover, Germany
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Molina F, Simancas A, Ramírez M, Tabla R, Roa I, Rebollo JE. A New Pipeline for Designing Phage Cocktails Based on Phage-Bacteria Infection Networks. Front Microbiol 2021; 12:564532. [PMID: 33664712 PMCID: PMC7920989 DOI: 10.3389/fmicb.2021.564532] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 01/18/2021] [Indexed: 12/17/2022] Open
Abstract
In recent years, the spread of antibiotic-resistant bacteria and efforts to preserve food microbiota have induced renewed interest in phage therapy. Phage cocktails, instead of a single phage, are commonly used as antibacterial agents since the hosts are unlikely to become resistant to several phages simultaneously. While the spectrum of activity might increase with cocktail complexity, excessive phages could produce side effects, such as the horizontal transfer of genes that augment the fitness of host strains, dysbiosis or high manufacturing costs. Therefore, cocktail formulation represents a compromise between achieving substantial reduction in the bacterial loads and restricting its complexity. Despite the abovementioned points, the observed bacterial load reduction does not increase significantly with the size of phage cocktails, indicating the requirement for a systematic approach to their design. In this work, the information provided by host range matrices was analyzed after building phage-bacteria infection networks (PBINs). To this end, we conducted a meta-analysis of 35 host range matrices, including recently published studies and new datasets comprising Escherichia coli strains isolated during ripening of artisanal raw milk cheese and virulent coliphages from ewes' feces. The nestedness temperature, which reflects the host range hierarchy of the phages, was determined from bipartite host range matrices using heuristic (Nestedness Temperature Calculator) and genetic (BinMatNest) algorithms. The latter optimizes matrix packing, leading to lower temperatures, i.e., it simplifies the identification of the phages with the broadest host range. The structure of infection networks suggests that generalist phages (and not specialist phages) tend to succeed in infecting less susceptible bacteria. A new metric (Φ), which considers some properties of the host range matrices (fill, temperature, and number of bacteria), is proposed as an estimator of phage cocktail size. To identify the best candidates, agglomerative hierarchical clustering using Ward's method was implemented. Finally, a cocktail was formulated for the biocontrol of cheese-isolated E. coli, reducing bacterial counts by five orders of magnitude.
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Affiliation(s)
- Felipe Molina
- Genetics, Department of Biochemistry Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
| | - Alfredo Simancas
- Genetics, Department of Biochemistry Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
| | - Manuel Ramírez
- Microbiology, Department of Biomedical Sciences, University of Extremadura, Badajoz, Spain
| | - Rafael Tabla
- Dairy Department, Scientific and Technological Research Centre of Extremadura, Technological Institute of Food and Agriculture, Junta de Extremadura, Badajoz, Spain
| | - Isidro Roa
- Dairy Department, Scientific and Technological Research Centre of Extremadura, Technological Institute of Food and Agriculture, Junta de Extremadura, Badajoz, Spain
| | - José Emilio Rebollo
- Genetics, Department of Biochemistry Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
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Balance between promiscuity and specificity in phage λ host range. ISME JOURNAL 2021; 15:2195-2205. [PMID: 33589767 DOI: 10.1038/s41396-021-00912-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 01/18/2021] [Accepted: 01/25/2021] [Indexed: 01/21/2023]
Abstract
As hosts acquire resistance to viruses, viruses must overcome that resistance to re-establish infectivity, or go extinct. Despite the significant hurdles associated with adapting to a resistant host, viruses are evolutionarily successful and maintain stable coevolutionary relationships with their hosts. To investigate the factors underlying how pathogens adapt to their hosts, we performed a deep mutational scan of the region of the λ tail fiber tip protein that mediates contact with the receptor on λ's host, Escherichia coli. Phages harboring amino acid substitutions were subjected to selection for infectivity on wild type E. coli, revealing a highly restrictive fitness landscape, in which most substitutions completely abrogate function. A subset of positions that are tolerant of mutation in this assay, but diverse over evolutionary time, are associated with host range expansion. Imposing selection for phage infectivity on three λ-resistant hosts, each harboring a different missense mutation in the λ receptor, reveals hundreds of adaptive variants in λ. We distinguish λ variants that confer promiscuity, a general ability to overcome host resistance, from those that drive host-specific infectivity. Both processes may be important in driving adaptation to a novel host.
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44
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Does over a century of aerobic phage work provide a solid framework for the study of phages in the gut? Anaerobe 2021; 68:102319. [PMID: 33465423 DOI: 10.1016/j.anaerobe.2021.102319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 01/09/2021] [Accepted: 01/11/2021] [Indexed: 12/13/2022]
Abstract
Bacterial viruses (bacteriophages, phages) of the gut have increasingly become a focus in microbiome studies, with an understanding that they are likely key players in health and disease. However, characterization of the virome remains largely based on bioinformatic approaches, with the impact of these viromes inferred based on a century of knowledge from aerobic phage work. Studying the phages infecting anaerobes is difficult, as they are often technically demanding to isolate and propagate. In this review, we primarily discuss the phages infecting three well-studied anaerobes in the gut: Bifidobacterium, Clostridia and Bacteroides, with a particular focus on the challenges in isolating and characterizing these phages. We contrast the lessons learned from these to other anaerobic work on phages infecting facultative anaerobes of the gut: Enterococcus and Lactobacillus. Phages from the gut do appear to adhere to the lessons learned from aerobic work, but the additional challenges of working on them has required ingenious new approaches to enable their study. This, in turn, has uncovered remarkable biology likely underpinning phage-host relationships in many stable environments.
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45
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Babenko V, Millard A, Kulikov E, Spasskaya N, Letarova M, Konanov D, Belalov I, Letarov A. The ecogenomics of dsDNA bacteriophages in feces of stabled and feral horses. Comput Struct Biotechnol J 2020; 18:3457-3467. [PMID: 33294140 PMCID: PMC7691681 DOI: 10.1016/j.csbj.2020.10.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/30/2020] [Accepted: 10/30/2020] [Indexed: 12/13/2022] Open
Abstract
The viromes of the mammalian lower gut were shown to be heavily dominated by bacteriophages; however, only for humans were the composition and intervariability of the bacteriophage communities studied in depth. Here we present an ecogenomics survey of dsDNA bacteriophage diversity in the feces of horses (Equus caballus), comparing two groups of stabled horses, and a further group of feral horses that were isolated on an island. Our results indicate that the dsDNA viromes of the horse feces feature higher richness than in human viromes, with more even distribution of genotypes. No over-represented phage genotypes, such as CrAssphage-related viruses found in humans, were identified. Additionally, many bacteriophage genus-level clusters were found to be present in all three geographically isolated populations. The diversity of the horse intestinal bacteriophages is severely undersampled, and so consequently only a minor fraction of the phage contigs could be linked with the bacteriophage genomes. Our study indicates that bacteriophage ecological parameters in the intestinal ecosystems in horses and humans differ significantly, leading them to shape their corresponding viromes in different ways. Therefore, the diversity and structure of the intestinal virome in different animal species needs to be experimentally studied.
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Affiliation(s)
| | - A. Millard
- Dept Genetics and Genome Biology, University of Leicester, UK
| | - E.E. Kulikov
- Winogradsky Institute of Microbiology RC Biotechnology RAS, Moscow, Russia
| | - N.N. Spasskaya
- Zoology Museum, Faculty of Biology, Lomonosov Moscow State University, Russia
| | - M.A. Letarova
- Winogradsky Institute of Microbiology RC Biotechnology RAS, Moscow, Russia
| | | | - I.S. Belalov
- Winogradsky Institute of Microbiology RC Biotechnology RAS, Moscow, Russia
| | - A.V. Letarov
- Winogradsky Institute of Microbiology RC Biotechnology RAS, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Russia
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Phages to shape the gut microbiota? Curr Opin Biotechnol 2020; 68:89-95. [PMID: 33176253 DOI: 10.1016/j.copbio.2020.09.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/22/2020] [Accepted: 09/29/2020] [Indexed: 12/13/2022]
Abstract
The concept of (bacterio)phage therapy is simple; target the phage to the bacterial pathogen causing disease. As phages are natural killers of bacteria, one could expect this to be an easy task. However, when it comes to phage therapy within the gut, it might not be quite that simple. Already without exogenous intervention, a multitude of phage-bacterial interactions occur within the human gut, some of which might play a direct role in disease progression. In this perspective, we aim to summarise the current understanding of phages within our gut, moving from infancy, adulthood, and then into disease progression. We then highlight recent advances in phage-based interventions, both conventional phage therapy and the progressing field of whole virome transplant.
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Mutalik VK, Adler BA, Rishi HS, Piya D, Zhong C, Koskella B, Kutter EM, Calendar R, Novichkov PS, Price MN, Deutschbauer AM, Arkin AP. High-throughput mapping of the phage resistance landscape in E. coli. PLoS Biol 2020; 18:e3000877. [PMID: 33048924 PMCID: PMC7553319 DOI: 10.1371/journal.pbio.3000877] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 09/08/2020] [Indexed: 12/18/2022] Open
Abstract
Bacteriophages (phages) are critical players in the dynamics and function of microbial communities and drive processes as diverse as global biogeochemical cycles and human health. Phages tend to be predators finely tuned to attack specific hosts, even down to the strain level, which in turn defend themselves using an array of mechanisms. However, to date, efforts to rapidly and comprehensively identify bacterial host factors important in phage infection and resistance have yet to be fully realized. Here, we globally map the host genetic determinants involved in resistance to 14 phylogenetically diverse double-stranded DNA phages using two model Escherichia coli strains (K-12 and BL21) with known sequence divergence to demonstrate strain-specific differences. Using genome-wide loss-of-function and gain-of-function genetic technologies, we are able to confirm previously described phage receptors as well as uncover a number of previously unknown host factors that confer resistance to one or more of these phages. We uncover differences in resistance factors that strongly align with the susceptibility of K-12 and BL21 to specific phage. We also identify both phage-specific mechanisms, such as the unexpected role of cyclic-di-GMP in host sensitivity to phage N4, and more generic defenses, such as the overproduction of colanic acid capsular polysaccharide that defends against a wide array of phages. Our results indicate that host responses to phages can occur via diverse cellular mechanisms. Our systematic and high-throughput genetic workflow to characterize phage-host interaction determinants can be extended to diverse bacteria to generate datasets that allow predictive models of how phage-mediated selection will shape bacterial phenotype and evolution. The results of this study and future efforts to map the phage resistance landscape will lead to new insights into the coevolution of hosts and their phage, which can ultimately be used to design better phage therapeutic treatments and tools for precision microbiome engineering.
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Affiliation(s)
- Vivek K. Mutalik
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Innovative Genomics Institute, Berkeley, California, United States of America
| | - Benjamin A. Adler
- Innovative Genomics Institute, Berkeley, California, United States of America
- Department of Bioengineering, University of California – Berkeley, Berkeley, California, United States of America
| | - Harneet S. Rishi
- Biophysics Graduate Group, University of California – Berkeley, Berkeley, California, United States of America
- Designated Emphasis Program in Computational and Genomic Biology, University of California – Berkeley, Berkeley, California, United States of America
| | - Denish Piya
- Innovative Genomics Institute, Berkeley, California, United States of America
- Department of Bioengineering, University of California – Berkeley, Berkeley, California, United States of America
| | - Crystal Zhong
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Britt Koskella
- Department of Integrative Biology, University of California – Berkeley, Berkeley, California, United States of America
| | | | - Richard Calendar
- Department of Molecular and Cell Biology, University of California – Berkeley, Berkeley, California, United States of America
| | - Pavel S. Novichkov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Morgan N. Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Innovative Genomics Institute, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California – Berkeley, Berkeley, California, United States of America
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Innovative Genomics Institute, Berkeley, California, United States of America
- Department of Bioengineering, University of California – Berkeley, Berkeley, California, United States of America
- Biophysics Graduate Group, University of California – Berkeley, Berkeley, California, United States of America
- Designated Emphasis Program in Computational and Genomic Biology, University of California – Berkeley, Berkeley, California, United States of America
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Olsen NS, Forero-Junco L, Kot W, Hansen LH. Exploring the Remarkable Diversity of Culturable Escherichia coli Phages in the Danish Wastewater Environment. Viruses 2020; 12:E986. [PMID: 32899836 PMCID: PMC7552041 DOI: 10.3390/v12090986] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/24/2020] [Accepted: 08/31/2020] [Indexed: 12/12/2022] Open
Abstract
Phages drive bacterial diversity, profoundly influencing microbial communities, from microbiomes to the drivers of global biogeochemical cycling. Aiming to broaden our understanding of Escherichiacoli (MG1655, K-12) phages, we screened 188 Danish wastewater samples and isolated 136 phages. Ninety-two of these have genomic sequences with less than 95% similarity to known phages, while most map to existing genera several represent novel lineages. The isolated phages are highly diverse, estimated to represent roughly one-third of the true diversity of culturable virulent dsDNA Escherichia phages in Danish wastewater, yet almost half (40%) are not represented in metagenomic databases, emphasising the importance of isolating phages to uncover diversity. Seven viral families, Myoviridae, Siphoviridae, Podoviridae,Drexlerviridae,Chaseviridae,Autographviridae, and Microviridae, are represented in the dataset. Their genomes vary drastically in length from 5.3 kb to 170.8 kb, with a guanine and cytosine (GC) content ranging from 35.3% to 60.0%. Hence, even for a model host bacterium, substantial diversity remains to be uncovered. These results expand and underline the range of coliphage diversity and demonstrate how far we are from fully disclosing phage diversity and ecology.
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Affiliation(s)
- Nikoline S. Olsen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark;
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark;
| | - Laura Forero-Junco
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark;
| | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark;
| | - Lars H. Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark;
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Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation. ISME JOURNAL 2020; 14:2980-2996. [PMID: 32732904 PMCID: PMC7784688 DOI: 10.1038/s41396-020-0726-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 07/15/2020] [Accepted: 07/20/2020] [Indexed: 01/21/2023]
Abstract
Klebsiella species are able to colonize a wide range of environments and include worrisome nosocomial pathogens. Here, we sought to determine the abundance and infectivity of prophages of Klebsiella to understand how the interactions between induced prophages and bacteria affect population dynamics and evolution. We identified many prophages in the species, placing these taxa among the top 5% of the most polylysogenic bacteria. We selected 35 representative strains of the Klebsiella pneumoniae species complex to establish a network of induced phage-bacteria interactions. This revealed that many prophages are able to enter the lytic cycle, and subsequently kill or lysogenize closely related Klebsiella strains. Although 60% of the tested strains could produce phages that infect at least one other strain, the interaction network of all pairwise cross-infections is very sparse and mostly organized in modules corresponding to the strains' capsule serotypes. Accordingly, capsule mutants remain uninfected showing that the capsule is a key factor for successful infections. Surprisingly, experiments in which bacteria are predated by their own prophages result in accelerated loss of the capsule. Our results show that phage infectiousness defines interaction modules between small subsets of phages and bacteria in function of capsule serotype. This limits the role of prophages as competitive weapons because they can infect very few strains of the species complex. This should also restrict phage-driven gene flow across the species. Finally, the accelerated loss of the capsule in bacteria being predated by their own phages, suggests that phages drive serotype switch in nature.
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McCallin S, Suh G, Sacher J, Koeris M, Barreto M, Blasdel B, Merril C, McCallin S. PHAGE Futures Congress Meeting Summary Washington, DC January 29 to 30, 2020. PHAGE (NEW ROCHELLE, N.Y.) 2020; 1:83-86. [PMID: 36147891 PMCID: PMC9041456 DOI: 10.1089/phage.2020.29006.fre] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Affiliation(s)
- Shawna McCallin
- Division of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
- Department of Neuro-Urology, Balgrist University Hospital, University of Zürich, Zürich, Switzerland
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