1
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Dougherty PE, Nielsen TK, Riber L, Lading HH, Forero-Junco LM, Kot W, Raaijmakers JM, Hansen LH. Widespread and largely unknown prophage activity, diversity, and function in two genera of wheat phyllosphere bacteria. THE ISME JOURNAL 2023; 17:2415-2425. [PMID: 37919394 PMCID: PMC10689766 DOI: 10.1038/s41396-023-01547-1] [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: 06/28/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023]
Abstract
Environmental bacteria host an enormous number of prophages, but their diversity and natural functions remain largely elusive. Here, we investigate prophage activity and diversity in 63 Erwinia and Pseudomonas strains isolated from flag leaves of wheat grown in a single field. Introducing and validating Virion Induction Profiling Sequencing (VIP-Seq), we identify and quantify the activity of 120 spontaneously induced prophages, discovering that some phyllosphere bacteria produce more than 108 virions/mL in overnight cultures, with significant induction also observed in planta. Sequence analyses and plaque assays reveal E. aphidicola prophages contribute a majority of intraspecies genetic diversity and divide their bacterial hosts into antagonistic factions engaged in widespread microbial warfare, revealing the importance of prophage-mediated microdiversity. When comparing spontaneously active prophages with predicted prophages we also find insertion sequences are strongly correlated with non-active prophages. In conclusion, we discover widespread and largely unknown prophage diversity and function in phyllosphere bacteria.
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Affiliation(s)
- Peter Erdmann Dougherty
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Tue Kjærgaard Nielsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Leise Riber
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Helen Helgå Lading
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark.
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2
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Zheng K, Liang Y, Paez-Espino D, Zou X, Gao C, Shao H, Sung YY, Mok WJ, Wong LL, Zhang YZ, Tian J, Chen F, Jiao N, Suttle CA, He J, McMinn A, Wang M. Identification of hidden N4-like viruses and their interactions with hosts. mSystems 2023; 8:e0019723. [PMID: 37702511 PMCID: PMC10654107 DOI: 10.1128/msystems.00197-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/19/2023] [Indexed: 09/14/2023] Open
Abstract
IMPORTANCE The findings of this study are significant, as N4-like viruses represent a unique viral lineage with a distinct replication mechanism and a conserved core genome. This work has resulted in a comprehensive global map of the entire N4-like viral lineage, including information on their distribution in different biomes, evolutionary divergence, genomic diversity, and the potential for viral-mediated host metabolic reprogramming. As such, this work significantly contributes to our understanding of the ecological function and viral-host interactions of bacteriophages.
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Affiliation(s)
- Kaiyang Zheng
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Yantao Liang
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - David Paez-Espino
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Mammoth Biosciences Inc., South San Francisco, California, USA
| | - Xiao Zou
- Qingdao Central Hospital, Qingdao, China
| | - Chen Gao
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Hongbing Shao
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Yeong Yik Sung
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), Kuala Terengganu, Malaysia
| | - Wen Jye Mok
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), Kuala Terengganu, Malaysia
| | - Li Lian Wong
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), Kuala Terengganu, Malaysia
| | - Yu-Zhong Zhang
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Jiwei Tian
- Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao, China
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Curtis A. Suttle
- Department of Earth, Ocean and Atmospheric Sciences, Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology and Immunology, Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jianfeng He
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
| | - Andrew McMinn
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Min Wang
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- The Affiliated Hospital of Qingdao University, Qingdao, China
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3
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Aghdam SA, Lahowetz RM, Brown AMV. Divergent endophytic viromes and phage genome repertoires among banana ( Musa) species. Front Microbiol 2023; 14:1127606. [PMID: 37362937 PMCID: PMC10288200 DOI: 10.3389/fmicb.2023.1127606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/02/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction Viruses generally cause disease, but some viruses may be beneficial as resident regulators of their hosts or host microbiomes. Plant-associated viruses can help plants survive by increasing stress tolerance or regulating endophytic communities. The goal of this study was to characterize endophytic virus communities in banana and plantain (Musa spp.) genotypes, including cultivated and wild species, to assess virome repertoires and detect novel viruses. Methods DNA viral communities were characterized by shotgun sequencing of an enriched endosphere extract from leaves and roots or corm of 7 distinct Musa genotypes (M. balbisiana, Thai Black, M. textilis, M. sikkimensis, Dwarf Cavendish, Williams Hybrid, and FHIA-25 Hybrid). Results Results showed abundant virus-like contigs up to 108,191 bp long with higher relative abundance in leaves than roots. Analyses predicted 733 phage species in 51 families, with little overlap in phage communities among plants. Phage diversity was higher in roots and in diploid wild hosts. Ackermanniviridae and Rhizobium phage were generally the most abundant taxa. A Rhizobium RR1-like phage related to a phage of an endophytic tumor-causing rhizobium was found, bearing a holin gene and a partial Shiga-like toxin gene, raising interest in its potential to regulate endophytic Rhizobiaceae. Klebsiella phages were of interest for possible protection against Fusarium wilt, and other phages were predicted with potential to regulate Erwinia, Pectobacterium, and Ralstonia-associated diseases. Although abundant phage-containing contigs were functionally annotated, revealing 1,038 predicted viral protein domains, gene repertoires showed high divergence from database sequences, suggesting novel phages in these banana cultivars. Plant DNA viruses included 56 species of Badnavirus and 26 additional non-Musa plant viruses with distributions that suggested a mixture of resident and transient plant DNA viruses in these samples. Discussion Together, the disparate viral communities in these plants from a shared environment suggest hosts drive the composition of these virus communities. This study forms a first step in understanding the endophytic virome in this globally important food crop, which is currently threatened by fungal, bacterial, and viral diseases.
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Zhang M, Hao Y, Yi Y, Liu S, Sun Q, Tan X, Tang S, Xiao X, Jian H. Unexplored diversity and ecological functions of transposable phages. THE ISME JOURNAL 2023:10.1038/s41396-023-01414-z. [PMID: 37069234 DOI: 10.1038/s41396-023-01414-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 04/02/2023] [Accepted: 04/05/2023] [Indexed: 04/19/2023]
Abstract
Phages are prevalent in diverse environments and play major ecological roles attributed to their tremendous diversity and abundance. Among these viruses, transposable phages (TBPs) are exceptional in terms of their unique lifestyle, especially their replicative transposition. Although several TBPs have been isolated and the life cycle of the representative phage Mu has been extensively studied, the diversity distribution and ecological functions of TBPs on the global scale remain unknown. Here, by mining TBPs from enormous microbial genomes and viromes, we established a TBP genome dataset (TBPGD), that expands the number of accessible TBP genomes 384-fold. TBPs are prevalent in diverse biomes and show great genetic diversity. Based on taxonomic evaluations, we propose the categorization of TBPs into four viral groups, including 11 candidate subfamilies. TBPs infect multiple bacterial phyla, and seem to infect a wider range of hosts than non-TBPs. Diverse auxiliary metabolic genes (AMGs) are identified in the TBP genomes, and genes related to glycoside hydrolases and pyrimidine deoxyribonucleotide biosynthesis are highly enriched. Finally, the influences of TBPs on their hosts are experimentally examined by using the marine bacterium Shewanella psychrophila WP2 and its infecting transposable phage SP2. Collectively, our findings greatly expand the genetic diversity of TBPs, and comprehensively reveal their potential influences in various ecosystems.
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Affiliation(s)
- Mujie Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yali Hao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Yi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shunzhang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qingyang Sun
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoli Tan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shan Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China.
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5
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Twenty Years of Collaboration to Sort out Phage Mu Replication and Its Dependence on the Mu Central Gyrase Binding Site. Viruses 2023; 15:v15030637. [PMID: 36992345 PMCID: PMC10052514 DOI: 10.3390/v15030637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/02/2023] Open
Abstract
For 20 years, the intricacies in bacteriophage Mu replication and its regulation were elucidated in collaboration between Ariane Toussaint and her co-workers in the Laboratory of Genetics at the Université Libre de Bruxelles, and the groups of Martin Pato and N. Patrick Higgins in the US. Here, to honor Martin Pato’s scientific passion and rigor, we tell the history of this long-term sharing of results, ideas and experiments between the three groups, and Martin’s final discovery of a very unexpected step in the initiation of Mu replication, the joining of Mu DNA ends separated by 38 kB with the assistance of the host DNA gyrase.
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6
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West PT, Chanin RB, Bhatt AS. From genome structure to function: insights into structural variation in microbiology. Curr Opin Microbiol 2022; 69:102192. [PMID: 36030622 PMCID: PMC9783807 DOI: 10.1016/j.mib.2022.102192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/07/2022] [Accepted: 07/19/2022] [Indexed: 12/27/2022]
Abstract
Structural variation in bacterial genomes is an important evolutionary driver. Genomic rearrangements, such as inversions, duplications, and insertions, can regulate gene expression and promote niche adaptation. Importantly, many of these variations are reversible and preprogrammed to generate heterogeneity. While many tools have been developed to detect structural variation in eukaryotic genomes, variation in bacterial genomes and metagenomes remains understudied. However, recent advances in genome sequencing technology and the development of new bioinformatic pipelines hold promise in further understanding microbial genomics.
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Affiliation(s)
- Patrick T West
- Department of Genetics, Stanford University, 269 Campus Dr, CCSR 1155b, Stanford, 94305 CA, USA; Department of Medicine (Hematology, Blood and Marrow Transplantation), 269 Campus Dr, CCSR 1155b, Stanford, CA 94305, USA
| | - Rachael B Chanin
- Department of Genetics, Stanford University, 269 Campus Dr, CCSR 1155b, Stanford, 94305 CA, USA; Department of Medicine (Hematology, Blood and Marrow Transplantation), 269 Campus Dr, CCSR 1155b, Stanford, CA 94305, USA
| | - Ami S Bhatt
- Department of Genetics, Stanford University, 269 Campus Dr, CCSR 1155b, Stanford, 94305 CA, USA; Department of Medicine (Hematology, Blood and Marrow Transplantation), 269 Campus Dr, CCSR 1155b, Stanford, CA 94305, USA.
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7
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Ribeiro HG, Nilsson A, Melo LDR, Oliveira A. Analysis of intact prophages in genomes of Paenibacillus larvae: An important pathogen for bees. Front Microbiol 2022; 13:903861. [PMID: 35923395 PMCID: PMC9341999 DOI: 10.3389/fmicb.2022.903861] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
Paenibacillus larvae is the etiological agent of American Foulbrood (AFB), a highly contagious and worldwide spread bacterial disease that affects honeybee brood. In this study, all complete P. larvae genomes available on the NCBI database were analyzed in order to detect presence of prophages using the PHASTER software. A total of 55 intact prophages were identified in 11 P. larvae genomes (5.0 ± 2.3 per genome) and were further investigated for the presence of genes encoding relevant traits related to P. larvae. A closer look at the prophage genomes revealed the presence of several putative genes such as metabolic and antimicrobial resistance genes, toxins or bacteriocins, potentially influencing host performance. Some of the coding DNA sequences (CDS) were present in all ERIC-genotypes, while others were only found in a specific genotype. While CDS encoding toxins and antitoxins such as HicB and MazE were found in prophages of all bacterial genotypes, others, from the same category, were provided by prophages particularly to ERIC I (enhancin-like toxin), ERIC II (antitoxin SocA) and ERIC V strains (subunit of Panton-Valentine leukocidin system (PVL) LukF-PV). This is the first in-depth analysis of P. larvae prophages. It provides better knowledge on their impact in the evolution of virulence and fitness of P. larvae, by discovering new features assigned by the viruses.
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Affiliation(s)
- Henrique G. Ribeiro
- LIBRO – Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS – Associate Laboratory on Biotechnology and Bioengineering, and Electromechanical Systems, Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Anna Nilsson
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Luís D. R. Melo
- LIBRO – Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS – Associate Laboratory on Biotechnology and Bioengineering, and Electromechanical Systems, Centre of Biological Engineering, University of Minho, Braga, Portugal
- *Correspondence: Luís D. R. Melo,
| | - Ana Oliveira
- LIBRO – Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS – Associate Laboratory on Biotechnology and Bioengineering, and Electromechanical Systems, Centre of Biological Engineering, University of Minho, Braga, Portugal
- Ana Oliveira,
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Abstract
The recovery of DNA from viromes is a major obstacle in the use of long-read sequencing to study their genomes. For this reason, the use of cellular metagenomes (>0.2-μm size range) emerges as an interesting complementary tool, since they contain large amounts of naturally amplified viral genomes from prelytic replication. We have applied second-generation (Illumina NextSeq; short reads) and third-generation (PacBio Sequel II; long reads) sequencing to compare the diversity and features of the viral community in a marine sample obtained from offshore waters of the western Mediterranean. We found that a major wedge of the expected marine viral diversity was directly recovered by the raw PacBio circular consensus sequencing (CCS) reads. More than 30,000 sequences were detected only in this data set, with no homologues in the long- and short-read assembly, and ca. 26,000 had no homologues in the large data set of the Global Ocean Virome 2 (GOV2), highlighting the information gap created by the assembly bias. At the level of complete viral genomes, the performance was similar in both approaches. However, the hybrid long- and short-read assembly provided the longest average length of the sequences and improved the host assignment. Although no novel major clades of viruses were found, there was an increase in the intraclade genomic diversity recovered by long reads that produced an enriched assessment of the real diversity and allowed the discovery of novel genes with biotechnological potential (e.g., endolysin genes). IMPORTANCE We explored the vast genetic diversity of environmental viruses by using a combination of cellular metagenome (as opposed to virome) sequencing using high-fidelity long-read sequences (in this case, PacBio CCS). This approach resulted in the recovery of a representative sample of the viral population, and it performed better (more phage contigs, larger average contig size) than Illumina sequencing applied to the same sample. By this approach, the many biases of assembly are avoided, as the CCS reads recovers (typically around 5 kb) complete genes and even operons, resulting in a better discovery of the viral gene diversity based on viral marker proteins. Thus, biotechnologically promising genes, such as endolysin genes, can be very efficiently searched with this approach. In addition, hybrid assembly produces more complete and longer contigs, which is particularly important for studying little-known viral groups such as the nucleocytoplasmic large DNA viruses (NCLDV).
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9
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Li M, Wang C, Guo Q, Xu C, Xie Z, Tan J, Wu S, Wang P, Guo J, Fang Z, Zhu S, Duan L, Jiang X, Zhu H. More Positive or More Negative? Metagenomic Analysis Reveals Roles of Virome in Human Disease-Related Gut Microbiome. Front Cell Infect Microbiol 2022; 12:846063. [PMID: 35493727 PMCID: PMC9040671 DOI: 10.3389/fcimb.2022.846063] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/07/2022] [Indexed: 12/04/2022] Open
Abstract
Viruses are increasingly viewed as vital components of the human gut microbiota, while their roles in health and diseases remain incompletely understood. Here, we first sequenced and analyzed the 37 metagenomic and 18 host metabolomic samples related to irritable bowel syndrome (IBS) and found that some shifted viruses between IBS and controls covaried with shifted bacteria and metabolites. Especially, phages that infect beneficial lactic acid bacteria depleted in IBS covaried with their hosts. We also retrieved public whole-genome metagenomic datasets of another four diseases (type 2 diabetes, Crohn’s disease, colorectal cancer, and liver cirrhosis), totaling 438 samples including IBS, and performed uniform analysis of the gut viruses in diseases. By constructing disease-specific co-occurrence networks, we found viruses actively interacting with bacteria, negatively correlated with possible dysbiosis-related and inflammation-mediating bacteria, increasing the connectivity between bacteria modules, and contributing to the robustness of the networks. Functional enrichment analysis showed that phages interact with bacteria through predation or expressing genes involved in the transporter and secretion system, metabolic enzymes, etc. We further built a viral database to facilitate systematic functional classification and explored the functions of viral genes on interacting with bacteria. Our analyses provided a systematic view of the gut virome in the disease-related microbial community and suggested possible positive roles of viruses concerning gut health.
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Affiliation(s)
- Mo Li
- Peking University-Tsinghua University-National Institute of Biological Sciences (PTN) Joint Ph.D. Program, School of Life Sciences, Peking University, Beijing, China
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Chunhui Wang
- Peking University-Tsinghua University-National Institute of Biological Sciences (PTN) Joint Ph.D. Program, School of Life Sciences, Peking University, Beijing, China
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Qian Guo
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
- Center for Quantitative Biology, Peking University, Beijing, China
| | - Congmin Xu
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Zhongjie Xie
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Jie Tan
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
- Center for Quantitative Biology, Peking University, Beijing, China
| | - Shufang Wu
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
- Center for Quantitative Biology, Peking University, Beijing, China
| | - Peihong Wang
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Jinyuan Guo
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Zhencheng Fang
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
- Center for Quantitative Biology, Peking University, Beijing, China
| | - Shiwei Zhu
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Liping Duan
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Xiaoqing Jiang
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
- Center for Quantitative Biology, Peking University, Beijing, China
- *Correspondence: Huaiqiu Zhu, ; Xiaoqing Jiang,
| | - Huaiqiu Zhu
- Peking University-Tsinghua University-National Institute of Biological Sciences (PTN) Joint Ph.D. Program, School of Life Sciences, Peking University, Beijing, China
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
- Center for Quantitative Biology, Peking University, Beijing, China
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
- *Correspondence: Huaiqiu Zhu, ; Xiaoqing Jiang,
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10
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Gauthier CH, Abad L, Venbakkam AK, Malnak J, Russell D, Hatfull G. OUP accepted manuscript. Nucleic Acids Res 2022; 50:e75. [PMID: 35451479 PMCID: PMC9303363 DOI: 10.1093/nar/gkac273] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/11/2022] [Accepted: 04/06/2022] [Indexed: 11/26/2022] Open
Abstract
Advances in genome sequencing have produced hundreds of thousands of bacterial genome sequences, many of which have integrated prophages derived from temperate bacteriophages. These prophages play key roles by influencing bacterial metabolism, pathogenicity, antibiotic resistance, and defense against viral attack. However, they vary considerably even among related bacterial strains, and they are challenging to identify computationally and to extract precisely for comparative genomic analyses. Here, we describe DEPhT, a multimodal tool for prophage discovery and extraction. It has three run modes that facilitate rapid screening of large numbers of bacterial genomes, precise extraction of prophage sequences, and prophage annotation. DEPhT uses genomic architectural features that discriminate between phage and bacterial sequences for efficient prophage discovery, and targeted homology searches for precise prophage extraction. DEPhT is designed for prophage discovery in Mycobacterium genomes but can be adapted broadly to other bacteria. We deploy DEPhT to demonstrate that prophages are prevalent in Mycobacterium strains but are absent not only from the few well-characterized Mycobacterium tuberculosis strains, but also are absent from all ∼30 000 sequenced M. tuberculosis strains.
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Affiliation(s)
| | | | - Ananya K Venbakkam
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Julia Malnak
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Graham F Hatfull
- To whom correspondence should be addressed. Tel: +1 412 624 6975;
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11
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Olo Ndela E, Enault F, Toussaint A. Transposable Prophages in Leptospira: An Ancient, Now Diverse, Group Predominant in Causative Agents of Weil's Disease. Int J Mol Sci 2021; 22:13434. [PMID: 34948244 PMCID: PMC8705779 DOI: 10.3390/ijms222413434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/06/2021] [Accepted: 12/11/2021] [Indexed: 12/24/2022] Open
Abstract
The virome associated with the corkscrew shaped bacterium Leptospira, responsible for Weil's disease, is scarcely known, and genetic tools available for these bacteria remain limited. To reduce these two issues, potential transposable prophages were searched in Leptospiraceae genomes. The 236 predicted transposable prophages were particularly abundant in the most pathogenic leptospiral clade, being potentially involved in the acquisition of virulent traits. According to genomic similarities and phylogenies, these prophages are distantly related to known transposable phages and are organized into six groups, one of them encompassing prophages with unusual TA-TA ends. Interestingly, structural and transposition proteins reconstruct different relationships between groups, suggesting ancestral recombinations. Based on the baseplate phylogeny, two large clades emerge, with specific gene-contents and high sequence divergence reflecting their ancient origin. Despite their high divergence, the size and overall genomic organization of all prophages are very conserved, a testimony to the highly constrained nature of their genomes. Finally, similarities between these prophages and the three known non-transposable phages infecting L. biflexa, suggest gene transfer between different Caudovirales inside their leptospiral host, and the possibility to use some of the transposable prophages in that model strain.
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Affiliation(s)
- Eric Olo Ndela
- Laboratoire Microorganismes: Genome Environment (LMGE), Université Clermont Auvergne, CNRS, F-63000 Clermont-Ferrand, France;
| | - François Enault
- Laboratoire Microorganismes: Genome Environment (LMGE), Université Clermont Auvergne, CNRS, F-63000 Clermont-Ferrand, France;
| | - Ariane Toussaint
- Microbiologie Cellulaire et Moléculaire, Université Libre de Bruxelles, IBMM-DBM, 12 Rue des Professeurs Jeneer et Brachet, B-6041 Gosselies, Belgium;
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Characterization and Genomic Analysis of ɸSHP3, a New Transposable Bacteriophage Infecting Stenotrophomonas maltophilia. J Virol 2021; 95:JVI.00019-21. [PMID: 33536173 DOI: 10.1128/jvi.00019-21] [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] [Received: 01/07/2021] [Accepted: 01/29/2021] [Indexed: 01/21/2023] Open
Abstract
This study describes a novel transposable bacteriophage, ɸSHP3, continuously released by Stenotrophomonas maltophilia strain c31. Morphological observation and genomic analysis revealed that ɸSHP3 is a siphovirus with a 37,611-bp genome that encodes 51 putative proteins. Genomic comparisons indicated that ɸSHP3 is a B3-like transposable phage. Its genome configuration is similar to that of Pseudomonas phage B3, except for the DNA modification module. Similar to B3-like phages, the putative transposase B of ɸSHP3 is a homolog of the type two secretion component ExeA, which is proposed to serve as a potential virulence factor. Moreover, most proteins of ɸSHP3 have homologs in transposable phages, but only ɸSHP3 carries an RdgC-like protein encoded by gene 3, which exhibits exonuclease activity in vitro Two genes and their promoters coding for ɸSHP3 regulatory proteins were identified and appear to control the lytic-lysogenic switch. One of the proteins represses one promoter activity and confers immunity to ɸSHP3 superinfection in vivo The short regulatory region, in addition to the canonical bacterial promoter sequences, displays one LexA and two CpxR recognition sequences. This suggests that LexA and the CpxR/CpxA two-component system might be involved in the control of the ɸSHP3 genetic switch.IMPORTANCE S. maltophilia is an emerging global pathogenic bacterium that displays genetic diversity in both environmental and clinical strains. Transposable phages have long been known to improve the genetic diversity of bacterial strains by transposition. More than a dozen phages of S. maltophilia have been characterized. However, no transposable phage infecting S. maltophilia has been reported to date. Characterization of the first transposable phage, ɸSHP3, from S. maltophilia will contribute to our understanding of host-phage interactions and genetic diversity, especially the interchange of genetic materials among S. maltophilia.
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Laanto E, Ravantti JJ, Sundberg LR. Prophages and Past Prophage-Host Interactions Revealed by CRISPR Spacer Content in a Fish Pathogen. Microorganisms 2020; 8:E1919. [PMID: 33276599 PMCID: PMC7761591 DOI: 10.3390/microorganisms8121919] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/26/2020] [Accepted: 11/30/2020] [Indexed: 12/20/2022] Open
Abstract
The role of prophages in the evolution, diversification, or virulence of the fish pathogen Flavobacterium columnare has not been studied thus far. Here, we describe a functional spontaneously inducing prophage fF4 from the F. columnare type strain ATCC 23463, which is not detectable with commonly used prophage search methods. We show that this prophage type has a global distribution and is present in strains isolated from Finland, Thailand, Japan, and North America. The virions of fF4 are myoviruses with contractile tails and infect only bacterial strains originating from Northern Finland. The fF4 resembles transposable phages by similar genome organization and several gene orthologs. Additional bioinformatic analyses reveal several species in the phylum Bacteroidetes that host a similar type of putative prophage, including bacteria that are important animal and human pathogens. Furthermore, a survey of F. columnare Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) spacers indicate a shared evolutionary history between F. columnare strains and the fF4 phage, and another putative prophage in the F. columnare strain ATCC 49512, named p49512. First, CRISPR spacer content from the two CRISPR loci (types II-C and VI-B) of the fF4 lysogen F. columnare ATCC 23463 revealed a phage terminase protein-matching spacer in the VI-B locus. This spacer is also present in two Chinese F. columnare strains. Second, CRISPR analysis revealed four F. columnare strains that contain unique spacers targeting different regions of the putative prophage p49512 in the F. columnare strain ATCC 49512, despite the geographical distance or genomovar of the different strains. This suggests a common ancestry for the F. columnare prophages and different host strains.
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Affiliation(s)
- Elina Laanto
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland;
| | - Janne J. Ravantti
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland;
| | - Lotta-Riina Sundberg
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland;
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Wang H, Wang J, Li S, Ding G, Wang K, Zhuang T, Huang X, Wang X. Synergistic effect of UV/chlorine in bacterial inactivation, resistance gene removal, and gene conjugative transfer blocking. WATER RESEARCH 2020; 185:116290. [PMID: 32818733 DOI: 10.1016/j.watres.2020.116290] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/19/2020] [Accepted: 08/09/2020] [Indexed: 05/21/2023]
Abstract
Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) were investigated from effluent of two hospital and two municipal wastewater treatment plants (WWTPs) before and after disinfection. The results of network analysis showed that 8 genera were identified to be the main potential hosts of ARGs, including Mycobacterium, Ferruginibacter, Thermomonas, Morganella, Enterococcus, Bacteroides, Myroides and Romboutsia. The removal of ARGs and their possible bacterialhosts were synchronous and consistent by chlorine or ultraviolet (UV) disinfection in WWTPs. The mechanisms of ARB and ARGs removal, and conjugation transfer of RP4 plasmids by UV, chlorine and synergistic UV/chlorine disinfection was revealed. Compared to UV alone, ARB inactivation was improved 1.4 log and photoreactivation was overcomeeffectively by UV/chlorine combination (8 mJ/cm2, chlorine 2 mg/L). However, ARGs degradation was more difficult than ARB inactivation. Until UV dosage enhanced to 320 mJ/cm2, ARGs achieved 0.58-1.60 log removal. Meanwhile, when 2 mg/L of chlorine was combined with UV combination, ARGs removal enhanced 1-1.5 log. The synergistic effect of adding low-dose chlorine (1-2 mg/L) during UV radiation effectively improved ARB and ARGs removal simultaneously. The same synergistic effect also occurred in the horizontal gene transfer (HGT). Non-lethal dose chlorine (0.5 mg/L) increased the conjugation transfer frequency,which confirmed that the mRNA expression levels of type IV secretion system (T4SS) proteins vir4D, vir5B and vir10B were significantly enhanced. The risk of RP4 plasmid conjugation transfer was significantly reduced with UV/chlorine (UV ≥ 4 mJ/cm2, chlorine ≥ 1 mg/L). These findings may serve as valuable implications for assessing and controlling the risk of ARGs transfer and propagation in the environment.
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Affiliation(s)
- Haichao Wang
- Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, School of Civil Engineering, Beijing Jiaotong University, Beijing 100044, China
| | - Jin Wang
- Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, School of Civil Engineering, Beijing Jiaotong University, Beijing 100044, China.
| | - Shuming Li
- Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, School of Civil Engineering, Beijing Jiaotong University, Beijing 100044, China
| | - Guoyu Ding
- Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, School of Civil Engineering, Beijing Jiaotong University, Beijing 100044, China
| | - Kun Wang
- Jinan Environmental Research Academy, Jinan, Shandong 250102, China
| | - Tao Zhuang
- Jinan Environmental Research Academy, Jinan, Shandong 250102, China
| | - Xue Huang
- Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, School of Civil Engineering, Beijing Jiaotong University, Beijing 100044, China
| | - Xiaoyue Wang
- Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, School of Civil Engineering, Beijing Jiaotong University, Beijing 100044, China
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Wang M, Zeng Z, Jiang F, Zheng Y, Shen H, Macedo N, Sun Y, Sahin O, Li G. Role of enterotoxigenic Escherichia coli prophage in spreading antibiotic resistance in a porcine-derived environment. Environ Microbiol 2020; 22:4974-4984. [PMID: 32419209 DOI: 10.1111/1462-2920.15084] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 05/13/2020] [Indexed: 11/27/2022]
Abstract
Enterotoxigenic Escherichia coli (ETEC) cause acute secretory diarrhoea in pigs, posing a great economic loss to the swine industry. This study analysed the prevalence and genetic characteristics of prophages from 132 ETEC isolates from symptomatic pigs to determine their potential for spreading antibiotic resistance. A total of 1105 potential prophages were identified, and the distribution of the genome size showed three 'overlapping' trends. Similarity matrix comparison showed that prophages correlated with the ETEC lineage distribution, and further identification of these prophages corroborated the lineage specificity. In total, 1206 antibiotic resistance genes (ARGs) of 52 different categories were identified in 132 ETEC strains; among these, 2.65% (32/1206) of ARGs were found to be carried by prophages. Analysis of flanking sequences showed that almost all the ARGs could be grouped into two types: 'blaTEM-1B ' and 'classic class 1 integron (IntI1)'. They co-occurred with a strictly conserved recombinase and transposon Tn3 family but with a difference: the 'blaTEM-1B type' prophages exhibited a classic Tn2 transposon structure with 100% sequence identity, whereas the 'IntI1 type' co-occurred with the TnAs2 transposon with only 84% sequence identity. These results imply that ARGs might be pervasive in natural bacterial populations through transmission by transposable bacteriophages.
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Affiliation(s)
- Mianzhi Wang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Zhenling Zeng
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Fengwei Jiang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Ying Zheng
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Huigang Shen
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Nubia Macedo
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Yongxue Sun
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Orhan Sahin
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Ganwu Li
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA.,State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
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A Novel Inducible Prophage from Burkholderia Vietnamiensis G4 is Widely Distributed across the Species and Has Lytic Activity against Pathogenic Burkholderia. Viruses 2020; 12:v12060601. [PMID: 32486377 PMCID: PMC7354579 DOI: 10.3390/v12060601] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/30/2022] Open
Abstract
Burkholderia species have environmental, industrial and medical significance, and are important opportunistic pathogens in individuals with cystic fibrosis (CF). Using a combination of existing and newly determined genome sequences, this study investigated prophage carriage across the species B. vietnamiensis, and also isolated spontaneously inducible prophages from a reference strain, G4. Eighty-one B. vietnamiensis genomes were bioinformatically screened for prophages using PHASTER (Phage Search Tool Enhanced Release) and prophage regions were found to comprise up to 3.4% of total genetic material. Overall, 115 intact prophages were identified and there was evidence of polylysogeny in 32 strains. A novel, inducible Mu-like phage (vB_BvM-G4P1) was isolated from B. vietnamiensis G4 that had lytic activity against strains of five Burkholderia species prevalent in CF infections, including the Boston epidemic B. dolosa strain SLC6. The cognate prophage to vB_BvM-G4P1 was identified in the lysogen genome and was almost identical (>93.5% tblastx identity) to prophages found in 13 other B. vietnamiensis strains (17% of the strain collection). Phylogenomic analysis determined that the G4P1-like prophages were widely distributed across the population structure of B. vietnamiensis. This study highlights how genomic characterization of Burkholderia prophages can lead to the discovery of novel bacteriophages with potential therapeutic or biotechnological applications.
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de Jonge PA, von Meijenfeldt FAB, van Rooijen LE, Brouns SJJ, Dutilh BE. Evolution of BACON Domain Tandem Repeats in crAssphage and Novel Gut Bacteriophage Lineages. Viruses 2019; 11:v11121085. [PMID: 31766550 PMCID: PMC6949934 DOI: 10.3390/v11121085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/17/2019] [Accepted: 11/19/2019] [Indexed: 12/12/2022] Open
Abstract
The human gut contains an expanse of largely unstudied bacteriophages. Among the most common are crAss-like phages, which were predicted to infect Bacteriodetes hosts. CrAssphage, the first crAss-like phage to be discovered, contains a protein encoding a Bacteroides-associated carbohydrate-binding often N-terminal (BACON) domain tandem repeat. Because protein domain tandem repeats are often hotspots of evolution, BACON domains may provide insight into the evolution of crAss-like phages. Here, we studied the biodiversity and evolution of BACON domains in bacteriophages by analysing over 2 million viral contigs. We found a high biodiversity of BACON in seven gut phage lineages, including five known crAss-like phage lineages and two novel gut phage lineages that are distantly related to crAss-like phages. In three BACON-containing phage lineages, we found that BACON domain tandem repeats were associated with phage tail proteins, suggestive of a possible role of these repeats in host binding. In contrast, individual BACON domains that did not occur in tandem were not found in the proximity of tail proteins. In two lineages, tail-associated BACON domain tandem repeats evolved largely through horizontal transfer of separate domains. In the third lineage that includes the prototypical crAssphage, the tandem repeats arose from several sequential domain duplications, resulting in a characteristic tandem array that is distinct from bacterial BACON domains. We conclude that phage tail-associated BACON domain tandem repeats have evolved in at least two independent cases in gut bacteriophages, including in the widespread gut phage crAssphage.
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Affiliation(s)
- Patrick A. de Jonge
- Theoretical Biology and Bioinformatics, Science4 Life, Utrecht University, 3584 CH Utrecht, The Netherlands; (P.A.d.J.); (F.A.B.v.M.); (L.E.v.R.)
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands;
| | - F. A. Bastiaan von Meijenfeldt
- Theoretical Biology and Bioinformatics, Science4 Life, Utrecht University, 3584 CH Utrecht, The Netherlands; (P.A.d.J.); (F.A.B.v.M.); (L.E.v.R.)
| | - Laura E. van Rooijen
- Theoretical Biology and Bioinformatics, Science4 Life, Utrecht University, 3584 CH Utrecht, The Netherlands; (P.A.d.J.); (F.A.B.v.M.); (L.E.v.R.)
| | - Stan J. J. Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands;
| | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Science4 Life, Utrecht University, 3584 CH Utrecht, The Netherlands; (P.A.d.J.); (F.A.B.v.M.); (L.E.v.R.)
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
- Correspondence:
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O'Brien S, Kümmerli R, Paterson S, Winstanley C, Brockhurst MA. Transposable temperate phages promote the evolution of divergent social strategies in Pseudomonas aeruginosa populations. Proc Biol Sci 2019; 286:20191794. [PMID: 31594506 DOI: 10.1098/rspb.2019.1794] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Transposable temperate phages randomly insert into bacterial genomes, providing increased supply and altered spectra of mutations available to selection, thus opening alternative evolutionary trajectories. Transposable phages accelerate bacterial adaptation to new environments, but their effect on adaptation to the social environment is unclear. Using experimental evolution of Pseudomonas aeruginosa in iron-limited and iron-rich environments, where the cost of producing cooperative iron-chelating siderophores is high and low, respectively, we show that transposable phages promote divergence into extreme siderophore production phenotypes. Iron-limited populations with transposable phages evolved siderophore overproducing clones alongside siderophore non-producing cheats. Low siderophore production was associated with parallel mutations in pvd genes, encoding pyoverdine biosynthesis, and pqs genes, encoding quinolone signalling, while high siderophore production was associated with parallel mutations in phenazine-associated gene clusters. Notably, some of these parallel mutations were caused by phage insertional inactivation. These data suggest that transposable phages, which are widespread in microbial communities, can mediate the evolutionary divergence of social strategies.
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Affiliation(s)
- Siobhán O'Brien
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Rolf Kümmerli
- Department of Plant and Microbial Biology, University of Zürich, Switzerland
| | - Steve Paterson
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Craig Winstanley
- Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK
| | - Michael A Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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20
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Grüll MP, Mulligan ME, Lang AS. Small extracellular particles with big potential for horizontal gene transfer: membrane vesicles and gene transfer agents. FEMS Microbiol Lett 2019; 365:5067299. [PMID: 30085064 DOI: 10.1093/femsle/fny192] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 08/04/2018] [Indexed: 12/18/2022] Open
Abstract
Bacteria are known to release different types of particles that serve various purposes such as the processing of metabolites, communication, and the transfer of genetic material. One of the most interesting aspects of the production of such particles is the biogenesis and trafficking of complex particles that can carry DNA, RNA, proteins or toxins into the surrounding environment to aid in bacterial survival or lead to gene transfer. Two important bacterial extracellular complexes are membrane vesicles and gene transfer agents. In this review, we will discuss the production, contents and functions of these two types of particles as related to their abilities to facilitate horizontal gene transfer.
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Affiliation(s)
| | - M E Mulligan
- Biochemistry, Memorial University of Newfoundland, St John's, NL, Canada
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21
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Diversity patterns of bacteriophages infecting Aggregatibacter and Haemophilus species across clades and niches. ISME JOURNAL 2019; 13:2500-2522. [PMID: 31201356 PMCID: PMC6776037 DOI: 10.1038/s41396-019-0450-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/07/2019] [Accepted: 05/26/2019] [Indexed: 12/19/2022]
Abstract
Aggregatibacter and Haemophilus species are relevant human commensals and opportunistic pathogens. Consequently, their bacteriophages may have significant impact on human microbial ecology and pathologies. Our aim was to reveal the prevalence and diversity of bacteriophages infecting Aggregatibacter and Haemophilus species that colonize the human body. Genome mining with comparative genomics, screening of clinical isolates, and profiling of metagenomes allowed characterization of 346 phages grouped in 52 clusters and 18 superclusters. Less than 10% of the identified phage clusters were represented by previously characterized phages. Prophage diversity patterns varied significantly for different phage types, host clades, and environmental niches. A more diverse phage community lysogenizes Haemophilus influenzae and Haemophilus parainfluenzae strains than Aggregatibacter actinomycetemcomitans and “Haemophilus ducreyi”. Co-infections occurred more often in “H. ducreyi”. Phages from Aggregatibacter actinomycetemcomitans preferably lysogenized strains of specific serotype. Prophage patterns shared by subspecies clades of different bacterial species suggest similar ecoevolutionary drivers. Changes in frequencies of DNA uptake signal sequences and guanine–cytosine content reflect phage-host long-term coevolution. Aggregatibacter and Haemophilus phages were prevalent at multiple oral sites. Together, these findings should help exploring the ecoevolutionary forces shaping virus-host interactions in the human microbiome. Putative lytic phages, especially phiKZ-like, may provide new therapeutic options.
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Abstract
Transposable elements (TEs) are ubiquitous in both prokaryotes and eukaryotes, and the dynamic character of their interaction with host genomes brings about numerous evolutionary innovations and shapes genome structure and function in a multitude of ways. In traditional classification systems, TEs are often being depicted in simplistic ways, based primarily on the key enzymes required for transposition, such as transposases/recombinases and reverse transcriptases. Recent progress in whole-genome sequencing and long-read assembly, combined with expansion of the familiar range of model organisms, resulted in identification of unprecedentedly long transposable units spanning dozens or even hundreds of kilobases, initially in prokaryotic and more recently in eukaryotic systems. Here, we focus on such oversized eukaryotic TEs, including retrotransposons and DNA transposons, outline their complex and often combinatorial nature and closely intertwined relationship with viruses, and discuss their potential for participating in transfer of long stretches of DNA in eukaryotes.
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Affiliation(s)
- Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts
- Corresponding author: E-mail:
| | - Irina A Yushenova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts
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23
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Moreno-Gallego JL, Chou SP, Di Rienzi SC, Goodrich JK, Spector TD, Bell JT, Youngblut ND, Hewson I, Reyes A, Ley RE. Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins. Cell Host Microbe 2019; 25:261-272.e5. [PMID: 30763537 PMCID: PMC6411085 DOI: 10.1016/j.chom.2019.01.019] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/31/2018] [Accepted: 01/24/2019] [Indexed: 01/01/2023]
Abstract
The virome is one of the most variable components of the human gut microbiome. Within twin pairs, viromes have been shown to be similar for infants, but not for adults, indicating that as twins age and their environments and microbiomes diverge, so do their viromes. The degree to which the microbiome drives the vast virome diversity is unclear. Here, we examine the relationship between microbiome and virome diversity in 21 adult monozygotic twin pairs selected for high or low microbiome concordance. Viromes derived from virus-like particles are unique to each individual, are dominated by Caudovirales and Microviridae, and exhibit a small core that includes crAssphage. Microbiome-discordant twins display more dissimilar viromes compared to microbiome-concordant twins, and the richer the microbiomes, the richer the viromes. These patterns are driven by bacteriophages, not eukaryotic viruses. Collectively, these observations support a strong role of the microbiome in patterning for the virome.
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Affiliation(s)
- J Leonardo Moreno-Gallego
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Shao-Pei Chou
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Sara C Di Rienzi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Julia K Goodrich
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Nicholas D Youngblut
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia; Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63108, USA
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany.
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Vale FF, Lehours P. Relating Phage Genomes to Helicobacter pylori Population Structure: General Steps Using Whole-Genome Sequencing Data. Int J Mol Sci 2018; 19:ijms19071831. [PMID: 29933614 PMCID: PMC6073503 DOI: 10.3390/ijms19071831] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/30/2018] [Accepted: 06/15/2018] [Indexed: 12/19/2022] Open
Abstract
The review uses the Helicobacter pylori, the gastric bacterium that colonizes the human stomach, to address how to obtain information from bacterial genomes about prophage biology. In a time of continuous growing number of genomes available, this review provides tools to explore genomes for prophage presence, or other mobile genetic elements and virulence factors. The review starts by covering the genetic diversity of H. pylori and then moves to the biologic basis and the bioinformatics approaches used for studding the H. pylori phage biology from their genomes and how this is related with the bacterial population structure. Aspects concerning H. pylori prophage biology, evolution and phylogeography are discussed.
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Affiliation(s)
- Filipa F Vale
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal.
| | - Philippe Lehours
- Laboratoire de Bacteriologie, Centre National de Référence des Campylobacters et Hélicobacters, Place Amélie Raba Léon, 33076 Bordeaux, France.
- INSERM U1053-UMR Bordeaux Research in Translational Oncology, BaRITOn, 33000 Bordeaux, France.
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Vergnaud G, Midoux C, Blouin Y, Bourkaltseva M, Krylov V, Pourcel C. Transposition Behavior Revealed by High-Resolution Description of Pseudomonas Aeruginosa Saltovirus Integration Sites. Viruses 2018; 10:v10050245. [PMID: 29735891 PMCID: PMC5977238 DOI: 10.3390/v10050245] [Citation(s) in RCA: 3] [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: 04/09/2018] [Revised: 04/27/2018] [Accepted: 05/04/2018] [Indexed: 01/08/2023] Open
Abstract
Transposable phages, also called saltoviruses, of which the Escherichia coli phage Mu is the reference, are temperate phages that multiply their genome through replicative transposition at multiple sites in their host chromosome. The viral genome is packaged together with host DNA at both ends. In the present work, genome sequencing of three Pseudomonas aeruginosa transposable phages, HW12, 2P1, and Ab30, incidentally gave us access to the location of thousands of replicative integration sites and revealed the existence of a variable number of hotspots. Taking advantage of deep sequencing, we then designed an experiment to study 13,000,000 transposon integration sites of bacteriophage Ab30. The investigation revealed the presence of 42 transposition hotspots adjacent to bacterial interspersed mosaic elements (BIME) accounting for 5% of all transposition sites. The rest of the sites appeared widely distributed with the exception of coldspots associated with low G-C content segments, including the putative O-antigen biosynthesis cluster. Surprisingly, 0.4% of the transposition events occurred in a copy of the phage genome itself, indicating that the previously described immunity against such events is slightly leaky. This observation allowed drawing an image of the phage chromosome supercoiling into four loops.
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Affiliation(s)
- Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette CEDEX, France.
| | - Cédric Midoux
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette CEDEX, France.
| | - Yann Blouin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette CEDEX, France.
| | - Maria Bourkaltseva
- I. I. Mechnikov Research Institute for Vaccines & Sera, Moscow 105064, Russia.
| | - Victor Krylov
- I. I. Mechnikov Research Institute for Vaccines & Sera, Moscow 105064, Russia.
| | - Christine Pourcel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette CEDEX, France.
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Toussaint A, Van Gijsegem F. Extension of the transposable bacterial virus family: two genomic organisations among phages and prophages with a Tn552-related transposase. Res Microbiol 2017; 169:495-499. [PMID: 29158161 DOI: 10.1016/j.resmic.2017.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 10/26/2017] [Accepted: 11/02/2017] [Indexed: 11/28/2022]
Abstract
Mu-like transposable phages and prophages have been isolated from, or predicted, in a wide range of bacterial phyla. However, related B3-like transposable phages, which differ in their genome organisation and the DDE transposase and transposition activator they code for have thus far been restricted to a very limited set of hosts. Through sequence similarity searches, we have now expanded the number of predicted B3-like prophages and uncovered a third genomic organisation. These new genomes, although only prophages, further illustrate the previously reported mosaicism existing in the proposed "Saltoviridae" family of Caudovirales, and further support the proposal to move morphology criteria (contractile vs. flexible or short tail, i.e. Myo-vs. Sipho- or Podoviridae) from the family to the subfamily level in the taxonomic classification of the Caudovirales.
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Affiliation(s)
- Ariane Toussaint
- Université Libre de Bruxelles, Génétique et Physiologie Bactérienne (LGPB), 12 Rue des Professeurs Jeener et Brachet, 6041 Charleroi Gosselies, Belgium.
| | - Frédérique Van Gijsegem
- Sorbonne Universités, UPMC Univ Paris 06, Diderot Univ Paris 07, UPEC Univ Paris 12, CNRS, INRA, IRD, Institut d'Ecologie et des Sciences de l'Environnement de Paris (UMR7618), 4 Place Jussieu, 75252 Paris Cedex 05, France
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Harrison E, Brockhurst MA. Ecological and Evolutionary Benefits of Temperate Phage: What Does or Doesn't Kill You Makes You Stronger. Bioessays 2017; 39. [PMID: 28983932 DOI: 10.1002/bies.201700112] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/30/2017] [Indexed: 01/04/2023]
Abstract
Infection by a temperate phage can lead to death of the bacterial cell, but sometimes these phages integrate into the bacterial chromosome, offering the potential for a more long-lasting relationship to be established. Here we define three major ecological and evolutionary benefits of temperate phage for bacteria: as agents of horizontal gene transfer (HGT), as sources of genetic variation for evolutionary innovation, and as weapons of bacterial competition. We suggest that a coevolutionary perspective is required to understand the roles of temperate phages in bacterial populations.
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Affiliation(s)
- Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Arthur Willis Environment Centre, Sheffield, UK
| | - Michael A Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Sheffield, UK
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