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Cook R, Brown N, Rihtman B, Michniewski S, Redgwell T, Clokie M, Stekel DJ, Chen Y, Scanlan DJ, Hobman JL, Nelson A, Jones MA, Smith D, Millard A. The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies. Microb Genom 2024; 10:001198. [PMID: 38376377 PMCID: PMC10926689 DOI: 10.1099/mgen.0.001198] [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: 02/25/2023] [Accepted: 01/25/2024] [Indexed: 02/21/2024] Open
Abstract
Viral metagenomics has fuelled a rapid change in our understanding of global viral diversity and ecology. Long-read sequencing and hybrid assembly approaches that combine long- and short-read technologies are now being widely implemented in bacterial genomics and metagenomics. However, the use of long-read sequencing to investigate viral communities is still in its infancy. While Nanopore and PacBio technologies have been applied to viral metagenomics, it is not known to what extent different technologies will impact the reconstruction of the viral community. Thus, we constructed a mock bacteriophage community of previously sequenced phage genomes and sequenced them using Illumina, Nanopore and PacBio sequencing technologies and tested a number of different assembly approaches. When using a single sequencing technology, Illumina assemblies were the best at recovering phage genomes. Nanopore- and PacBio-only assemblies performed poorly in comparison to Illumina in both genome recovery and error rates, which both varied with the assembler used. The best Nanopore assembly had errors that manifested as SNPs and INDELs at frequencies 41 and 157 % higher than found in Illumina only assemblies, respectively. While the best PacBio assemblies had SNPs at frequencies 12 and 78 % higher than found in Illumina-only assemblies, respectively. Despite high-read coverage, long-read-only assemblies recovered a maximum of one complete genome from any assembly, unless reads were down-sampled prior to assembly. Overall the best approach was assembly by a combination of Illumina and Nanopore reads, which reduced error rates to levels comparable with short-read-only assemblies. When using a single technology, Illumina only was the best approach. The differences in genome recovery and error rates between technology and assembler had downstream impacts on gene prediction, viral prediction, and subsequent estimates of diversity within a sample. These findings will provide a starting point for others in the choice of reads and assembly algorithms for the analysis of viromes.
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Affiliation(s)
- Ryan Cook
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
| | - Nathan Brown
- Centre for Phage Research, Dept Genetics and Genome Biology, University of Leicester, University Road, Leicester, Leicestershire, LE1 7RH, UK
| | - Branko Rihtman
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Slawomir Michniewski
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Tamsin Redgwell
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820, Gentofte, Denmark
| | - Martha Clokie
- Centre for Phage Research, Dept Genetics and Genome Biology, University of Leicester, University Road, Leicester, Leicestershire, LE1 7RH, UK
| | - Dov J. Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
- Department of Mathematics and Applied Mathematics, University of Johannesburg, Rossmore 2029, South Africa
| | - Yin Chen
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - David J. Scanlan
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Jon L. Hobman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
| | - Andrew Nelson
- Faculty of Health and Life Sciences, University of Northumbria, Newcastle upon Tyne, NE1 8ST, UK
| | - Michael A. Jones
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
| | - Darren Smith
- Faculty of Health and Life Sciences, University of Northumbria, Newcastle upon Tyne, NE1 8ST, UK
| | - Andrew Millard
- Centre for Phage Research, Dept Genetics and Genome Biology, University of Leicester, University Road, Leicester, Leicestershire, LE1 7RH, UK
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Kar P, Das TK, Ghosh S, Pradhan S, Chakrabarti S, Mondal KC, Ghosh K. Characterization of a Vibrio-infecting bacteriophage, VPMCC5, and proposal of its incorporation as a new genus in the Zobellviridae family. Virus Res 2022; 321:198904. [PMID: 36044930 DOI: 10.1016/j.virusres.2022.198904] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/24/2022]
Abstract
Vibrio harveyi is a Gram-negative pathogenic bacterium responsible for luminous vibriosis in shrimp and causes mass mortality of shrimp that leads to economic losses. Considering the emergence of multi-drug resistant bacteria, there is always a need for an alternative to antibiotics. In this study, we have aimed to characterize the Vibrio-infecting bacteriophage VPMCC5 (isolated from an environmental sample by using V. harveyi S2A) and evaluate its efficacy in controlling the pathogen. The bacteriophage exhibited an isometric head and short non-contractile tail. The latent period of the bacteriophage was 10 min and the burst size was 20. The genome of the bacteriophage was 48938 bp long with 40.7 mol% G+C content. A total of 71 ORFs were identified and no tRNA and antibiotic-associated genes were detected. Comparative genomic analyses (CLANS, dot plot, progressiveMauve alignment, and phylogenetic tree) strongly suggest that the bacteriophage VPMCC5 might be a new genus in the family of Zobellviridae. A distinguishing feature of this bacteriophage among the other reported Vibrio-infecting bacteriophages is the presence of putative alginate lyase family protein-coding open reading frame. The bacteriophage was found to be surviving at pH 3-9 and in a wide range of temperatures (4-45 ᵒC). In liquid culture inhibition, the bacteriophage could completely lyse the host bacteria after 3 h. This bacteriophage might be used as a biocontrol agent in the extreme environment of shrimp culture.
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Affiliation(s)
- Priyanka Kar
- Department of Biological Sciences, Midnapore City College, Midnapore, West Bengal 721129, India
| | - Tridip Kr Das
- Department of Biological Sciences, Midnapore City College, Midnapore, West Bengal 721129, India
| | - Smita Ghosh
- Department of Biological Sciences, Midnapore City College, Midnapore, West Bengal 721129, India
| | - Shrabani Pradhan
- Department of Biological Sciences, Midnapore City College, Midnapore, West Bengal 721129, India
| | - Sudipta Chakrabarti
- Department of Biological Sciences, Midnapore City College, Midnapore, West Bengal 721129, India
| | - Keshab Ch Mondal
- Department of Microbiology, Vidyasagar University, West Bengal, India
| | - Kuntal Ghosh
- Department of Biological Sciences, Midnapore City College, Midnapore, West Bengal 721129, India.
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Martinez J, Ant TH, Murdochy SM, Tong L, da Silva Filipe A, Sinkins SP. Genome sequencing and comparative analysis of Wolbachia strain wAlbA reveals Wolbachia-associated plasmids are common. PLoS Genet 2022; 18:e1010406. [PMID: 36121852 PMCID: PMC9560607 DOI: 10.1371/journal.pgen.1010406] [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: 07/04/2022] [Revised: 10/13/2022] [Accepted: 09/02/2022] [Indexed: 11/18/2022] Open
Abstract
Wolbachia are widespread maternally-transmitted bacteria of arthropods that often spread by manipulating their host's reproduction through cytoplasmic incompatibility (CI). Their invasive potential is currently being harnessed in field trials aiming to control mosquito-borne diseases. Wolbachia genomes commonly harbour prophage regions encoding the cif genes which confer their ability to induce CI. Recently, a plasmid-like element was discovered in wPip, a Wolbachia strain infecting Culex mosquitoes; however, it is unclear how common such extra-chromosomal elements are in Wolbachia. Here we sequenced the complete genome of wAlbA, a strain of the symbiont found in Aedes albopictus, after eliminating the co-infecting and higher density wAlbB strain that previously made sequencing of wAlbA challenging. We show that wAlbA is associated with two new plasmids and identified additional Wolbachia plasmids and related chromosomal islands in over 20% of publicly available Wolbachia genome datasets. These plasmids encode a variety of accessory genes, including several phage-like DNA packaging genes as well as genes potentially contributing to host-symbiont interactions. In particular, we recovered divergent homologues of the cif genes in both Wolbachia- and Rickettsia-associated plasmids. Our results indicate that plasmids are common in Wolbachia and raise fundamental questions around their role in symbiosis. In addition, our comparative analysis provides useful information for the future development of genetic tools to manipulate and study Wolbachia symbionts.
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Affiliation(s)
- Julien Martinez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Thomas H. Ant
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Shivan M. Murdochy
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Steven P. Sinkins
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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Djihinto OY, Medjigbodo AA, Gangbadja ARA, Saizonou HM, Lagnika HO, Nanmede D, Djossou L, Bohounton R, Sovegnon PM, Fanou MJ, Agonhossou R, Akoton R, Mousse W, Djogbénou LS. Malaria-Transmitting Vectors Microbiota: Overview and Interactions With Anopheles Mosquito Biology. Front Microbiol 2022; 13:891573. [PMID: 35668761 PMCID: PMC9164165 DOI: 10.3389/fmicb.2022.891573] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/04/2022] [Indexed: 11/20/2022] Open
Abstract
Malaria remains a vector-borne infectious disease that is still a major public health concern worldwide, especially in tropical regions. Malaria is caused by a protozoan parasite of the genus Plasmodium and transmitted through the bite of infected female Anopheles mosquitoes. The control interventions targeting mosquito vectors have achieved significant success during the last two decades and rely mainly on the use of chemical insecticides through the insecticide-treated nets (ITNs) and indoor residual spraying (IRS). Unfortunately, resistance to conventional insecticides currently being used in public health is spreading in the natural mosquito populations, hampering the long-term success of the current vector control strategies. Thus, to achieve the goal of malaria elimination, it appears necessary to improve vector control approaches through the development of novel environment-friendly tools. Mosquito microbiota has by now given rise to the expansion of innovative control tools, such as the use of endosymbionts to target insect vectors, known as "symbiotic control." In this review, we will present the viral, fungal and bacterial diversity of Anopheles mosquitoes, including the bacteriophages. This review discusses the likely interactions between the vector microbiota and its fitness and resistance to insecticides.
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Affiliation(s)
- Oswald Y. Djihinto
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Adandé A. Medjigbodo
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Albert R. A. Gangbadja
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Helga M. Saizonou
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Hamirath O. Lagnika
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Dyane Nanmede
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Laurette Djossou
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Roméo Bohounton
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Pierre Marie Sovegnon
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Marie-Joel Fanou
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Romuald Agonhossou
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Romaric Akoton
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Wassiyath Mousse
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Luc S. Djogbénou
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
- Regional Institute of Public Health, University of Abomey-Calavi, Ouidah, Benin
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Fallon AM. Muramidase, nuclease, or hypothetical protein genes intervene between paired genes encoding DNA packaging terminase and portal proteins in Wolbachia phages and prophages. Virus Genes 2022; 58:327-349. [PMID: 35538383 DOI: 10.1007/s11262-022-01907-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/11/2022] [Indexed: 12/25/2022]
Abstract
Genomes of the obligate intracellular alpha proteobacterium Wolbachia pipientis often encode prophage-like regions, and in a few cases, purified particles have been recovered. Because the structure of a conserved WO phage genome has been difficult to establish, we examined paired terminase and portal genes in Wolbachia phages and prophages, relative to those encoded by the gene transfer agent RcGTA from the free-living alpha proteobacterium Rhodobacter capsulatus. Terminase and portal proteins from Wolbachia have higher similarity to orthologs encoded by RcGTA than to orthologs encoded by bacteriophage lambda. In lambdoid phages, these proteins play key roles in assembly of mature phage particles, while in less well-studied gene transfer agents, terminase and portal proteins package random fragments of bacterial DNA, which could confound elucidation of WO phage genomes. In WO phages and prophages, terminase genes followed by a short gpW gene may be separated from the downstream portal gene by open-reading frames encoding a GH_25 hydrolase/muramidase, a PD-(D/E)XK nuclease, a hypothetical protein and/or a RelE/ParE toxin-antitoxin module. These aspects of gene organization, coupled with evidence for a low, non-inducible yield of WO phages, and the small size of WO phage particles described in the literature raise the possibility that Wolbachia prophage regions participate in processes that extend beyond conventional bacteriophage lysogeny and lytic replication. These intervening genes, and their possible relation to functions associated with GTAs, may contribute to variability among WO phage genomes recovered from physical particles and impact the ability of WO phages to act as transducing agents.
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Affiliation(s)
- Ann M Fallon
- Department of Entomology, University of Minnesota, 1980 Folwell Ave, St. Paul, MN, 55108, USA.
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Quek S, Cerdeira L, Jeffries CL, Tomlinson S, Walker T, Hughes GL, Heinz E. Wolbachia endosymbionts in two Anopheles species indicates independent acquisitions and lack of prophage elements. Microb Genom 2022; 8. [PMID: 35446252 PMCID: PMC9453072 DOI: 10.1099/mgen.0.000805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Wolbachia is a genus of obligate bacterial endosymbionts that infect a diverse range of arthropod species as well as filarial nematodes, with its single described species, Wolbachia pipientis, divided into several ‘supergroups’ based on multilocus sequence typing. Wolbachia strains in mosquitoes have been shown to inhibit the transmission of human pathogens, including Plasmodium malaria parasites and arboviruses. Despite their large host range, Wolbachia strains within the major malaria vectors of the Anopheles gambiae and Anopheles funestus complexes appear at low density, established solely on PCR-based methods. Questions have been raised as to whether this represents a true endosymbiotic relationship. However, recent definitive evidence for two distinct, high-density strains of supergroup B Wolbachia within Anopheles demeilloni and Anopheles moucheti has opened exciting possibilities to explore naturally occurring Wolbachia endosymbionts in Anopheles for biocontrol strategies to block Plasmodium transmission. Here, we utilize genomic analyses to demonstrate that both Wolbachia strains have retained all key metabolic and transport pathways despite their smaller genome size, with this reduction potentially attributable to degenerated prophage regions. Even with this reduction, we confirmed the presence of cytoplasmic incompatibility (CI) factor genes within both strains, with wAnD maintaining intact copies of these genes while the cifB gene was interrupted in wAnM, so functional analysis is required to determine whether wAnM can induce CI. Additionally, phylogenetic analysis indicates that these Wolbachia strains may have been introduced into these two Anopheles species via horizontal transmission events, rather than by ancestral acquisition and subsequent loss events in the Anopheles gambiae species complex. These are the first Wolbachia genomes, to our knowledge, that enable us to study the relationship between natural strain Plasmodium malaria parasites and their anopheline hosts.
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Affiliation(s)
- Shannon Quek
- Department of Tropical Disease Biology, Centre for Neglected Tropical Diseases, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Louise Cerdeira
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Claire L Jeffries
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Sean Tomlinson
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Thomas Walker
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Grant L Hughes
- Department of Tropical Disease Biology, Centre for Neglected Tropical Diseases, Liverpool School of Tropical Medicine, Liverpool, UK.,Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Eva Heinz
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK.,Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
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