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Sundaramoorthy NS, Thothathri S, Bhaskaran M, GaneshPrasad A, Nagarajan S. Phages from Ganges River curtail in vitro biofilms and planktonic growth of drug resistant Klebsiella pneumoniae in a zebrafish infection model. AMB Express 2021; 11:27. [PMID: 33587215 PMCID: PMC7884498 DOI: 10.1186/s13568-021-01181-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/11/2021] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages are a promising alternative for curtailing infections caused by multi drug resistant (MDR) bacteria. The objective of the present study is to evaluate phage populations from water bodies to inhibit planktonic and biofilm mode of growth of drug resistant Klebsiella pneumoniae in vitro and curtail planktonic growth in vivo in a zebrafish model. Phage specific to K. pneumoniae (MTCC 432) was isolated from Ganges River (designated as KpG). One-step growth curve, in vitro time kill curve study and in vivo infection model were performed to evaluate the ability of phage to curtail planktonic growth. Crystal violet assay and colony biofilm assay were performed to determine the action of phages on biofilms. KpG phages had a greater burst size, better bactericidal potential and enhanced inhibitory effect against biofilms formed at liquid air and solid air interfaces. In vitro time kill assay showed a 3 log decline and a 6 log decline in K. pneumoniae colony counts, when phages were administered individually and in combination with streptomycin, respectively. In vivo injection of KpG phages revealed that it did not pose any toxicity to zebrafish as evidenced by liver/brain enzyme profiles and by histopathological analysis. The muscle tissue of zebrafish, infected with K. pneumoniae and treated with KpG phages alone and in combination with streptomycin showed a significant 77.7% and 97.2% decline in CFU/ml, respectively, relative to untreated control. Our study reveals that KpG phages has the potential to curtail plantonic and biofilm mode of growth in higher animal models.
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2
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Teixeira H, Sousa AL, Azevedo AS. Bioinformatic Tools and Guidelines for the Design of Fluorescence In Situ Hybridization Probes. Methods Mol Biol 2021; 2246:35-50. [PMID: 33576981 DOI: 10.1007/978-1-0716-1115-9_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Fluorescence in situ hybridization (FISH) is a well-established technique that allows the detection of microorganisms in diverse types of samples (e.g., clinical, food, environmental samples, and biofilm communities). The FISH probe design is an essential step in this technique. For this, two strategies can be used, the manual form based on multiple sequence alignment to identify conserved regions and programs/software specifically developed for the selection of the sequence of the probe. Additionally, databases/software for the theoretical evaluation of the probes in terms of specificity, sensitivity, and thermodynamic parameters (melting temperature and Gibbs free energy change) are used. The purpose of this chapter is to describe the essential steps and guidelines for the design of FISH probes (e.g., DNA and Nucleic Acid Mimic (NAM) probes), and its theoretical evaluation through the application of diverse bioinformatic tools.
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Affiliation(s)
- Helena Teixeira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Ana L Sousa
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal.,INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Lugar da Madalena, Vairão, Vila do Conde, Portugal
| | - Andreia S Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal. .,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal. .,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal. .,CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal.
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3
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Newase SK, Gupta A, Dastager SG, Kapadnis BP, Shashidhar R. Development and evaluation of taxon-specific primers for the selected Caudovirales taxa. Virus Res 2019; 263:184-188. [PMID: 30769122 DOI: 10.1016/j.virusres.2019.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 01/16/2019] [Accepted: 02/11/2019] [Indexed: 11/30/2022]
Abstract
The phage taxonomy is primarily based on the morphology derived from Transmission Electron Microscopic (TEM) studies. TEM based characterization is authentic and accepted by scientific community. However, TEM based identification is expensive and time consuming. After the phage isolation, before analysis TEM, a DNA based rapid method could be introduced. The DNA based method could dramatically reduce the number of samples analyzed by TEM and thereby increase the speed and reduce the cost of identification. In the present work, four environmental phage isolates were identified based on TEM studies and genome size. The identification of these four phages was validated using DNA based method. The taxon-specific DNA markers were identified through multiple sequence alignments. The primers were designed at conserved genes (DNA polymerase or integrase) of 4 different phage taxa viz. family Ackermannviridae, genus Jerseyvirus, genus T4virus, and genus P22virus. These primers were evaluated using both in vitro and in silico approach for the amplification of the target taxons. Majority of the primer sets were found to amplify member species of the targeted taxa in vitro. In In silico analysis, six primer sets intended for identification of family Ackermannviridae showed positive amplification of ≥86.7% classified species. Further, the primers targeting the genus Jerseyvirus and T4virus showed the amplification of 53.8% and ≥84.6% species, respectively. The present work is a case study performed to explore the possibility of use of taxon-specific primers for identification and taxonomic studies of newly isolated phages to supplement the TEM.
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Affiliation(s)
- Sandeep K Newase
- Department of Microbiology, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India; Food Technology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Alka Gupta
- Molecular Biology Division, Bhabha Atomic Research Center, Mumbai, 400085, India
| | - Syed G Dastager
- National Collection of Industrial Micro-organisms (NCIM) Resource Center, Biochemical Sciences Division, CSIR-NCL, Pune, 411008, India
| | - Balu P Kapadnis
- Department of Microbiology, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India.
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Cobián Güemes AG, Youle M, Cantú VA, Felts B, Nulton J, Rohwer F. Viruses as Winners in the Game of Life. Annu Rev Virol 2016; 3:197-214. [DOI: 10.1146/annurev-virology-100114-054952] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | - Vito Adrian Cantú
- Computational Sciences Research Center, San Diego State University, San Diego, California 92182
| | - Ben Felts
- Department of Mathematics and Statistics, San Diego State University, San Diego, California 92182
| | - James Nulton
- Department of Mathematics and Statistics, San Diego State University, San Diego, California 92182
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, California 92182;
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5
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Kim H, Kang N, An K, Koo J, Kim MS. MRPrimerW: a tool for rapid design of valid high-quality primers for multiple target qPCR experiments. Nucleic Acids Res 2016; 44:W259-66. [PMID: 27154272 PMCID: PMC4987926 DOI: 10.1093/nar/gkw380] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 04/25/2016] [Indexed: 01/25/2023] Open
Abstract
Design of high-quality primers for multiple target sequences is essential for qPCR experiments, but is challenging due to the need to consider both homology tests on off-target sequences and the same stringent filtering constraints on the primers. Existing web servers for primer design have major drawbacks, including requiring the use of BLAST-like tools for homology tests, lack of support for ranking of primers, TaqMan probes and simultaneous design of primers against multiple targets. Due to the large-scale computational overhead, the few web servers supporting homology tests use heuristic approaches or perform homology tests within a limited scope. Here, we describe the MRPrimerW, which performs complete homology testing, supports batch design of primers for multi-target qPCR experiments, supports design of TaqMan probes and ranks the resulting primers to return the top-1 best primers to the user. To ensure high accuracy, we adopted the core algorithm of a previously reported MapReduce-based method, MRPrimer, but completely redesigned it to allow users to receive query results quickly in a web interface, without requiring a MapReduce cluster or a long computation. MRPrimerW provides primer design services and a complete set of 341 963 135 in silico validated primers covering 99% of human and mouse genes. Free access: http://MRPrimerW.com.
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Affiliation(s)
- Hyerin Kim
- Department of Information and Communication Engineering, DGIST, Daegu 42988, South Korea
| | - NaNa Kang
- Department of Brain and Cognitive Sciences, DGIST, Daegu 42988, South Korea
| | - KyuHyeon An
- Department of Information and Communication Engineering, DGIST, Daegu 42988, South Korea
| | - JaeHyung Koo
- Department of Brain and Cognitive Sciences, DGIST, Daegu 42988, South Korea
| | - Min-Soo Kim
- Department of Information and Communication Engineering, DGIST, Daegu 42988, South Korea
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Keegan KP, Glass EM, Meyer F. MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function. Methods Mol Biol 2016; 1399:207-33. [PMID: 26791506 DOI: 10.1007/978-1-4939-3369-3_13] [Citation(s) in RCA: 232] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Approaches in molecular biology, particularly those that deal with high-throughput sequencing of entire microbial communities (the field of metagenomics), are rapidly advancing our understanding of the composition and functional content of microbial communities involved in climate change, environmental pollution, human health, biotechnology, etc. Metagenomics provides researchers with the most complete picture of the taxonomic (i.e., what organisms are there) and functional (i.e., what are those organisms doing) composition of natively sampled microbial communities, making it possible to perform investigations that include organisms that were previously intractable to laboratory-controlled culturing; currently, these constitute the vast majority of all microbes on the planet. All organisms contained in environmental samples are sequenced in a culture-independent manner, most often with 16S ribosomal amplicon methods to investigate the taxonomic or whole-genome shotgun-based methods to investigate the functional content of sampled communities. Metagenomics allows researchers to characterize the community composition and functional content of microbial communities, but it cannot show which functional processes are active; however, near parallel developments in transcriptomics promise a dramatic increase in our knowledge in this area as well. Since 2008, MG-RAST (Meyer et al., BMC Bioinformatics 9:386, 2008) has served as a public resource for annotation and analysis of metagenomic sequence data, providing a repository that currently houses more than 150,000 data sets (containing 60+ tera-base-pairs) with more than 23,000 publically available. MG-RAST, or the metagenomics RAST (rapid annotation using subsystems technology) server makes it possible for users to upload raw metagenomic sequence data in (preferably) fastq or fasta format. Assessments of sequence quality, annotation with respect to multiple reference databases, are performed automatically with minimal input from the user (see Subheading 4 at the end of this chapter for more details). Post-annotation analysis and visualization are also possible, directly through the web interface, or with tools like matR (metagenomic analysis tools for R, covered later in this chapter) that utilize the MG-RAST API ( http://api.metagenomics.anl.gov/api.html ) to easily download data from any stage in the MG-RAST processing pipeline. Over the years, MG-RAST has undergone substantial revisions to keep pace with the dramatic growth in the number, size, and types of sequence data that accompany constantly evolving developments in metagenomics and related -omic sciences (e.g., metatranscriptomics).
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Affiliation(s)
- Kevin P Keegan
- Argonne National Laboratory, 9700 South Cass Ave, Argonne, IL, 60439, USA.
- University of Chicago, Chicago, IL, USA.
| | - Elizabeth M Glass
- Argonne National Laboratory, 9700 South Cass Ave, Argonne, IL, 60439, USA.
| | - Folker Meyer
- Argonne National Laboratory, 9700 South Cass Ave, Argonne, IL, 60439, USA.
- University of Chicago, Chicago, IL, USA.
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Edwards RA, McNair K, Faust K, Raes J, Dutilh BE. Computational approaches to predict bacteriophage-host relationships. FEMS Microbiol Rev 2015; 40:258-72. [PMID: 26657537 PMCID: PMC5831537 DOI: 10.1093/femsre/fuv048] [Citation(s) in RCA: 274] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2015] [Indexed: 01/21/2023] Open
Abstract
Metagenomics has changed the face of virus discovery by enabling the accurate identification of viral genome sequences without requiring isolation of the viruses. As a result, metagenomic virus discovery leaves the first and most fundamental question about any novel virus unanswered: What host does the virus infect? The diversity of the global virosphere and the volumes of data obtained in metagenomic sequencing projects demand computational tools for virus–host prediction. We focus on bacteriophages (phages, viruses that infect bacteria), the most abundant and diverse group of viruses found in environmental metagenomes. By analyzing 820 phages with annotated hosts, we review and assess the predictive power of in silico phage–host signals. Sequence homology approaches are the most effective at identifying known phage–host pairs. Compositional and abundance-based methods contain significant signal for phage–host classification, providing opportunities for analyzing the unknowns in viral metagenomes. Together, these computational approaches further our knowledge of the interactions between phages and their hosts. Importantly, we find that all reviewed signals significantly link phages to their hosts, illustrating how current knowledge and insights about the interaction mechanisms and ecology of coevolving phages and bacteria can be exploited to predict phage–host relationships, with potential relevance for medical and industrial applications. New viruses infecting bacteria are increasingly being discovered in many environments through sequence-based explorations. To understand their role in microbial ecosystems, computational tools are indispensable to prioritize and guide experimental efforts. This review assesses and discusses a range of bioinformatic approaches to predict bacteriophage–host relationships when all that is known is their genome sequence.
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Affiliation(s)
- Robert A Edwards
- Department of Computer Science, San Diego State University, 5500 Campanile Dr., San Diego, CA 92182, USA Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, CEP 21941-902, Brazil Division of Mathematics and Computer Science, Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL 60439, USA
| | - Katelyn McNair
- Department of Computer Science, San Diego State University, 5500 Campanile Dr., San Diego, CA 92182, USA
| | - Karoline Faust
- Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium Laboratory of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium Laboratory of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Bas E Dutilh
- Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, CEP 21941-902, Brazil Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen, the Netherlands
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8
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Using signature genes as tools to assess environmental viral ecology and diversity. Appl Environ Microbiol 2015; 80:4470-80. [PMID: 24837394 DOI: 10.1128/aem.00878-14] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viruses (including bacteriophages) are the most abundant biological entities on the planet. As such, they are thought to have a major impact on all aspects of microbial community structure and function. Despite this critical role in ecosystem processes, the study of virus/phage diversity has lagged far behind parallel studies of the bacterial and eukaryotic kingdoms, largely due to the absence of any universal phylogenetic marker. Here we review the development and use of signature genes to investigate viral diversity, as a viable strategy for data sets of specific virus groups. Genes that have been used include those encoding structural proteins, such as portal protein, major capsid protein, and tail sheath protein, auxiliary metabolism genes, such as psbA, psbB,and phoH, and several polymerase genes. These marker genes have been used in combination with PCR-based fingerprinting and/or sequencing strategies to investigate spatial, temporal, and seasonal variations and diversity in a wide range of habitats.
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9
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Kim H, Kang N, Chon KW, Kim S, Lee N, Koo J, Kim MS. MRPrimer: a MapReduce-based method for the thorough design of valid and ranked primers for PCR. Nucleic Acids Res 2015; 43:e130. [PMID: 26109350 PMCID: PMC4787749 DOI: 10.1093/nar/gkv632] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 06/05/2015] [Indexed: 11/24/2022] Open
Abstract
Primer design is a fundamental technique that is widely used for polymerase chain reaction (PCR). Although many methods have been proposed for primer design, they require a great deal of manual effort to generate feasible and valid primers, including homology tests on off-target sequences using BLAST-like tools. That approach is inconvenient for many target sequences of quantitative PCR (qPCR) due to considering the same stringent and allele-invariant constraints. To address this issue, we propose an entirely new method called MRPrimer that can design all feasible and valid primer pairs existing in a DNA database at once, while simultaneously checking a multitude of filtering constraints and validating primer specificity. Furthermore, MRPrimer suggests the best primer pair for each target sequence, based on a ranking method. Through qPCR analysis using 343 primer pairs and the corresponding sequencing and comparative analyses, we showed that the primer pairs designed by MRPrimer are very stable and effective for qPCR. In addition, MRPrimer is computationally efficient and scalable and therefore useful for quickly constructing an entire collection of feasible and valid primers for frequently updated databases like RefSeq. Furthermore, we suggest that MRPrimer can be utilized conveniently for experiments requiring primer design, especially real-time qPCR.
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Affiliation(s)
- Hyerin Kim
- Department of Information and Communication Engineering, DGIST, 333, Techno Jungang Daero, Daegu, 711-873, South Korea
| | - NaNa Kang
- Department of Brain and Cognitive Sciences, DGIST, 333, Techno Jungang Daero, Daegu, 711-873, South Korea
| | - Kang-Wook Chon
- Department of Information and Communication Engineering, DGIST, 333, Techno Jungang Daero, Daegu, 711-873, South Korea
| | - Seonho Kim
- Department of Information and Communication Engineering, DGIST, 333, Techno Jungang Daero, Daegu, 711-873, South Korea
| | - NaHye Lee
- Department of Brain and Cognitive Sciences, DGIST, 333, Techno Jungang Daero, Daegu, 711-873, South Korea
| | - JaeHyung Koo
- Department of Brain and Cognitive Sciences, DGIST, 333, Techno Jungang Daero, Daegu, 711-873, South Korea
| | - Min-Soo Kim
- Department of Information and Communication Engineering, DGIST, 333, Techno Jungang Daero, Daegu, 711-873, South Korea
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10
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Goldsmith DB, Parsons RJ, Beyene D, Salamon P, Breitbart M. Deep sequencing of the viral phoH gene reveals temporal variation, depth-specific composition, and persistent dominance of the same viral phoH genes in the Sargasso Sea. PeerJ 2015; 3:e997. [PMID: 26157645 PMCID: PMC4476143 DOI: 10.7717/peerj.997] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 05/13/2015] [Indexed: 11/20/2022] Open
Abstract
Deep sequencing of the viral phoH gene, a host-derived auxiliary metabolic gene, was used to track viral diversity throughout the water column at the Bermuda Atlantic Time-series Study (BATS) site in the summer (September) and winter (March) of three years. Viral phoH sequences reveal differences in the viral communities throughout a depth profile and between seasons in the same year. Variation was also detected between the same seasons in subsequent years, though these differences were not as great as the summer/winter distinctions. Over 3,600 phoH operational taxonomic units (OTUs; 97% sequence identity) were identified. Despite high richness, most phoH sequences belong to a few large, common OTUs whereas the majority of the OTUs are small and rare. While many OTUs make sporadic appearances at just a few times or depths, a small number of OTUs dominate the community throughout the seasons, depths, and years.
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Affiliation(s)
- Dawn B Goldsmith
- College of Marine Science, University of South Florida , St. Petersburg, FL , USA
| | | | - Damitu Beyene
- Department of Mathematics and Statistics, San Diego State University , San Diego, CA , USA
| | - Peter Salamon
- Department of Mathematics and Statistics, San Diego State University , San Diego, CA , USA
| | - Mya Breitbart
- College of Marine Science, University of South Florida , St. Petersburg, FL , USA
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11
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Hopkins M, Kailasan S, Cohen A, Roux S, Tucker KP, Shevenell A, Agbandje-McKenna M, Breitbart M. Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein. THE ISME JOURNAL 2014; 8:2093-103. [PMID: 24694711 PMCID: PMC4184009 DOI: 10.1038/ismej.2014.43] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 02/24/2014] [Indexed: 11/15/2022]
Abstract
The small single-stranded DNA (ssDNA) bacteriophages of the subfamily Gokushovirinae were traditionally perceived as narrowly targeted, niche-specific viruses infecting obligate parasitic bacteria, such as Chlamydia. The advent of metagenomics revealed gokushoviruses to be widespread in global environmental samples. This study expands knowledge of gokushovirus diversity in the environment by developing a degenerate PCR assay to amplify a portion of the major capsid protein (MCP) gene of gokushoviruses. Over 500 amplicons were sequenced from 10 environmental samples (sediments, sewage, seawater and freshwater), revealing the ubiquity and high diversity of this understudied phage group. Residue-level conservation data generated from multiple alignments was combined with a predicted 3D structure, revealing a tendency for structurally internal residues to be more highly conserved than surface-presenting protein-protein or viral-host interaction domains. Aggregating this data set into a phylogenetic framework, many gokushovirus MCP clades contained samples from multiple environments, although distinct clades dominated the different samples. Antarctic sediment samples contained the most diverse gokushovirus communities, whereas freshwater springs from Florida were the least diverse. Whether the observed diversity is being driven by environmental factors or host-binding interactions remains an open question. The high environmental diversity of this previously overlooked ssDNA viral group necessitates further research elucidating their natural hosts and exploring their ecological roles.
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Affiliation(s)
- Max Hopkins
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Shweta Kailasan
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
| | - Allison Cohen
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Simon Roux
- Laboratoire ‘Microorganismes: Génome et Environnement', Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | | | - Amelia Shevenell
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
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12
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Fancello L, Monteil S, Popgeorgiev N, Rivet R, Gouriet F, Fournier PE, Raoult D, Desnues C. Viral communities associated with human pericardial fluids in idiopathic pericarditis. PLoS One 2014; 9:e93367. [PMID: 24690743 PMCID: PMC3972187 DOI: 10.1371/journal.pone.0093367] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 03/04/2014] [Indexed: 12/14/2022] Open
Abstract
Pericarditis is a common human disease defined by inflammation of the pericardium. Currently, 40% to 85% of pericarditis cases have no identified etiology. Most of these cases are thought to be caused by an infection of undetected, unsuspected or unknown viruses. In this work, we used a culture- and sequence-independent approach to investigate the viral DNA communities present in human pericardial fluids. Seven viral metagenomes were generated from the pericardial fluid of patients affected by pericarditis of unknown etiology and one metagenome was generated from the pericardial fluid of a sudden infant death case. As a positive control we generated one metagenome from the pericardial fluid of a patient affected by pericarditis caused by herpesvirus type 3. Furthermore, we used as negative controls a total of 6 pericardial fluids from 6 different individuals affected by pericarditis of non-infectious origin: 5 of them were sequenced as a unique pool and the remaining one was sequenced separately. The results showed a significant presence of torque teno viruses especially in one patient, while herpesviruses and papillomaviruses were present in the positive control. Co-infections by different genotypes of the same viral type (torque teno viruses) or different viruses (herpesviruses and papillomaviruses) were observed. Sequences related to bacteriophages infecting Staphylococcus, Enterobacteria, Streptococcus, Burkholderia and Pseudomonas were also detected in three patients. This study detected torque teno viruses and papillomaviruses, for the first time, in human pericardial fluids.
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Affiliation(s)
- Laura Fancello
- Unité de recherche sur les maladies infectieuses et tropicales émergentes, URMITE CNRS-IRD UMR 7278, Aix-Marseille Université, Marseille, France
| | - Sonia Monteil
- Unité de recherche sur les maladies infectieuses et tropicales émergentes, URMITE CNRS-IRD UMR 7278, Aix-Marseille Université, Marseille, France
| | - Nikolay Popgeorgiev
- Unité de recherche sur les maladies infectieuses et tropicales émergentes, URMITE CNRS-IRD UMR 7278, Aix-Marseille Université, Marseille, France
| | - Romain Rivet
- Unité de recherche sur les maladies infectieuses et tropicales émergentes, URMITE CNRS-IRD UMR 7278, Aix-Marseille Université, Marseille, France
| | - Frédérique Gouriet
- Unité de recherche sur les maladies infectieuses et tropicales émergentes, URMITE CNRS-IRD UMR 7278, Aix-Marseille Université, Marseille, France
| | - Pierre-Edouard Fournier
- Unité de recherche sur les maladies infectieuses et tropicales émergentes, URMITE CNRS-IRD UMR 7278, Aix-Marseille Université, Marseille, France
| | - Didier Raoult
- Unité de recherche sur les maladies infectieuses et tropicales émergentes, URMITE CNRS-IRD UMR 7278, Aix-Marseille Université, Marseille, France
| | - Christelle Desnues
- Unité de recherche sur les maladies infectieuses et tropicales émergentes, URMITE CNRS-IRD UMR 7278, Aix-Marseille Université, Marseille, France
- * E-mail:
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13
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Complete genome sequence of the naphthalene-degrading bacterium Pseudomonas stutzeri AN10 (CCUG 29243). J Bacteriol 2013; 194:6642-3. [PMID: 23144395 DOI: 10.1128/jb.01753-12] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Pseudomonas stutzeri AN10 (CCUG 29243) can be considered a model strain for aerobic naphthalene degradation. We report the complete genome sequence of this bacterium. Its 4.71-Mb chromosome provides insights into other biodegradative capabilities of strain AN10 (i.e., benzoate catabolism) and suggests a high number of horizontal gene transfer events.
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Gemi: PCR primers prediction from multiple alignments. Comp Funct Genomics 2012; 2012:783138. [PMID: 23316117 PMCID: PMC3535827 DOI: 10.1155/2012/783138] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 10/19/2012] [Indexed: 12/31/2022] Open
Abstract
Designing primers and probes for polymerase chain reaction (PCR) is a preliminary and critical step that requires the identification of highly conserved regions in a given set of sequences. This task can be challenging if the targeted sequences display a high level of diversity, as frequently encountered in microbiologic studies. We developed Gemi, an automated, fast, and easy-to-use bioinformatics tool with a user-friendly interface to design primers and probes based on multiple aligned sequences. This tool can be used for the purpose of real-time and conventional PCR and can deal efficiently with large sets of sequences of a large size.
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Gulvik CA, Effler TC, Wilhelm SW, Buchan A. De-MetaST-BLAST: a tool for the validation of degenerate primer sets and data mining of publicly available metagenomes. PLoS One 2012. [PMID: 23189198 PMCID: PMC3506598 DOI: 10.1371/journal.pone.0050362] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Development and use of primer sets to amplify nucleic acid sequences of interest is fundamental to studies spanning many life science disciplines. As such, the validation of primer sets is essential. Several computer programs have been created to aid in the initial selection of primer sequences that may or may not require multiple nucleotide combinations (i.e., degeneracies). Conversely, validation of primer specificity has remained largely unchanged for several decades, and there are currently few available programs that allows for an evaluation of primers containing degenerate nucleotide bases. To alleviate this gap, we developed the program De-MetaST that performs an in silico amplification using user defined nucleotide sequence dataset(s) and primer sequences that may contain degenerate bases. The program returns an output file that contains the in silico amplicons. When De-MetaST is paired with NCBI’s BLAST (De-MetaST-BLAST), the program also returns the top 10 nr NCBI database hits for each recovered in silico amplicon. While the original motivation for development of this search tool was degenerate primer validation using the wealth of nucleotide sequences available in environmental metagenome and metatranscriptome databases, this search tool has potential utility in many data mining applications.
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Affiliation(s)
- Christopher A. Gulvik
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - T. Chad Effler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Steven W. Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Alison Buchan
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail:
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