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Zhang H, Zhang H, Du H, Yu X, Xu Y. The insights into the phage communities of fermented foods in the age of viral metagenomics. Crit Rev Food Sci Nutr 2024:1-13. [PMID: 38214674 DOI: 10.1080/10408398.2023.2299323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Phages play a critical role in the assembly and regulation of fermented food microbiome through lysis and lysogenic lifestyle, which in turn affects the yield and quality of fermented foods. Therefore, it is important to investigate and characterize the diversity and function of phages under complex microbial communities and nutrient substrate conditions to provide novel insights into the regulation of traditional spontaneous fermentation. Viral metagenomics has gradually garnered increasing attention in fermented food research to elucidate phage functions and characterize the interactions between phages and the microbial community. Advances in this technology have uncovered a wide range of phages associated with the production of traditional fermented foods and beverages. This paper reviews the common methods of viral metagenomics applied in fermented food research, and summarizes the ecological functions of phages in traditional fermented foods. In the future, combining viral metagenomics with culturable methods and metagenomics will broaden the scope of research on fermented food systems, revealing the complex role of phages and intricate phage-bacterium interactions.
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Affiliation(s)
- Huadong Zhang
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hongxia Zhang
- College of Life Sciences, Shanxi Normal University, Taiyuan, Shanxi, China
| | - Hai Du
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiaowei Yu
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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2
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Li C, Wang W, Zhang X, Xiao P, Li Z, Wang P, Shi N, Zhou H, Lu H, Gao X, Zhang H, Jin N. Metavirome Analysis and Identification of Midge-Borne Viruses from Yunnan Province, China, in 2021. Viruses 2023; 15:1817. [PMID: 37766224 PMCID: PMC10535587 DOI: 10.3390/v15091817] [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: 07/07/2023] [Revised: 08/24/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Midges are widely distributed globally and can transmit various human and animal diseases through blood-sucking. As part of this study, 259,300 midges were collected from four districts in Yunnan province, China, to detect the viral richness and diversity using metavirome analysis techniques. As many as 26 virus families were detected, and the partial sequences of bluetongue virus (BTV), dengue virus (DENV), and Getah virus (GETV) were identified by phylogenetic analysis and PCR amplification. Two BTV gene fragments, 866 bps for the VP2 gene of BTV type 16 and 655 bps for the VP5 gene of BTV type 21, were amplified. The nucleotide sequence identities of the two amplified BTV fragments were 94.46% and 98.81%, respectively, with two classical BTV-16 (GenBank: JN671907) and BTV-21 strains (GenBank: MK250961) isolated in Yunnan province. Furthermore, the BTV-16 DH2021 strain was successfully isolated in C6/36 cells, and the peak value of the copy number reached 3.13 × 107 copies/μL after five consecutive BHK-21 cell passages. Moreover, two 2054 bps fragments including the E gene of DENV genotype Asia II were amplified and shared the highest identity with the DENV strain isolated in New Guinea in 1944. A length of 656 bps GETV gene sequence encoded the partial capsid protein, and it shared the highest identity of 99.68% with the GETV isolated from Shandong province, China, in 2017. Overall, this study emphasizes the importance of implementing prevention and control strategies for viral diseases transmitted by midges in China.
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Affiliation(s)
- Chenghui Li
- College of Agriculture, Yanbian University, Yanji 133002, China; (C.L.); (X.G.)
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (X.Z.); (Z.L.); (P.W.); (H.L.)
| | - Wei Wang
- Institute of Virology, Wenzhou University, Wenzhou 325035, China; (W.W.); (P.X.)
| | - Xuancheng Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (X.Z.); (Z.L.); (P.W.); (H.L.)
- College of Veterinary Medicine, Jilin University, Changchun 130062, China;
| | - Pengpeng Xiao
- Institute of Virology, Wenzhou University, Wenzhou 325035, China; (W.W.); (P.X.)
| | - Zhuoxin Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (X.Z.); (Z.L.); (P.W.); (H.L.)
| | - Peng Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (X.Z.); (Z.L.); (P.W.); (H.L.)
| | - Ning Shi
- College of Veterinary Medicine, Jilin University, Changchun 130062, China;
| | - Hongning Zhou
- Yunnan Institute of Parasitic Diseases, Puer 665000, China;
| | - Huijun Lu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (X.Z.); (Z.L.); (P.W.); (H.L.)
| | - Xu Gao
- College of Agriculture, Yanbian University, Yanji 133002, China; (C.L.); (X.G.)
| | - He Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (X.Z.); (Z.L.); (P.W.); (H.L.)
| | - Ningyi Jin
- College of Agriculture, Yanbian University, Yanji 133002, China; (C.L.); (X.G.)
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (X.Z.); (Z.L.); (P.W.); (H.L.)
- Institute of Virology, Wenzhou University, Wenzhou 325035, China; (W.W.); (P.X.)
- College of Veterinary Medicine, Jilin University, Changchun 130062, China;
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3
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Raza A, Wu Q. Diagnosis of Viral Diseases Using Deep Sequencing and Metagenomics Analyses. Methods Mol Biol 2022; 2400:225-243. [PMID: 34905206 DOI: 10.1007/978-1-0716-1835-6_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Viruses are ubiquitous in nature and exist in a variety of habitats. The advancement in sequencing technologies has revolutionized the understanding of viral biodiversity associated with plant diseases. Deep sequencing combined with metagenomics is a powerful approach that has proven to be revolutionary in the last decade and involves the direct analysis of viral genomes present in a diseased tissue sample. This protocol describes the details of RNA extraction and purification from wild rice plant and their yield, RNA purity, and integrity assessment. As a final step, bioinformatics data analysis including demultiplexing, quality control, de novo transcriptome assembly, taxonomic allocation and read mapping following Illumina HiSeq small and total RNA sequencing are described. Furthermore, the total RNAs extraction protocol and an additional ribosomal rRNAs depletion step which are significantly important for viral genomes construction are provided.
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Affiliation(s)
- Ali Raza
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Qingfa Wu
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China.
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4
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Runa V, Wenk J, Bengtsson S, Jones BV, Lanham AB. Bacteriophages in Biological Wastewater Treatment Systems: Occurrence, Characterization, and Function. Front Microbiol 2021; 12:730071. [PMID: 34803947 PMCID: PMC8600467 DOI: 10.3389/fmicb.2021.730071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/25/2021] [Indexed: 12/20/2022] Open
Abstract
Phage bacteria interactions can affect structure, dynamics, and function of microbial communities. In the context of biological wastewater treatment (BWT), the presence of phages can alter the efficiency of the treatment process and influence the quality of the treated effluent. The active role of phages in BWT has been demonstrated, but many questions remain unanswered regarding the diversity of phages in these engineered environments, the dynamics of infection, the determination of bacterial hosts, and the impact of their activity in full-scale processes. A deeper understanding of the phage ecology in BWT can lead the improvement of process monitoring and control, promote higher influent quality, and potentiate the use of phages as biocontrol agents. In this review, we highlight suitable methods for studying phages in wastewater adapted from other research fields, provide a critical overview on the current state of knowledge on the effect of phages on structure and function of BWT bacterial communities, and highlight gaps, opportunities, and priority questions to be addressed in future research.
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Affiliation(s)
- Viviane Runa
- Centre for Sustainable and Circular Technologies, University of Bath, Bath, United Kingdom.,Department of Chemical Engineering, University of Bath, Bath, United Kingdom
| | - Jannis Wenk
- Department of Chemical Engineering, University of Bath, Bath, United Kingdom.,Water Innovation and Research Centre, University of Bath, Bath, United Kingdom
| | | | - Brian V Jones
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Ana B Lanham
- Centre for Sustainable and Circular Technologies, University of Bath, Bath, United Kingdom.,Department of Chemical Engineering, University of Bath, Bath, United Kingdom.,Water Innovation and Research Centre, University of Bath, Bath, United Kingdom
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5
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Trubl G, Roux S, Solonenko N, Li YF, Bolduc B, Rodríguez-Ramos J, Eloe-Fadrosh EA, Rich VI, Sullivan MB. Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils. PeerJ 2019; 7:e7265. [PMID: 31309007 PMCID: PMC6612421 DOI: 10.7717/peerj.7265] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/07/2019] [Indexed: 11/29/2022] Open
Abstract
Soils impact global carbon cycling and their resident microbes are critical to their biogeochemical processing and ecosystem outputs. Based on studies in marine systems, viruses infecting soil microbes likely modulate host activities via mortality, horizontal gene transfer, and metabolic control. However, their roles remain largely unexplored due to technical challenges with separating, isolating, and extracting DNA from viruses in soils. Some of these challenges have been overcome by using whole genome amplification methods and while these have allowed insights into the identities of soil viruses and their genomes, their inherit biases have prevented meaningful ecological interpretations. Here we experimentally optimized steps for generating quantitatively-amplified viral metagenomes to better capture both ssDNA and dsDNA viruses across three distinct soil habitats along a permafrost thaw gradient. First, we assessed differing DNA extraction methods (PowerSoil, Wizard mini columns, and cetyl trimethylammonium bromide) for quantity and quality of viral DNA. This established PowerSoil as best for yield and quality of DNA from our samples, though ∼1/3 of the viral populations captured by each extraction kit were unique, suggesting appreciable differential biases among DNA extraction kits. Second, we evaluated the impact of purifying viral particles after resuspension (by cesium chloride gradients; CsCl) and of viral lysis method (heat vs bead-beating) on the resultant viromes. DNA yields after CsCl particle-purification were largely non-detectable, while unpurified samples yielded 1–2-fold more DNA after lysis by heat than by bead-beating. Virome quality was assessed by the number and size of metagenome-assembled viral contigs, which showed no increase after CsCl-purification, but did from heat lysis relative to bead-beating. We also evaluated sample preparation protocols for ssDNA virus recovery. In both CsCl-purified and non-purified samples, ssDNA viruses were successfully recovered by using the Accel-NGS 1S Plus Library Kit. While ssDNA viruses were identified in all three soil types, none were identified in the samples that used bead-beating, suggesting this lysis method may impact recovery. Further, 13 ssDNA vOTUs were identified compared to 582 dsDNA vOTUs, and the ssDNA vOTUs only accounted for ∼4% of the assembled reads, implying dsDNA viruses were dominant in these samples. This optimized approach was combined with the previously published viral resuspension protocol into a sample-to-virome protocol for soils now available at protocols.io, where community feedback creates ‘living’ protocols. This collective approach will be particularly valuable given the high physicochemical variability of soils, which will may require considerable soil type-specific optimization. This optimized protocol provides a starting place for developing quantitatively-amplified viromic datasets and will help enable viral ecogenomic studies on organic-rich soils.
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Affiliation(s)
- Gareth Trubl
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America.,Current affiliation: Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States of America
| | - Simon Roux
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, United States of America
| | - Natalie Solonenko
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America
| | - Yueh-Fen Li
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America
| | - Benjamin Bolduc
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America
| | - Josué Rodríguez-Ramos
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America.,Current affiliation: Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States of America
| | - Emiley A Eloe-Fadrosh
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, United States of America
| | - Virginia I Rich
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America.,Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, United States of America
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Trubl G, Jang HB, Roux S, Emerson JB, Solonenko N, Vik DR, Solden L, Ellenbogen J, Runyon AT, Bolduc B, Woodcroft BJ, Saleska SR, Tyson GW, Wrighton KC, Sullivan MB, Rich VI. Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing. mSystems 2018; 3:e00076-18. [PMID: 30320215 PMCID: PMC6172770 DOI: 10.1128/msystems.00076-18] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 08/24/2018] [Indexed: 01/10/2023] Open
Abstract
Rapidly thawing permafrost harbors ∼30 to 50% of global soil carbon, and the fate of this carbon remains unknown. Microorganisms will play a central role in its fate, and their viruses could modulate that impact via induced mortality and metabolic controls. Because of the challenges of recovering viruses from soils, little is known about soil viruses or their role(s) in microbial biogeochemical cycling. Here, we describe 53 viral populations (viral operational taxonomic units [vOTUs]) recovered from seven quantitatively derived (i.e., not multiple-displacement-amplified) viral-particle metagenomes (viromes) along a permafrost thaw gradient at the Stordalen Mire field site in northern Sweden. Only 15% of these vOTUs had genetic similarity to publicly available viruses in the RefSeq database, and ∼30% of the genes could be annotated, supporting the concept of soils as reservoirs of substantial undescribed viral genetic diversity. The vOTUs exhibited distinct ecology, with different distributions along the thaw gradient habitats, and a shift from soil-virus-like assemblages in the dry palsas to aquatic-virus-like assemblages in the inundated fen. Seventeen vOTUs were linked to microbial hosts (in silico), implicating viruses in infecting abundant microbial lineages from Acidobacteria, Verrucomicrobia, and Deltaproteobacteria, including those encoding key biogeochemical functions such as organic matter degradation. Thirty auxiliary metabolic genes (AMGs) were identified and suggested virus-mediated modulation of central carbon metabolism, soil organic matter degradation, polysaccharide binding, and regulation of sporulation. Together, these findings suggest that these soil viruses have distinct ecology, impact host-mediated biogeochemistry, and likely impact ecosystem function in the rapidly changing Arctic. IMPORTANCE This work is part of a 10-year project to examine thawing permafrost peatlands and is the first virome-particle-based approach to characterize viruses in these systems. This method yielded >2-fold-more viral populations (vOTUs) per gigabase of metagenome than vOTUs derived from bulk-soil metagenomes from the same site (J. B. Emerson, S. Roux, J. R. Brum, B. Bolduc, et al., Nat Microbiol 3:870-880, 2018, https://doi.org/10.1038/s41564-018-0190-y). We compared the ecology of the recovered vOTUs along a permafrost thaw gradient and found (i) habitat specificity, (ii) a shift in viral community identity from soil-like to aquatic-like viruses, (iii) infection of dominant microbial hosts, and (iv) carriage of host metabolic genes. These vOTUs can impact ecosystem carbon processing via top-down (inferred from lysing dominant microbial hosts) and bottom-up (inferred from carriage of auxiliary metabolic genes) controls. This work serves as a foundation which future studies can build upon to increase our understanding of the soil virosphere and how viruses affect soil ecosystem services.
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Affiliation(s)
- Gareth Trubl
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Ho Bin Jang
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Simon Roux
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Joanne B. Emerson
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Natalie Solonenko
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Dean R. Vik
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Lindsey Solden
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Jared Ellenbogen
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | | | - Benjamin Bolduc
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Ben J. Woodcroft
- Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, Queensland, Australia
| | - Scott R. Saleska
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | - Gene W. Tyson
- Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, Queensland, Australia
| | - Kelly C. Wrighton
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Matthew B. Sullivan
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Virginia I. Rich
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
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Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa's Environmental Regimes. Viruses 2018; 10:v10080429. [PMID: 30110939 PMCID: PMC6115975 DOI: 10.3390/v10080429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/03/2018] [Accepted: 08/10/2018] [Indexed: 12/19/2022] Open
Abstract
There has been an increase in the quest for metagenomics as an approach for the identification and study of the diversity of human viruses found in aquatic systems, both for their role as waterborne pathogens and as water quality indicators. In the last few years, environmental viral metagenomics has grown significantly and has enabled the identification, diversity and entire genome sequencing of viruses in environmental and clinical samples extensively. Prior to the arrival of metagenomics, traditional molecular procedures such as the polymerase chain reaction (PCR) and sequencing, were mostly used to identify and classify enteric viral species in different environmental milieu. After the advent of metagenomics, more detailed reports have emerged about the important waterborne viruses identified in wastewater treatment plant effluents and surface water. This paper provides a review of methods that have been used for the concentration, detection and identification of viral species from different environmental matrices. The review also takes into consideration where metagenomics has been explored in different African countries, as well as the limitations and challenges facing the approach. Procedures including sample processing, experimental design, sequencing technology, and bioinformatics analysis are discussed. The review concludes by summarising the current thinking and practices in the field and lays bare key issues that those venturing into this field need to consider and address.
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8
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Segobola J, Adriaenssens E, Tsekoa T, Rashamuse K, Cowan D. Exploring Viral Diversity in a Unique South African Soil Habitat. Sci Rep 2018; 8:111. [PMID: 29311639 PMCID: PMC5758573 DOI: 10.1038/s41598-017-18461-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 12/12/2017] [Indexed: 02/06/2023] Open
Abstract
The Kogelberg Biosphere Reserve in the Cape Floral Kingdom in South Africa is known for its unique plant biodiversity. The potential presence of unique microbial and viral biodiversity associated with this unique plant biodiversity led us to explore the fynbos soil using metaviromic techniques. In this study, metaviromes of a soil community from the Kogelberg Biosphere Reserve has been characterised in detail for the first time. Metaviromic DNA was recovered from soil and sequenced by Next Generation Sequencing. The MetaVir, MG-RAST and VIROME bioinformatics pipelines were used to analyse taxonomic composition, phylogenetic and functional assessments of the sequences. Taxonomic composition revealed members of the order Caudovirales, in particular the family Siphoviridae, as prevalent in the soil samples and other compared viromes. Functional analysis and other metaviromes showed a relatively high frequency of phage-related and structural proteins. Phylogenetic analysis of PolB, PolB2, terL and T7gp17 genes indicated that many viral sequences are closely related to the order Caudovirales, while the remainder were distinct from known isolates. The use of single virome which only includes double stranded DNA viruses limits this study. Novel phage sequences were detected, presenting an opportunity for future studies aimed at targeting novel genetic resources for applied biotechnology.
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Affiliation(s)
- Jane Segobola
- Biosciences Unit, Council for Scientific and Industrial Research (CSIR), Pretoria, South Africa
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Evelien Adriaenssens
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Tsepo Tsekoa
- Biosciences Unit, Council for Scientific and Industrial Research (CSIR), Pretoria, South Africa
| | - Konanani Rashamuse
- Biosciences Unit, Council for Scientific and Industrial Research (CSIR), Pretoria, South Africa
| | - Don Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa.
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Rihtman B, Meaden S, Clokie MRJ, Koskella B, Millard AD. Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes. PeerJ 2016; 4:e2055. [PMID: 27280068 PMCID: PMC4893331 DOI: 10.7717/peerj.2055] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 04/29/2016] [Indexed: 11/20/2022] Open
Abstract
Bacteriophages are the most abundant biological entities on the planet, playing crucial roles in the shaping of bacterial populations. Phages have smaller genomes than their bacterial hosts, yet there are currently fewer fully sequenced phage than bacterial genomes. We assessed the suitability of Illumina technology for high-throughput sequencing and subsequent assembly of phage genomes. In silico datasets reveal that 30× coverage is sufficient to correctly assemble the complete genome of ~98.5% of known phages, with experimental data confirming that the majority of phage genomes can be assembled at 30× coverage. Furthermore, in silico data demonstrate it is possible to co-sequence multiple phages from different hosts, without introducing assembly errors.
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Affiliation(s)
- Branko Rihtman
- School of Life Sciences, University of Warwick , Coventry , United Kingdom
| | - Sean Meaden
- College of Life and Environmental Sciences, University of Exeter , United Kingdom
| | - Martha R J Clokie
- Department of Infection, Immunity and Inflammation, University of Leicester
| | - Britt Koskella
- College of Life and Environmental Sciences, University of Exeter, United Kingdom; Department of Integrative Biology, University of California, Berkeley, California, United States
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10
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Wu Q, Ding SW, Zhang Y, Zhu S. Identification of viruses and viroids by next-generation sequencing and homology-dependent and homology-independent algorithms. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:425-44. [PMID: 26047558 DOI: 10.1146/annurev-phyto-080614-120030] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
A fast, accurate, and full indexing of viruses and viroids in a sample for the inspection and quarantine services and disease management is desirable but was unrealistic until recently. This article reviews the rapid and exciting recent progress in the use of next-generation sequencing (NGS) technologies for the identification of viruses and viroids in plants. A total of four viroids/viroid-like RNAs and 49 new plant RNA and DNA viruses from 18 known or unassigned virus families have been identified from plants since 2009. A comparison of enrichment strategies reveals that full indexing of RNA and DNA viruses as well as viroids in a plant sample at single-nucleotide resolution is made possible by one NGS run of total small RNAs, followed by data mining with homology-dependent and homology-independent computational algorithms. Major challenges in the application of NGS technologies to pathogen discovery are discussed.
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Affiliation(s)
- Qingfa Wu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 China;
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11
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Wang Y, Wang H, Xu K, Ni P, Zhang H, Ma J, Yang H, Xu F. A survey of overlooked viral infections in biological experiment systems. PLoS One 2014; 9:e105348. [PMID: 25144530 PMCID: PMC4140767 DOI: 10.1371/journal.pone.0105348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 07/23/2014] [Indexed: 12/04/2022] Open
Abstract
It is commonly accepted that there are many unknown viruses on the planet. For the known viruses, do we know their prevalence, even in our experimental systems? Here we report a virus survey using recently published small (s)RNA sequencing datasets. The sRNA reads were assembled and contigs were screened for virus homologues against the NCBI nucleotide (nt) database using the BLASTn program. To our surprise, approximately 30% (28 out of 94) of publications had highly scored viral sequences in their datasets. Among them, only two publications reported virus infections. Though viral vectors were used in some of the publications, virus sequences without any identifiable source appeared in more than 20 publications. By determining the distributions of viral reads and the antiviral RNA interference (RNAi) pathways using the sRNA profiles, we showed evidence that many of the viruses identified were indeed infecting and generated host RNAi responses. As virus infections affect many aspects of host molecular biology and metabolism, the presence and impact of viruses needs to be actively investigated in experimental systems.
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Affiliation(s)
- Yajing Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
| | - Hui Wang
- NERC/Centre for Ecology and Hydrology, Wallingford, Oxfordshire, United Kingdom
- Beijing Genome Institute (BGI), Yantian District, Shenzhen, China
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kunhan Xu
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
| | - Peixiang Ni
- BGI-Tianjin, Airport Economic Area, Tianjin, China
| | - Huan Zhang
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
| | - Jinmin Ma
- Beijing Genome Institute (BGI), Yantian District, Shenzhen, China
| | - Huanming Yang
- Beijing Genome Institute (BGI), Yantian District, Shenzhen, China
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Prince Aljawhra Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- James D. Watson Institute of Genome Science, Hangzhou, China
| | - Feng Xu
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
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Gonzalez-Martin C, Teigell-Perez N, Valladares B, Griffin DW. The Global Dispersion of Pathogenic Microorganisms by Dust Storms and Its Relevance to Agriculture. ADVANCES IN AGRONOMY 2014; 127. [PMCID: PMC7150032 DOI: 10.1016/b978-0-12-800131-8.00001-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Dust storms move an estimated 500–5000 Tg of soil through Earth’s atmosphere every year. Dust-storm transport of topsoils may have positive effects such as fertilization of aquatic and terrestrial ecosystems and the evolution of soils in proximal and distal environments. Negative effects may include the stripping of nutrient-rich topsoils from source regions, sandblasting of plant life in downwind environments, the fertilization of harmful algal blooms, and the transport of toxins (e.g., metals, pesticides, herbicides, etc.) and pathogenic microorganisms. With respect to the long-range dispersion of microorganisms and more specifically pathogens, research is just beginning to demonstrate the quantity and diversity of organisms that can survive this type of transport. Most studies to date have utilized different assays to identify microorganisms and microbial communities using predominately culture-based, and more recently nonculture-based, methodologies. There is a clear need for international-scale research efforts that apply standardized methods to advance this field of science. Here we present a review of dust-borne microorganisms with a focus on their relevance to agronomy.
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Affiliation(s)
- Cristina Gonzalez-Martin
- University Institute of Tropical Diseases and Public Health of the Canary Islands, University of La Laguna, Avda, Astrofisico Francisco Sanchez, San Cristóbal de La Laguna, Tenerife, Canary Islands, Spain
- Corresponding author: e-mail address:
| | - Nuria Teigell-Perez
- University Institute of Tropical Diseases and Public Health of the Canary Islands, University of La Laguna, Avda, Astrofisico Francisco Sanchez, San Cristóbal de La Laguna, Tenerife, Canary Islands, Spain
| | - Basilio Valladares
- University Institute of Tropical Diseases and Public Health of the Canary Islands, University of La Laguna, Avda, Astrofisico Francisco Sanchez, San Cristóbal de La Laguna, Tenerife, Canary Islands, Spain
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