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Colombo S, Arioli S, Gargari G, Neri E, Della Scala G, Mora D. Characterization of airborne viromes in cheese production plants. J Appl Microbiol 2018; 125:1444-1454. [DOI: 10.1111/jam.14046] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/28/2018] [Accepted: 07/05/2018] [Indexed: 12/29/2022]
Affiliation(s)
- S. Colombo
- Department of Food, Environmental and Nutritional Sciences; University of Milan; Milan Italy
| | - S. Arioli
- Department of Food, Environmental and Nutritional Sciences; University of Milan; Milan Italy
| | - G. Gargari
- Department of Food, Environmental and Nutritional Sciences; University of Milan; Milan Italy
| | - E. Neri
- Department of Food, Environmental and Nutritional Sciences; University of Milan; Milan Italy
| | - G. Della Scala
- Department of Food, Environmental and Nutritional Sciences; University of Milan; Milan Italy
| | - D. Mora
- Department of Food, Environmental and Nutritional Sciences; University of Milan; Milan Italy
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52
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Wu YT, Yang CY, Chiang PW, Tseng CH, Chiu HH, Saeed I, Baatar B, Rogozin D, Halgamuge S, Degermendzhi A, Tang SL. Comprehensive Insights Into Composition, Metabolic Potentials, and Interactions Among Archaeal, Bacterial, and Viral Assemblages in Meromictic Lake Shunet in Siberia. Front Microbiol 2018; 9:1763. [PMID: 30177915 PMCID: PMC6109700 DOI: 10.3389/fmicb.2018.01763] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 07/16/2018] [Indexed: 11/20/2022] Open
Abstract
Microorganisms are critical to maintaining stratified biogeochemical characteristics in meromictic lakes; however, their community composition and potential roles in nutrient cycling are not thoroughly described. Both metagenomics and metaviromics were used to determine the composition and capacity of archaea, bacteria, and viruses along the water column in the landlocked meromictic Lake Shunet in Siberia. Deep sequencing of 265 Gb and high-quality assembly revealed a near-complete genome corresponding to Nonlabens sp. sh3vir. in a viral sample and 38 bacterial bins (0.2–5.3 Mb each). The mixolimnion (3.0 m) had the most diverse archaeal, bacterial, and viral communities, followed by the monimolimnion (5.5 m) and chemocline (5.0 m). The bacterial and archaeal communities were dominated by Thiocapsa and Methanococcoides, respectively, whereas the viral community was dominated by Siphoviridae. The archaeal and bacterial assemblages and the associated energy metabolism were significantly related to the various depths, in accordance with the stratification of physicochemical parameters. Reconstructed elemental nutrient cycles of the three layers were interconnected, including co-occurrence of denitrification and nitrogen fixation in each layer and involved unique processes due to specific biogeochemical properties at the respective depths. According to the gene annotation, several pre-dominant yet unknown and uncultured bacteria also play potentially important roles in nutrient cycling. Reciprocal BLAST analysis revealed that the viruses were specific to the host archaea and bacteria in the mixolimnion. This study provides insights into the bacterial, archaeal, and viral assemblages and the corresponding capacity potentials in Lake Shunet, one of the three meromictic lakes in central Asia. Lake Shunet was determined to harbor specific and diverse viral, bacterial, and archaeal communities that intimately interacted, revealing patterns shaped by indigenous physicochemical parameters.
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Affiliation(s)
- Yu-Ting Wu
- Department of Forestry, National Pingtung University of Science and Technology, Neipu, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Cheng-Yu Yang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ching-Hung Tseng
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Germark Biotechnology Co., Ltd., Taichung, Taiwan
| | - Hsiu-Hui Chiu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Isaam Saeed
- Optimisation and Pattern Recognition Group, Melbourne School of Engineering, The University of Melbourne, Melbourne, VIC, Australia
| | - Bayanmunkh Baatar
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Department of Life Sciences, Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
| | - Denis Rogozin
- Institute of Biophysics, Siberian Division of Russian Academy of Sciences, Krasnoyarsk, Russia.,Siberian Federal University, Krasnoyarsk, Russia
| | - Saman Halgamuge
- Optimisation and Pattern Recognition Group, Melbourne School of Engineering, The University of Melbourne, Melbourne, VIC, Australia
| | - Andrei Degermendzhi
- Institute of Biophysics, Siberian Division of Russian Academy of Sciences, Krasnoyarsk, Russia
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Department of Life Sciences, Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
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53
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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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54
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Creasy A, Rosario K, Leigh BA, Dishaw LJ, Breitbart M. Unprecedented Diversity of ssDNA Phages from the Family Microviridae Detected within the Gut of a Protochordate Model Organism ( Ciona robusta). Viruses 2018; 10:v10080404. [PMID: 30065169 PMCID: PMC6116155 DOI: 10.3390/v10080404] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 07/23/2018] [Accepted: 07/27/2018] [Indexed: 12/13/2022] Open
Abstract
Phages (viruses that infect bacteria) play important roles in the gut ecosystem through infection of bacterial hosts, yet the gut virome remains poorly characterized. Mammalian gut viromes are dominated by double-stranded DNA (dsDNA) phages belonging to the order Caudovirales and single-stranded DNA (ssDNA) phages belonging to the family Microviridae. Since the relative proportion of each of these phage groups appears to correlate with age and health status in humans, it is critical to understand both ssDNA and dsDNA phages in the gut. Building upon prior research describing dsDNA viruses in the gut of Ciona robusta, a marine invertebrate model system used to study gut microbial interactions, this study investigated ssDNA phages found in the Ciona gut. We identified 258 Microviridae genomes, which were dominated by novel members of the Gokushovirinae subfamily, but also represented several proposed phylogenetic groups (Alpavirinae, Aravirinae, Group D, Parabacteroides prophages, and Pequeñovirus) and a novel group. Comparative analyses between Ciona specimens with full and cleared guts, as well as the surrounding water, indicated that Ciona retains a distinct and highly diverse community of ssDNA phages. This study significantly expands the known diversity within the Microviridae family and demonstrates the promise of Ciona as a model system for investigating their role in animal health.
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Affiliation(s)
- Alexandria Creasy
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
- Department of Pediatrics, Children's Research Institute, University of South Florida, St. Petersburg, FL 33701, USA.
| | - Karyna Rosario
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
| | - Brittany A Leigh
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
- Department of Pediatrics, Children's Research Institute, University of South Florida, St. Petersburg, FL 33701, USA.
| | - Larry J Dishaw
- Department of Pediatrics, Children's Research Institute, University of South Florida, St. Petersburg, FL 33701, USA.
| | - Mya Breitbart
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
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55
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Gu X, Tay QXM, Te SH, Saeidi N, Goh SG, Kushmaro A, Thompson JR, Gin KYH. Geospatial distribution of viromes in tropical freshwater ecosystems. WATER RESEARCH 2018; 137:220-232. [PMID: 29550725 PMCID: PMC7112100 DOI: 10.1016/j.watres.2018.03.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/02/2018] [Accepted: 03/07/2018] [Indexed: 05/05/2023]
Abstract
This study seeks to understand the general distribution of virome abundance and diversity in tropical freshwater ecosystems in Singapore and the geospatial distribution of the virome under different landuse patterns. Correlations between diversity, environmental parameters and land use patterns were analyzed and significant correlations were highlighted. Overall, the majority (65.5%) of the annotated virome belonged to bacteriophages. The percentage of Caudovirales was higher in reservoirs whereas the percentages of Dicistroviridae, Microviridae and Circoviridae were higher in tributaries. Reservoirs showed a higher Shannon-index virome diversity compared to upstream tributaries. Land use (urbanized, agriculture and parkland areas) influenced the characteristics of the virome distribution pattern. Dicistroviridae and Microviridae were enriched in urbanized tributaries while Mimiviridae, Phycodnaviridae, Siphoviridae and Podoviridae were enriched in parkland reservoirs. Several sequences closely related to the emerging zoonotic virus, cyclovirus, and the human-related virus (human picobirnavirus), were also detected. In addition, the relative abundance of PMMoV (pepper mild mottle virus) sequences was significantly correlated with RT-qPCR measurements (0.588 < r < 0.879, p < 0.05). This study shows that spatial factors (e.g., reservoirs/tributaries, land use) are the main drivers of the viral community structure in tropical freshwater ecosystems.
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Affiliation(s)
- Xiaoqiong Gu
- Department of Civil and Environmental Engineering, National University of Singapore, Engineering Drive 1, T-lab Building, TL08-03, 117576, Singapore
| | | | - Shu Harn Te
- Department of Civil and Environmental Engineering, National University of Singapore, Engineering Drive 1, T-lab Building, TL08-03, 117576, Singapore
| | - Nazanin Saeidi
- Department of Civil and Environmental Engineering, National University of Singapore, Engineering Drive 1, T-lab Building, TL08-03, 117576, Singapore
| | - Shin Giek Goh
- Department of Civil and Environmental Engineering, National University of Singapore, Engineering Drive 1, T-lab Building, TL08-03, 117576, Singapore
| | - Ariel Kushmaro
- School of Material Science and Engineering, Nanyang Technological University, 637819, Singapore
| | | | - Karina Yew-Hoong Gin
- Department of Civil and Environmental Engineering, National University of Singapore, Engineering Drive 1, T-lab Building, TL08-03, 117576, Singapore.
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56
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White Iii RA, Wong HL, Ruvindy R, Neilan BA, Burns BP. Viral Communities of Shark Bay Modern Stromatolites. Front Microbiol 2018; 9:1223. [PMID: 29951046 PMCID: PMC6008428 DOI: 10.3389/fmicb.2018.01223] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 05/22/2018] [Indexed: 01/21/2023] Open
Abstract
Single stranded DNA viruses have been previously shown to populate the oceans on a global scale, and are endemic in microbialites of both marine and freshwater systems. We undertook for the first time direct viral metagenomic shotgun sequencing to explore the diversity of viruses in the modern stromatolites of Shark Bay Australia. The data indicate that Shark Bay marine stromatolites have similar diversity of ssDNA viruses to that of Highbourne Cay, Bahamas. ssDNA viruses in cluster uniquely in Shark Bay and Highbourne Cay, potentially due to enrichment by phi29-mediated amplification bias. Further, pyrosequencing data was assembled from the Shark Bay systems into two putative viral genomes that are related to Genomoviridae family of ssDNA viruses. In addition, the cellular fraction was shown to be enriched for antiviral defense genes including CRISPR-Cas, BREX (bacteriophage exclusion), and DISARM (defense island system associated with restriction-modification), a potentially novel finding for these systems. This is the first evidence for viruses in the Shark Bay stromatolites, and these viruses may play key roles in modulating microbial diversity as well as potentially impacting ecosystem function through infection and the recycling of key nutrients.
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Affiliation(s)
- Richard Allen White Iii
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States.,Crop and Soil Sciences, Washington State University, Pullman, WA, United States.,Plant Pathology, Washington State University, Pullman, WA, United States.,Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia.,RAW Molecular Systems (RMS) LLC, Spokane, WA, United States
| | - Hon L Wong
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia.,School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW, Australia
| | - Rendy Ruvindy
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia.,School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW, Australia
| | - Brett A Neilan
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia.,School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW, Australia
| | - Brendan P Burns
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia.,School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW, Australia
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57
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Garner E, Chen C, Xia K, Bowers J, Engelthaler DM, McLain J, Edwards MA, Pruden A. Metagenomic Characterization of Antibiotic Resistance Genes in Full-Scale Reclaimed Water Distribution Systems and Corresponding Potable Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:6113-6125. [PMID: 29741366 DOI: 10.1021/acs.est.7b05419] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Water reclamation provides a valuable resource for meeting nonpotable water demands. However, little is known about the potential for wastewater reuse to disseminate antibiotic resistance genes (ARGs). Here, samples were collected seasonally in 2014-2015 from four U.S. utilities' reclaimed and potable water distribution systems before treatment, after treatment, and at five points of use (POU). Shotgun metagenomic sequencing was used to profile the resistome (i.e., full contingent of ARGs) of a subset ( n = 38) of samples. Four ARGs ( qnrA, blaTEM, vanA, sul1) were quantified by quantitative polymerase chain reaction. Bacterial community composition (via 16S rRNA gene amplicon sequencing), horizontal gene transfer (via quantification of intI1 integrase and plasmid genes), and selection pressure (via detection of metals and antibiotics) were investigated as potential factors governing the presence of ARGs. Certain ARGs were elevated in all ( sul1; p ≤ 0.0011) or some ( blaTEM, qnrA; p ≤ 0.0145) reclaimed POU samples compared to corresponding potable samples. Bacterial community composition was weakly correlated with ARGs (Adonis, R2 = 0.1424-0.1734) and associations were noted between 193 ARGs and plasmid-associated genes. This study establishes that reclaimed water could convey greater abundances of certain ARGs than potable waters and provides observations regarding factors that likely control ARG occurrence in reclaimed water systems.
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Affiliation(s)
- Emily Garner
- Via Department of Civil and Environmental Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Chaoqi Chen
- Department of Crop and Soil Environmental Sciences , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Kang Xia
- Department of Crop and Soil Environmental Sciences , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Jolene Bowers
- Translational Genomics Research Institute , Flagstaff , Arizona 86005 , United States
| | - David M Engelthaler
- Translational Genomics Research Institute , Flagstaff , Arizona 86005 , United States
| | - Jean McLain
- Water Resources Research Center , University of Arizona , Tucson , Arizona 85719 , United States
| | - Marc A Edwards
- Via Department of Civil and Environmental Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Amy Pruden
- Via Department of Civil and Environmental Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
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58
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Assis ASF, Fumian TM, Miagostovich MP, Drumond BP, da Rosa E Silva ML. Adenovirus and rotavirus recovery from a treated effluent through an optimized skimmed-milk flocculation method. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:17025-17032. [PMID: 29633189 DOI: 10.1007/s11356-018-1873-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/26/2018] [Indexed: 06/08/2023]
Abstract
Sewage treatment may be insufficient for the complete removal of enteric viruses, such as human adenoviruses (HAdV) and group A rotavirus (RVA). The differences in the efficiency of the treatment methodologies used may interfere with the detection of these viruses. The objective of this study was to optimize a skimmed-milk flocculation technique for the recovery of HAdV and RVA in the samples of treated effluent. The treated effluent collected at the wastewater treatment plant (WWTP) was processed via four protocols including modifications in the initial centrifugation step and the final concentration of skimmed-milk. The viral load and recovery rate were determined by quantitative PCR TaqMan® System. The highest recovery rates of HAdV, RVA, and bacteriophage PP7 (internal control process) were obtained when the concentration of skimmed-milk was doubled and no centrifugation step was used for the sample clarification. The optimized protocol was assessed in a field study conducted with 24 treated effluent samples collected bi-monthly during 2015. HAdV and RVA were detected in 50.0% (12/24) and 33.3% (08/24) of the samples tested, respectively, throughout the year, without seasonal variation (p > 0.05). This study corroborates the use of the organic flocculation method for virus recovery in environmental samples with the adaptation of the protocols to different aquatic matrices.
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Affiliation(s)
- Andrêssa Silvino Ferreira Assis
- Laboratory of Virology, Department of Parasitology, Microbiology and Immunology, Institute of Biological Science, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil.
| | - Tulio Machado Fumian
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marize Pereira Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Betânia Paiva Drumond
- Laboratory of Virology, Department of Parasitology, Microbiology and Immunology, Institute of Biological Science, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil.
- Laboratory of Virus, Department of Microbiology, Institute of Biological Science, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
| | - Maria Luzia da Rosa E Silva
- Laboratory of Virology, Department of Parasitology, Microbiology and Immunology, Institute of Biological Science, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
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59
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The Geographic Structure of Viruses in the Cuatro Ciénegas Basin, a Unique Oasis in Northern Mexico, Reveals a Highly Diverse Population on a Small Geographic Scale. Appl Environ Microbiol 2018; 84:AEM.00465-18. [PMID: 29625974 DOI: 10.1128/aem.00465-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/21/2018] [Indexed: 12/28/2022] Open
Abstract
The Cuatro Ciénegas Basin (CCB) is located in the Chihuahuan desert in the Mexican state of Coahuila; it has been characterized as a site with high biological diversity despite its extreme oligotrophic conditions. It has the greatest number of endemic species in North America, containing abundant living microbialites (including stromatolites and microbial mats) and diverse microbial communities. With the hypothesis that this high biodiversity and the geographic structure should be reflected in the virome, the viral communities in 11 different locations of three drainage systems, Churince, La Becerra, and Pozas Rojas, and in the intestinal contents of 3 different fish species, were analyzed for both eukaryotic and prokaryotic RNA and DNA viruses using next-generation sequencing methods. Double-stranded DNA (dsDNA) virus families were the most abundant (72.5% of reads), followed by single-stranded DNA (ssDNA) viruses (2.9%) and ssRNA and dsRNA virus families (0.5%). Thirteen families had dsDNA genomes, five had ssDNA, three had dsRNA, and 16 had ssRNA. A highly diverse viral community was found, with an ample range of hosts and a strong geographical structure, with very even distributions and signals of endemicity in the phylogenetic trees from several different virus families. The majority of viruses found were bacteriophages but eukaryotic viruses were also frequent, and the large diversity of viruses related to algae were a surprise, since algae are not evident in the previously analyzed aquatic systems of this ecosystem. Animal viruses were also frequently found, showing the large diversity of aquatic animals in this oasis, where plants, protozoa, and archaea are rare.IMPORTANCE In this study, we tested whether the high biodiversity and geographic structure of CCB is reflected in its virome. CCB is an extraordinarily biodiverse oasis in the Chihuahuan desert, where a previous virome study suggested that viruses had followed the marine ancestry of the marine bacteria and, as a result of their long isolation, became endemic to the site. In this study, which includes a larger sequencing coverage and water samples from other sites within the valley, we confirmed the high virus biodiversity and uniqueness as well as the strong biogeographical diversification of the CCB. In addition, we also analyzed fish intestinal contents, finding that each fish species eats different prey and, as a result, presents different viral compositions even if they coexist in the same pond. These facts highlight the high and novel virus diversity of CCB and its "lost world" status.
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60
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Haramoto E, Kitajima M, Hata A, Torrey JR, Masago Y, Sano D, Katayama H. A review on recent progress in the detection methods and prevalence of human enteric viruses in water. WATER RESEARCH 2018; 135:168-186. [PMID: 29471200 DOI: 10.1016/j.watres.2018.02.004] [Citation(s) in RCA: 240] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 05/17/2023]
Abstract
Waterborne human enteric viruses, such as noroviruses and adenoviruses, are excreted in the feces of infected individuals and transmitted via the fecal-oral route including contaminated food and water. Since viruses are normally present at low concentrations in aquatic environments, they should be concentrated into smaller volumes prior to downstream molecular biological applications, such as quantitative polymerase chain reaction (qPCR). This review describes recent progress made in the development of concentration and detection methods of human enteric viruses in water, and discusses their applications for providing a better understanding of the prevalence of the viruses in various types of water worldwide. Maximum concentrations of human enteric viruses in water that have been reported in previous studies are summarized to assess viral abundances in aquatic environments. Some descriptions are also available on recent applications of sequencing analyses used to determine the genetic diversity of viral genomes in water samples, including those of novel viruses. Furthermore, the importance and significance of utilizing appropriate process controls during viral analyses are discussed, and three types of process controls are considered: whole process controls, molecular process controls, and (reverse transcription (RT)-)qPCR controls. Although no standards have been established for acceptable values of virus recovery and/or extraction-(RT-)qPCR efficiency, use of at least one of these appropriate control types is highly recommended for more accurate interpretation of observed data.
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Affiliation(s)
- Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan.
| | - Akihiko Hata
- Integrated Research System for Sustainability Science, Institutes for Advanced Study, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.
| | - Jason R Torrey
- School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
| | - Yoshifumi Masago
- Institute for the Advanced Study of Sustainability, United Nations University, 5-53-70 Jingumae, Shibuya-ku, Tokyo 150-8925, Japan.
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan.
| | - Hiroyuki Katayama
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; Vietnam Japan University, Luu Huu Phuoc Road, My Dinh 1 Ward, Nam Tu Liem District, Ha Noi, Vietnam.
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61
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Oshiki M, Miura T, Kazama S, Segawa T, Ishii S, Hatamoto M, Yamaguchi T, Kubota K, Iguchi A, Tagawa T, Okubo T, Uemura S, Harada H, Kobayashi N, Araki N, Sano D. Microfluidic PCR Amplification and MiSeq Amplicon Sequencing Techniques for High-Throughput Detection and Genotyping of Human Pathogenic RNA Viruses in Human Feces, Sewage, and Oysters. Front Microbiol 2018; 9:830. [PMID: 29755444 PMCID: PMC5934477 DOI: 10.3389/fmicb.2018.00830] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/11/2018] [Indexed: 01/31/2023] Open
Abstract
Detection and genotyping of pathogenic RNA viruses in human and environmental samples are useful for monitoring the circulation and prevalence of these pathogens, whereas a conventional PCR assay followed by Sanger sequencing is time-consuming and laborious. The present study aimed to develop a high-throughput detection-and-genotyping tool for 11 human RNA viruses [Aichi virus; astrovirus; enterovirus; norovirus genogroup I (GI), GII, and GIV; hepatitis A virus; hepatitis E virus; rotavirus; sapovirus; and human parechovirus] using a microfluidic device and next-generation sequencer. Microfluidic nested PCR was carried out on a 48.48 Access Array chip, and the amplicons were recovered and used for MiSeq sequencing (Illumina, Tokyo, Japan); genotyping was conducted by homology searching and phylogenetic analysis of the obtained sequence reads. The detection limit of the 11 tested viruses ranged from 100 to 103 copies/μL in cDNA sample, corresponding to 101–104 copies/mL-sewage, 105–108 copies/g-human feces, and 102–105 copies/g-digestive tissues of oyster. The developed assay was successfully applied for simultaneous detection and genotyping of RNA viruses to samples of human feces, sewage, and artificially contaminated oysters. Microfluidic nested PCR followed by MiSeq sequencing enables efficient tracking of the fate of multiple RNA viruses in various environments, which is essential for a better understanding of the circulation of human pathogenic RNA viruses in the human population.
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Affiliation(s)
- Mamoru Oshiki
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Takayuki Miura
- Department of Environmental Health, National Institute of Public Health, Wako, Japan
| | - Shinobu Kazama
- Center for Simulation Sciences and Informational Biology, Ochanomizu University, Bunkyô, Japan
| | - Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, Kofu, Japan
| | - Satoshi Ishii
- Department of Soil, Water and Climate, University of Minnesota, Minneapolis, MN, United States
| | - Masashi Hatamoto
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, Japan
| | - Kengo Kubota
- Department of Civil and Environmental Engineering, Tohoku University, Sendai, Japan
| | - Akinori Iguchi
- Faculty of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Tadashi Tagawa
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Tsutomu Okubo
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Shigeki Uemura
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Hideki Harada
- New Industry Creation Hatchery Center, Tohoku University, Sendai, Japan
| | - Naohiro Kobayashi
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Nobuo Araki
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Tohoku University, Sendai, Japan
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Abstract
Viruses represent the most abundant and diverse of the biological entities in environmental waters, including the seas and probably also freshwater systems. They are important players in ecological networks in waters and influence global biochemical cycling and community composition dynamics. Among the many diverse viruses from terrestrial environments found in environmental waters, some are plant, animal, and/or human pathogens. The majority of pathogenic viral species found in waters are very stable and can survive outside host cells for long periods. The occurrence of such viruses in environmental waters has raised concerns because of the confirmation of the infectivity of waterborne viruses even at very low concentrations. This chapter focuses mainly on the survival of human, animal, and plant pathogenic viruses in aqueous environments, the possibility of their water-mediated transmission, the ecological implications of viruses in water, the methods adapted for detecting such viruses, and how to minimize the risk of viruses spreading through water.
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63
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Jones RAC. Plant and Insect Viruses in Managed and Natural Environments: Novel and Neglected Transmission Pathways. Adv Virus Res 2018; 101:149-187. [PMID: 29908589 DOI: 10.1016/bs.aivir.2018.02.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The capacity to spread by diverse transmission pathways enhances a virus' ability to spread effectively and survive when circumstances change. This review aims to improve understanding of how plant and insect viruses spread through natural and managed environments by drawing attention to 12 novel or neglected virus transmission pathways whose contribution is underestimated. For plant viruses, the pathways reviewed are vertical and horizontal transmission via pollen, and horizontal transmission by parasitic plants, natural root grafts, wind-mediated contact, chewing insects, and contaminated water or soil. For insect viruses, they are transmission by plants serving as passive "vectors," arthropod vectors, and contamination of pollen and nectar. Based on current understanding of the spatiotemporal dynamics of virus spread, the likely roles of each pathway in creating new primary infection foci, enlarging previously existing infection foci, and promoting generalized virus spread are estimated. All pathways except transmission via parasitic plants, root grafts, and wind-mediated contact transmission are likely to produce new primary infection foci. All 12 pathways have the capability to enlarge existing infection foci, but only to a limited extent when spread occurs via virus-contaminated soil or vertical pollen transmission. All pathways except those via parasitic plant, root graft, contaminated soil, and vertical pollen transmission likely contribute to generalized virus spread, but to different extents. For worst-case scenarios, where mixed populations of host species occur under optimal virus spread conditions, the risk that host species jumps or virus emergence events will arise is estimated to be "high" for all four insect virus pathways considered, and, "very high" or "moderate" for plant viruses transmitted by parasitic plant and root graft pathways, respectively. To establish full understanding of virus spread and thereby optimize effective virus disease management, it is important to examine all transmission pathways potentially involved, regardless of whether the virus' ecology is already presumed to be well understood or otherwise.
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Affiliation(s)
- Roger A C Jones
- Institute of Agriculture, Faculty of Science, University of Western Australia, Crawley, WA, Australia; Department of Primary Industries and Regional Development, South Perth, WA, Australia.
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64
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Teleosts Genomics: Progress and Prospects in Disease Prevention and Control. Int J Mol Sci 2018; 19:ijms19041083. [PMID: 29617353 PMCID: PMC5979277 DOI: 10.3390/ijms19041083] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 03/11/2018] [Accepted: 03/29/2018] [Indexed: 12/26/2022] Open
Abstract
Genome wide studies based on conventional molecular tools and upcoming omics technologies are beginning to gain functional applications in the control and prevention of diseases in teleosts fish. Herein, we provide insights into current progress and prospects in the use genomics studies for the control and prevention of fish diseases. Metagenomics has emerged to be an important tool used to identify emerging infectious diseases for the timely design of rational disease control strategies, determining microbial compositions in different aquatic environments used for fish farming and the use of host microbiota to monitor the health status of fish. Expounding the use of antimicrobial peptides (AMPs) as therapeutic agents against different pathogens as well as elucidating their role in tissue regeneration is another vital aspect of genomics studies that had taken precedent in recent years. In vaccine development, prospects made include the identification of highly immunogenic proteins for use in recombinant vaccine designs as well as identifying gene signatures that correlate with protective immunity for use as benchmarks in optimizing vaccine efficacy. Progress in quantitative trait loci (QTL) mapping is beginning to yield considerable success in identifying resistant traits against some of the highly infectious diseases that have previously ravaged the aquaculture industry. Altogether, the synopsis put forth shows that genomics studies are beginning to yield positive contribution in the prevention and control of fish diseases in aquaculture.
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65
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Reducing inherent biases introduced during DNA viral metagenome analyses of municipal wastewater. PLoS One 2018; 13:e0195350. [PMID: 29614100 PMCID: PMC5882159 DOI: 10.1371/journal.pone.0195350] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/20/2018] [Indexed: 01/21/2023] Open
Abstract
Metagenomics is a powerful tool for characterizing viral composition within environmental samples, but sample and molecular processing steps can bias the estimation of viral community structure. The objective of this study is to understand the inherent variability introduced when conducting viral metagenomic analyses of wastewater and provide a bioinformatic strategy to accurately analyze sequences for viral community analyses. A standard approach using a combination of ultrafiltration, membrane filtration, and DNase treatment, and multiple displacement amplification (MDA) produced DNA preparations without any bacterial derived genes. Results showed recoveries in wastewater matrix ranged between 60–100%. A bias towards small single stranded DNA (ssDNA; polyomavirus) virus types vs larger double stranded DNA (dsDNA; adenovirus) viruses was also observed with a total estimated recovery of small circular viruses to be as much as 173-fold higher. Notably, ssDNA abundance decreased with sample dilution while large dsDNA genomes (e.g., Caudovirales) initially increased in abundance with dilution before gradually decreasing with further dilution in wastewater samples. The present study revealed the inherent biases associated with different components of viral metagenomic methods applied to wastewater. Overall, these results provide a well-characterized approach for effectively conducting viral metagenomics analysis of wastewater and reveal that dilution can effectively mitigate MDA bias.
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66
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Abstract
We present the complete genome sequence of a virus found in raw sewage collected in Pittsburgh, PA, USA. Pittsburgh sewage-associated virus 1 (PSAV1) encodes one large open reading frame with conserved domains typically found in the Picornavirales order of viruses. PSAV1 is closely related to Biomphalaria virus 2 (BV2).
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67
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Fernandez-Cassi X, Timoneda N, Martínez-Puchol S, Rusiñol M, Rodriguez-Manzano J, Figuerola N, Bofill-Mas S, Abril JF, Girones R. Metagenomics for the study of viruses in urban sewage as a tool for public health surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 618:870-880. [PMID: 29108696 DOI: 10.1016/j.scitotenv.2017.08.249] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 04/14/2023]
Abstract
The application of next-generation sequencing (NGS) techniques for the identification of viruses present in urban sewage has not been fully explored. This is partially due to a lack of reliable and sensitive protocols for studying viral diversity and to the highly complex analysis required for NGS data processing. One important step towards this goal is finding methods that can efficiently concentrate viruses from sewage samples. Here the application of a virus concentration method based on skimmed milk organic flocculation (SMF) using 10L of sewage collected in different seasons enabled the detection of many viruses. However, some viruses, such as human adenoviruses, could not always be detected using metagenomics, even when quantitative PCR (qPCR) assessments were positive. A targeted metagenomic assay for adenoviruses was conducted and 59.41% of the obtained reads were assigned to murine adenoviruses. However, up to 20 different human adenoviruses (HAdV) were detected by this targeted assay being the most abundant HAdV-41 (29.24%) and HAdV-51 (1.63%). To improve metagenomics' sensitivity, two different protocols for virus concentration were comparatively analysed: an ultracentrifugation protocol and a lower-volume SMF protocol. The sewage virome contained 41 viral families, including pathogenic viral species from families Caliciviridae, Adenoviridae, Astroviridae, Picornaviridae, Polyomaviridae, Papillomaviridae and Hepeviridae. The contribution of urine to sewage metavirome seems to be restricted to a few specific DNA viral families, including the polyomavirus and papillomavirus species. In experimental infections with sewage in a rhesus macaque model, infective human hepatitis E and JC polyomavirus were identified. Urban raw sewage consists of the excreta of thousands of inhabitants; therefore, it is a representative sample for epidemiological surveillance purposes. The knowledge of the metavirome is of significance to public health, highlighting the presence of viral strains that are circulating within a population while acting as a complex matrix for viral discovery.
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Affiliation(s)
- X Fernandez-Cassi
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain.
| | - N Timoneda
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain; Computational Genomics Lab, University of Barcelona and Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Catalonia, Spain
| | - S Martínez-Puchol
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
| | - M Rusiñol
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
| | - J Rodriguez-Manzano
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London, United Kingdom
| | - N Figuerola
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
| | - S Bofill-Mas
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
| | - J F Abril
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain; Computational Genomics Lab, University of Barcelona and Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Catalonia, Spain
| | - R Girones
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
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68
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Kitajima M, Rachmadi AT, Iker BC, Haramoto E, Gerba CP. Temporal variations in genotype distribution of human sapoviruses and Aichi virus 1 in wastewater in Southern Arizona, United States. J Appl Microbiol 2018; 124:1324-1332. [PMID: 29377502 DOI: 10.1111/jam.13712] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/23/2018] [Accepted: 01/23/2018] [Indexed: 01/21/2023]
Abstract
AIMS To investigate the molecular epidemiology, especially temporal variations in genotype distribution, of sapoviruses and Aichi virus 1 (AiV-1) in Arizona, United States, by examining wastewater. METHODS AND RESULTS A total of 26 wastewater samples (13 influent and 13 effluent) were collected monthly from a wastewater treatment plant and viral strains were identified through nested reverse transcription-PCR followed by cloning and sequencing analysis. Identified sapovirus strains were classified into seven genotypes belonging to three genogroups (GI, GII, and GV): GI.1, GI.2, GI.3, GII.1, GII.2, GII.8 and GV.1, with a clear temporal shift. The majority of AiV-1 strains identified from the wastewater samples were classified into genotype B, and genotype A strains were identified in only two samples. CONCLUSIONS We identified a number of sapovirus and AiV-1 strains belonging to multiple genotypes in wastewater samples collected over a 13-month period. Our results suggested a temporal shift in prevalent genotypes in the community. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first study elucidating the genotype distribution of human sapoviruses and AiV-1 in wastewater in the United States. Wastewater surveillance is especially useful for understanding molecular epidemiology of viruses that are less commonly tested in clinical diagnosis, including sapoviruses and AiV-1.
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Affiliation(s)
- M Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido, Japan
| | - A T Rachmadi
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido, Japan
| | - B C Iker
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ, USA
| | - E Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, Kofu, Yamanashi, Japan
| | - C P Gerba
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ, USA
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69
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Yu DT, Han LL, Zhang LM, He JZ. Diversity and Distribution Characteristics of Viruses in Soils of a Marine-Terrestrial Ecotone in East China. MICROBIAL ECOLOGY 2018; 75:375-386. [PMID: 28825127 DOI: 10.1007/s00248-017-1049-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/20/2017] [Indexed: 06/07/2023]
Abstract
A substantial gap remains in our understanding of the abundance, diversity, and ecology of viruses in soil although some advances have been achieved in recent years. In this study, four soil samples according to the salinity gradient from shore to inland in East China have been characterized. Results showed that spherical virus particles represented the largest viral component in all of the four samples. The viromes had remarkably different taxonomic compositions, and most of the sequences were derived from single-stranded DNA viruses, especially from families Microviridae and Circoviridae. Compared with viromes from other aquatic and sediment samples, the community compositions of our four soil viromes resembled each other, meanwhile coastal sample virome closely congregated with sediment and hypersaline viromes, and high salinity paddy soil sample virome was similar with surface sediment virome. Phylogenetic analysis of functional genes showed that four viromes have high diversity of the subfamily Gokushovirinae in family Microviridae and most of Circoviridae replicase protein sequences grouped within the CRESS-DNA viruses. This work provided an initial outline of the viral communities in marine-terrestrial ecotone and will improve our understanding of the ecological functions of soil viruses.
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Affiliation(s)
- Dan-Ting Yu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, 3010, Australia.
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70
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Fernandez-Cassi X, Timoneda N, Gonzales-Gustavson E, Abril JF, Bofill-Mas S, Girones R. A metagenomic assessment of viral contamination on fresh parsley plants irrigated with fecally tainted river water. Int J Food Microbiol 2017. [PMID: 28646670 DOI: 10.1016/j.ijfoodmicro.2017.06.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microbial food-borne diseases are still frequently reported despite the implementation of microbial quality legislation to improve food safety. Among all the microbial agents, viruses are the most important causative agents of food-borne outbreaks. The development and application of a new generation of sequencing techniques to test for viral contaminants in fresh produce is an unexplored field that allows for the study of the viral populations that might be transmitted by the fecal-oral route through the consumption of contaminated food. To advance this promising field, parsley was planted and grown under controlled conditions and irrigated using contaminated river water. Viruses polluting the irrigation water and the parsley leaves were studied by using metagenomics. To address possible contamination due to sample manipulation, library preparation, and other sources, parsley plants irrigated with nutritive solution were used as a negative control. In parallel, viruses present in the river water used for plant irrigation were analyzed using the same methodology. It was possible to assign viral taxons from 2.4 to 74.88% of the total reads sequenced depending on the sample. Most of the viral reads detected in the river water were related to the plant viral families Tymoviridae (66.13%) and Virgaviridae (14.45%) and the phage viral families Myoviridae (5.70%), Siphoviridae (5.06%), and Microviridae (2.89%). Less than 1% of the viral reads were related to viral families that infect humans, including members of the Adenoviridae, Reoviridae, Picornaviridae and Astroviridae families. On the surface of the parsley plants, most of the viral reads that were detected were assigned to the Dicistroviridae family (41.52%). Sequences related to important viral pathogens, such as the hepatitis E virus, several picornaviruses from species A and B as well as human sapoviruses and GIV noroviruses were detected. The high diversity of viral sequences found in the parsley plants suggests that irrigation on fecally-tainted food may have a role in the transmission of a wide diversity of viral families. This finding reinforces the idea that the best way to avoid food-borne viral diseases is to introduce good field irrigation and production practices. New strains have been identified that are related to the Picornaviridae and distantly related to the Hepeviridae family. However, the detection of a viral genome alone does not necessarily indicate there is a risk of infection or disease development. Thus, further investigation is crucial for correlating the detection of viral metagenomes in samples with the risk of infection. There is also an urgent need to develop new methods to improve the sensitivity of current Next Generation Sequencing (NGS) techniques in the food safety area.
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Affiliation(s)
- X Fernandez-Cassi
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain.
| | - N Timoneda
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain; Computational Genomics Lab, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain; Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Catalonia, Spain
| | - E Gonzales-Gustavson
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - J F Abril
- Computational Genomics Lab, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain; Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Catalonia, Spain
| | - S Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - R Girones
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
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71
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Colson P, Aherfi S, La Scola B. Evidence of giant viruses of amoebae in the human gut. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.humic.2017.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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72
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Culley A. New insight into the RNA aquatic virosphere via viromics. Virus Res 2017; 244:84-89. [PMID: 29138044 DOI: 10.1016/j.virusres.2017.11.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/07/2017] [Accepted: 11/07/2017] [Indexed: 01/09/2023]
Abstract
RNA viruses that infect microbes are now recognized as an active, persistent and important component of the aquatic microbial community. While some information about the diversity and dynamics of the RNA virioplankton has been derived from culture-based and single gene approaches, research based on viromic and metatransciptomic methods has generated unprecedented insight into this relatively understudied class of microbes. Here, the relevant literature is summarized and discussed, including viromic studies of extracellular aquatic RNA viral assemblages, and transcriptomic studies of active and associated RNA viruses from aquatic environments followed by commentary on the present challenges and future directions of this field of research.
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Affiliation(s)
- Alexander Culley
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Québec, G1V 0A6, Canada; Centre d'études nordiques (CEN), Université Laval, Québec, Québec, G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, G1V 0A6, Canada; Takuvik, Unité Mixte Interntionale (UMI 3376) Université Laval (Canada) & Centre National de la Recherche Scientifique (France), Québec QC GIV 0A6, Canada.
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73
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Metagenomics reshapes the concepts of RNA virus evolution by revealing extensive horizontal virus transfer. Virus Res 2017; 244:36-52. [PMID: 29103997 PMCID: PMC5801114 DOI: 10.1016/j.virusres.2017.10.020] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/30/2017] [Accepted: 10/31/2017] [Indexed: 12/22/2022]
Abstract
Virus metagenomics is a young research filed but it has already transformed our understanding of virus diversity and evolution, and illuminated at a new level the connections between virus evolution and the evolution and ecology of the hosts. In this review article, we examine the new picture of the evolution of RNA viruses, the dominant component of the eukaryotic virome, that is emerging from metagenomic data analysis. The major expansion of many groups of RNA viruses through metagenomics allowed the construction of substantially improved phylogenetic trees for the conserved virus genes, primarily, the RNA-dependent RNA polymerases (RdRp). In particular, a new superfamily of widespread, small positive-strand RNA viruses was delineated that unites tombus-like and noda-like viruses. Comparison of the genome architectures of RNA viruses discovered by metagenomics and by traditional methods reveals an extent of gene module shuffling among diverse virus genomes that far exceeds the previous appreciation of this evolutionary phenomenon. Most dramatically, inclusion of the metagenomic data in phylogenetic analyses of the RdRp resulted in the identification of numerous, strongly supported groups that encompass RNA viruses from diverse hosts including different groups of protists, animals and plants. Notwithstanding potential caveats, in particular, incomplete and uneven sampling of eukaryotic taxa, these highly unexpected findings reveal horizontal virus transfer (HVT) between diverse hosts as the central aspect of RNA virus evolution. The vast and diverse virome of invertebrates, particularly nematodes and arthropods, appears to be the reservoir, from which the viromes of plants and vertebrates evolved via multiple HVT events.
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74
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Wong K, Molina M. Applying Quantitative Molecular Tools for Virus Transport Studies: Opportunities and Challenges. GROUND WATER 2017; 55:778-783. [PMID: 28542984 PMCID: PMC6146963 DOI: 10.1111/gwat.12531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 04/02/2017] [Accepted: 04/05/2017] [Indexed: 05/31/2023]
Abstract
Bacteriophages have been used in soil column studies for the last several decades as surrogates to study the fate and transport behavior of enteric viruses in groundwater. However, recent studies have shown that the transport behavior of bacteriophages and enteric viruses in porous media can be very different. The next generation of virus transport science must therefore provide more data on mobility of enteric viruses and the relationship between transport behaviors of enteric viruses and bacteriophages. To achieve this new paradigm, labor intensity devoted to enteric virus quantification method must be reduced. Recent studies applied quantitative polymerase chain reaction (qPCR) to column filtration experiments to study the transport behavior of human adenovirus (HAdV) in porous media under a variety of conditions. A similar approach can be used to study the transport of other enteric viruses such as norovirus. Analyzing the column samples with both qPCR and culture assays and applying multiplex qPCR to study cotransport behavior of more than one virus will provide information to under-explored areas in virus transport science. Both nucleic acid extraction kits and one-step lysis protocols have been used in these column studies to extract viral nucleic acid for qPCR quantification. The pros and cons of both methods are compared herein and solutions for overcoming problems are suggested. As better understanding of the transport behavior of enteric viruses is clearly needed, we strongly advocate for application of rapid molecular tools in future studies as well as optimization of protocols to overcome their current limitations.
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Affiliation(s)
- Kelvin Wong
- Ecosystem Research Division, USEPA Office of Research and Development, National Exposure Research Laboratory, 960 College Station Road, Athens, GA, 30605
- Oak Ridge Institute for Science and Education, 1299 Bethel Valley Road, Oak Ridge, TN, 37831
| | - Marirosa Molina
- Ecosystem Research Division, USEPA Office of Research and Development, National Exposure Research Laboratory, 960 College Station Road, Athens, GA, 30605
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75
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Mahmoud H, Jose L. Phage and Nucleocytoplasmic Large Viral Sequences Dominate Coral Viromes from the Arabian Gulf. Front Microbiol 2017; 8:2063. [PMID: 29114244 PMCID: PMC5660727 DOI: 10.3389/fmicb.2017.02063] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 10/09/2017] [Indexed: 11/25/2022] Open
Abstract
Corals that naturally thrive under extreme conditions are gaining increasing attention due to their importance as living models to understand the impact of global warming on world corals. Here, we present the first metagenomic study of viral communities in corals thriving in a thermally variable water body in which the temperature fluctuates between 11 and 39°C in different seasons. The viral assemblages of two of the most abundant massive (Porites harrisoni) and branching (Acropora downingi) corals in offshore and inshore reef systems in the northern Arabian Gulf were investigated. Samples were collected from five reef systems during summer, autumn and winter of 2011/2012. The two coral viromes contain 12 viral families, including 10 dsDNA viral families [Siphoviridae, Podoviridae, Myoviridae, Phycodnaviridae, Baculoviridae, Herpesviridae, Adenoviridae, Alloherpesviridae, Mimiviridae and one unclassified family], one-ssDNA viral family (Microviridae) and one RNA viral family (Retroviridae). Overall, sequences significantly similar to Podoviridae were the most abundant in the P. harrisoni and A. downingi viromes. Various morphological types of virus-like particles (VLPs) were confirmed in the healthy coral tissue by transmission electron microscopy, including large tailless VLPs and electron-dense core VLPs. Tailed bacteriophages were isolated from coral tissue using a plaque assay. Higher functional gene diversity was recorded in A. downingi than in P. harrisoni, and comparative metagenomics revealed that the Gulf viral assemblages are functionally distinct from Pacific Ocean coral viral communities.
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Affiliation(s)
- Huda Mahmoud
- Faculty of Science, Department of Biological Sciences, Kuwait University, Safat, Kuwait
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76
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Gerba CP, Betancourt WQ. Viral Aggregation: Impact on Virus Behavior in the Environment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:7318-7325. [PMID: 28599109 DOI: 10.1021/acs.est.6b05835] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Aggregates of viruses can have a significant impact on quantification and behavior of viruses in the environment. Viral aggregates may be formed in numerous ways. Viruses may form crystal like structures and aggregates in the host cell during replication or may form due to changes in environmental conditions after virus particles are released from the host cells. Aggregates tend to form near the isoelectric point of the virus, under the influence of certain salts and salt concentrations in solution, cationic polymers, and suspended organic matter. The given conditions under which aggregates form in the environment are highly dependent on the type of virus, type of salts in solution (cation, anion. monovalent, divalent) and pH. However, virus type greatly influences the conditions when aggregation/disaggregation will occur, making predictions difficult under any given set of water quality conditions. Most studies have shown that viral aggregates increase the survival of viruses in the environment and resistance to disinfectants, especially with more reactive disinfectants. The presence of viral aggregates may also result in overestimation of removal by filtration processes. Virus aggregation-disaggregation is a complex process and predicting the behavior of any individual virus is difficult under a given set of environmental circumstances without actual experimental data.
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Affiliation(s)
- Charles P Gerba
- Department of Soil, Water and Environmental Science Water & Energy Sustainable Technology (WEST) Center, The University of Arizona , 2959 W. Calle Agua, Nueva Tucson, Arizona 85745, United States
| | - Walter Q Betancourt
- Department of Soil, Water and Environmental Science Water & Energy Sustainable Technology (WEST) Center, The University of Arizona , 2959 W. Calle Agua, Nueva Tucson, Arizona 85745, United States
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77
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Colombo S, Arioli S, Neri E, Della Scala G, Gargari G, Mora D. Viromes As Genetic Reservoir for the Microbial Communities in Aquatic Environments: A Focus on Antimicrobial-Resistance Genes. Front Microbiol 2017; 8:1095. [PMID: 28663745 PMCID: PMC5471338 DOI: 10.3389/fmicb.2017.01095] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/30/2017] [Indexed: 11/16/2022] Open
Abstract
Despite studies of viromes isolated from aquatic environments are becoming increasingly frequent, most of them are limited to the characterization of viral taxonomy. Bacterial reads in viromes are abundant but the extent to which this genetic material is playing a role in the ecology of aquatic microbiology remains unclear. To this aim, we developed of a useful approach for the characterization of viral and microbial communities of aquatic environments with a particular focus on the identification of microbial genes harbored in the viromes. Virus-like particles were isolated from water samples collected across the Lambro River, from the spring to the high urbanized Milan area. The derived viromes were analyzed by shotgun metagenomic sequencing looking for the presence, relative abundance of bacterial genes with particular focus on those genes involved in antimicrobial resistance mechanisms. Antibiotic and heavy metal resistance genes have been identified in all virome samples together with a high abundance of reads assigned to cellular processes and signaling. Virome data compared to those identified in the microbiome isolated from the same sample revealed differences in terms of functional categories and their relative abundance. To verify the role of aquatic viral population in bacterial gene transfer, water-based mesocosms were perturbed or not perturbed with a low dose of tetracycline. The results obtained by qPCR assays revealed variation in abundance of tet genes in the virome and microbiome highlighting a relevant role of viral populations in microbial gene mobilization.
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Affiliation(s)
- Stefano Colombo
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| | - Stefania Arioli
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| | - Eros Neri
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| | - Giulia Della Scala
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| | - Giorgio Gargari
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
| | - Diego Mora
- Department of Food, Environmental and Nutritional Sciences, University of MilanMilan, Italy
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78
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Watkins SC, Putonti C. The use of informativity in the development of robust viromics-based examinations. PeerJ 2017; 5:e3281. [PMID: 28480148 PMCID: PMC5417064 DOI: 10.7717/peerj.3281] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 04/07/2017] [Indexed: 01/08/2023] Open
Abstract
Metagenomics-based studies have provided insight into many of the complex microbial communities responsible for maintaining life on this planet. Sequencing efforts often uncover novel genetic content; this is most evident for phage communities, in which upwards of 90% of all sequences exhibit no similarity to any sequence in current data repositories. For the small fraction that can be identified, the top BLAST hit is generally posited as being representative of a viral taxon present in the sample of origin. Homology-based classification, however, can be misleading as sequence repositories capture but a small fraction of phage diversity. Furthermore, lateral gene transfer is pervasive within phage communities. As such, the presence of a particular gene may not be indicative of the presence of a particular viral species. Rather, it is just that: an indication of the presence of a specific gene. To circumvent this limitation, we have developed a new method for the analysis of viral metagenomic datasets. BLAST hits are weighted, integrating the sequence identity and length of alignments as well as a taxonomic signal, such that each gene is evaluated with respect to its information content. Through this quantifiable metric, predictions of viral community structure can be made with confidence. As a proof-of-concept, the approach presented here was implemented and applied to seven freshwater viral metagenomes. While providing a robust method for evaluating viral metagenomic data, the tool is versatile and can easily be customized to investigations of any environment or biome.
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Affiliation(s)
- Siobhan C Watkins
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, United States of America.,Department of Biology, Loyola University of Chicago, Chicago, IL, United States of America
| | - Catherine Putonti
- Department of Biology, Loyola University of Chicago, Chicago, IL, United States of America.,Department of Computer Science, Loyola University of Chicago, Chicago, IL, United States of America.,Bioinformatics Program, Loyola University of Chicago, Chicago, IL, United States of America.,Department of Microbiology and Immunology, Loyola University of Chicago, Maywood, IL, United States of America
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79
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Munang'andu HM, Mugimba KK, Byarugaba DK, Mutoloki S, Evensen Ø. Current Advances on Virus Discovery and Diagnostic Role of Viral Metagenomics in Aquatic Organisms. Front Microbiol 2017; 8:406. [PMID: 28382024 PMCID: PMC5360701 DOI: 10.3389/fmicb.2017.00406] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 02/27/2017] [Indexed: 12/20/2022] Open
Abstract
The global expansion of the aquaculture industry has brought with it a corresponding increase of novel viruses infecting different aquatic organisms. These emerging viral pathogens have proved to be a challenge to the use of traditional cell-cultures and immunoassays for identification of new viruses especially in situations where the novel viruses are unculturable and no antibodies exist for their identification. Viral metagenomics has the potential to identify novel viruses without prior knowledge of their genomic sequence data and may provide a solution for the study of unculturable viruses. This review provides a synopsis on the contribution of viral metagenomics to the discovery of viruses infecting different aquatic organisms as well as its potential role in viral diagnostics. High throughput Next Generation sequencing (NGS) and library construction used in metagenomic projects have simplified the task of generating complete viral genomes unlike the challenge faced in traditional methods that use multiple primers targeted at different segments and VPs to generate the entire genome of a novel virus. In terms of diagnostics, studies carried out this far show that viral metagenomics has the potential to serve as a multifaceted tool able to study and identify etiological agents of single infections, co-infections, tissue tropism, profiling viral infections of different aquatic organisms, epidemiological monitoring of disease prevalence, evolutionary phylogenetic analyses, and the study of genomic diversity in quasispecies viruses. With sequencing technologies and bioinformatics analytical tools becoming cheaper and easier, we anticipate that metagenomics will soon become a routine tool for the discovery, study, and identification of novel pathogens including viruses to enable timely disease control for emerging diseases in aquaculture.
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Affiliation(s)
- Hetron M. Munang'andu
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life SciencesOslo, Norway
| | - Kizito K. Mugimba
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life SciencesOslo, Norway
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere UniversityKampala, Uganda
| | - Denis K. Byarugaba
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere UniversityKampala, Uganda
| | - Stephen Mutoloki
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life SciencesOslo, Norway
| | - Øystein Evensen
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life SciencesOslo, Norway
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80
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O'Brien E, Munir M, Marsh T, Heran M, Lesage G, Tarabara VV, Xagoraraki I. Diversity of DNA viruses in effluents of membrane bioreactors in Traverse City, MI (USA) and La Grande Motte (France). WATER RESEARCH 2017; 111:338-345. [PMID: 28107747 DOI: 10.1016/j.watres.2017.01.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 01/03/2017] [Accepted: 01/06/2017] [Indexed: 05/03/2023]
Abstract
This study assesses diversity of DNA viruses in the effluents of two membrane bioreactor (MBR) wastewater treatment plants (WWTPs): an MBR in the United States and an MBR in France. Viral diversity of these effluents is compared to that of a conventional activated sludge WWTP in the U.S. Diversity analysis indicates Herpesvirales to be the most abundant order of potentially pathogenic human DNA viruses in wastewater treated effluent in all utilities. Other potentially pathogenic human viruses detected include Adenoviridae, Parvoviridae, and Polyomaviridae. Bacteriophage order Caudovirales comprises the majority of DNA virus sequences in the effluent of all utilities. The choice of treatment process (MBR versus activated sludge reactor) utilized had no impact on effluent DNA viral diversity. In contrast, the type of disinfection applied had an impact on the viral diversity present in the effluent.
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Affiliation(s)
- Evan O'Brien
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48823, USA
| | - Mariya Munir
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48823, USA
| | - Terence Marsh
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48823, USA
| | - Marc Heran
- Institut Européen des Membranes, IEM, UMR-5635, Université de Montpellier, ENSCM, CNRS, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | - Geoffroy Lesage
- Institut Européen des Membranes, IEM, UMR-5635, Université de Montpellier, ENSCM, CNRS, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | - Volodymyr V Tarabara
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48823, USA
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48823, USA.
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81
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Thannesberger J, Hellinger HJ, Klymiuk I, Kastner MT, Rieder FJJ, Schneider M, Fister S, Lion T, Kosulin K, Laengle J, Bergmann M, Rattei T, Steininger C. Viruses comprise an extensive pool of mobile genetic elements in eukaryote cell cultures and human clinical samples. FASEB J 2017; 31:1987-2000. [PMID: 28179422 DOI: 10.1096/fj.201601168r] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/09/2017] [Indexed: 01/09/2023]
Abstract
Viruses shape a diversity of ecosystems by modulating their microbial, eukaryotic, or plant host metabolism. The complexity of virus-host interaction networks is progressively fathomed by novel metagenomic approaches. By using a novel metagenomic method, we explored the virome in mammalian cell cultures and clinical samples to identify an extensive pool of mobile genetic elements in all of these ecosystems. Despite aseptic treatment, cell cultures harbored extensive and diverse phage populations with a high abundance of as yet unknown and uncharacterized viruses (viral dark matter). Unknown phages also predominated in the oropharynx and urine of healthy individuals and patients infected with cytomegalovirus despite demonstration of active cytomegalovirus replication. The novelty of viral sequences correlated primarily with the individual evaluated, whereas relative abundance of encoded protein functions was associated with the ecologic niches probed. Together, these observations demonstrate the extensive presence of viral dark matter in human and artificial ecosystems.-Thannesberger, J., Hellinger, H.-J., Klymiuk, I., Kastner, M.-T., Rieder, F. J. J., Schneider, M., Fister, S., Lion, T., Kosulin, K., Laengle, J., Bergmann, M., Rattei, T., Steininger, C. Viruses comprise an extensive pool of mobile genetic elements in eukaryote cell cultures and human clinical samples.
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Affiliation(s)
- Jakob Thannesberger
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria
| | - Hans-Joerg Hellinger
- CUBE-Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Ingeborg Klymiuk
- Center for Medical Research, Core Facility Molecular Biology, Medical University of Graz, Graz, Austria
| | - Marie-Theres Kastner
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria
| | - Franz J J Rieder
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria
| | - Martina Schneider
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria
| | - Susanne Fister
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, University of Veterinary Medicine, Vienna, Austria
| | - Thomas Lion
- Children's Cancer Research Institute, Vienna, Austria
| | - Karin Kosulin
- Children's Cancer Research Institute, Vienna, Austria
| | - Johannes Laengle
- Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Michael Bergmann
- Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Thomas Rattei
- CUBE-Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Christoph Steininger
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria;
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82
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Hjelmsø MH, Hellmér M, Fernandez-Cassi X, Timoneda N, Lukjancenko O, Seidel M, Elsässer D, Aarestrup FM, Löfström C, Bofill-Mas S, Abril JF, Girones R, Schultz AC. Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing. PLoS One 2017; 12:e0170199. [PMID: 28099518 PMCID: PMC5242460 DOI: 10.1371/journal.pone.0170199] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/02/2017] [Indexed: 01/18/2023] Open
Abstract
Viral sewage metagenomics is a novel field of study used for surveillance, epidemiological studies, and evaluation of waste water treatment efficiency. In raw sewage human waste is mixed with household, industrial and drainage water, and virus particles are, therefore, only found in low concentrations. This necessitates a step of sample concentration to allow for sensitive virus detection. Additionally, viruses harbor a large diversity of both surface and genome structures, which makes universal viral genomic extraction difficult. Current studies have tackled these challenges in many different ways employing a wide range of viral concentration and extraction procedures. However, there is limited knowledge of the efficacy and inherent biases associated with these methods in respect to viral sewage metagenomics, hampering the development of this field. By the use of next generation sequencing this study aimed to evaluate the efficiency of four commonly applied viral concentrations techniques (precipitation with polyethylene glycol, organic flocculation with skim milk, monolithic adsorption filtration and glass wool filtration) and extraction methods (Nucleospin RNA XS, QIAamp Viral RNA Mini Kit, NucliSENS® miniMAG®, or PowerViral® Environmental RNA/DNA Isolation Kit) to determine the viriome in a sewage sample. We found a significant influence of concentration and extraction protocols on the detected viriome. The viral richness was largest in samples extracted with QIAamp Viral RNA Mini Kit or PowerViral® Environmental RNA/DNA Isolation Kit. Highest viral specificity were found in samples concentrated by precipitation with polyethylene glycol or extracted with Nucleospin RNA XS. Detection of viral pathogens depended on the method used. These results contribute to the understanding of method associated biases, within the field of viral sewage metagenomics, making evaluation of the current literature easier and helping with the design of future studies.
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Affiliation(s)
- Mathis Hjort Hjelmsø
- Research Group for Genomic Epidemiology, The National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
- * E-mail:
| | - Maria Hellmér
- Division of Microbiology and Production, The National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Xavier Fernandez-Cassi
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Natàlia Timoneda
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
- Institute of Biomedicine of the University of Barcelona, University of Barcelona, Barcelona, Catalonia, Spain
| | - Oksana Lukjancenko
- Research Group for Genomic Epidemiology, The National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Michael Seidel
- Institute of Hydrochemistry, Chair of Analytical Chemistry, Technical University of Munich, Munich, Germany
| | - Dennis Elsässer
- Institute of Hydrochemistry, Chair of Analytical Chemistry, Technical University of Munich, Munich, Germany
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, The National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Charlotta Löfström
- Division of Microbiology and Production, The National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Sílvia Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Josep F. Abril
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
- Institute of Biomedicine of the University of Barcelona, University of Barcelona, Barcelona, Catalonia, Spain
| | - Rosina Girones
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Anna Charlotte Schultz
- Division of Microbiology and Production, The National Food Institute, Technical University of Denmark, Søborg, Denmark
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83
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Munang'andu HM. Environmental Viral Metagenomics Analyses in Aquaculture: Applications in Epidemiology and Disease Control. Front Microbiol 2016; 7:1986. [PMID: 28018317 PMCID: PMC5155513 DOI: 10.3389/fmicb.2016.01986] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/28/2016] [Indexed: 11/17/2022] Open
Abstract
Studies on the epidemiology of viral diseases in aquaculture have for a long time depended on isolation of viruses from infected aquatic organisms. The role of aquatic environments in the epidemiology of viral diseases in aquaculture has not been extensively expounded mainly because of the lack of appropriate tools for environmental studies on aquatic viruses. However, the upcoming of metagenomics analyses opens great avenues in which environmental samples can be used to study the epidemiology of viral diseases outside their host species. Hence, in this review I have shown that epidemiological factors that influence the composition of viruses in different aquatic environments include ecological factors, anthropogenic activities and stocking densities of cultured organisms based on environmental metagenomics studies carried out this far. Ballast water transportation and global trade of aquatic organisms are the most common virus dispersal process identified this far. In terms of disease control for outdoor aquaculture systems, baseline data on viruses found in different environments intended for aquaculture use can be obtained to enable the design of effective disease control strategies. And as such, high-risk areas having a high specter of pathogenic viruses can be identified as an early warning system. As for the control of viral diseases for indoor recirculation aquaculture systems (RAS), the most effective disinfection methods able to eliminate pathogenic viruses from water used in RAS can be identified. Overall, the synopsis I have put forth in this review shows that environmental samples can be used to study the epidemiology of viral diseases in aquaculture using viral metagenomics analysis as an overture for the design of rational disease control strategies.
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Affiliation(s)
- Hetron M Munang'andu
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences Oslo, Norway
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84
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Roux S, Solonenko NE, Dang VT, Poulos BT, Schwenck SM, Goldsmith DB, Coleman ML, Breitbart M, Sullivan MB. Towards quantitative viromics for both double-stranded and single-stranded DNA viruses. PeerJ 2016; 4:e2777. [PMID: 28003936 PMCID: PMC5168678 DOI: 10.7717/peerj.2777] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/08/2016] [Indexed: 01/06/2023] Open
Abstract
Background Viruses strongly influence microbial population dynamics and ecosystem functions. However, our ability to quantitatively evaluate those viral impacts is limited to the few cultivated viruses and double-stranded DNA (dsDNA) viral genomes captured in quantitative viral metagenomes (viromes). This leaves the ecology of non-dsDNA viruses nearly unknown, including single-stranded DNA (ssDNA) viruses that have been frequently observed in viromes, but not quantified due to amplification biases in sequencing library preparations (Multiple Displacement Amplification, Linker Amplification or Tagmentation). Methods Here we designed mock viral communities including both ssDNA and dsDNA viruses to evaluate the capability of a sequencing library preparation approach including an Adaptase step prior to Linker Amplification for quantitative amplification of both dsDNA and ssDNA templates. We then surveyed aquatic samples to provide first estimates of the abundance of ssDNA viruses. Results Mock community experiments confirmed the biased nature of existing library preparation methods for ssDNA templates (either largely enriched or selected against) and showed that the protocol using Adaptase plus Linker Amplification yielded viromes that were ±1.8-fold quantitative for ssDNA and dsDNA viruses. Application of this protocol to community virus DNA from three freshwater and three marine samples revealed that ssDNA viruses as a whole represent only a minor fraction (<5%) of DNA virus communities, though individual ssDNA genomes, both eukaryote-infecting Circular Rep-Encoding Single-Stranded DNA (CRESS-DNA) viruses and bacteriophages from the Microviridae family, can be among the most abundant viral genomes in a sample. Discussion Together these findings provide empirical data for a new virome library preparation protocol, and a first estimate of ssDNA virus abundance in aquatic systems.
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Affiliation(s)
- Simon Roux
- Department of Microbiology, The Ohio State University , Columbus , OH , United States
| | - Natalie E Solonenko
- Department of Microbiology, The Ohio State University , Columbus , OH , United States
| | - Vinh T Dang
- Department of Microbiology, Ha Long University , Uong Bi , Quang Ninh , Vietnam
| | - Bonnie T Poulos
- Department of Ecology and Evolutionary Biology, University of Arizona , Tucson , AZ , United States
| | - Sarah M Schwenck
- Department of Ecology and Evolutionary Biology, University of Arizona , Tucson , AZ , United States
| | - Dawn B Goldsmith
- College of Marine Science, University of South Florida , St. Petersburg , FL , United States
| | - Maureen L Coleman
- Department of the Geophysical Sciences, University of Chicago , Chicago , IL , United States
| | - Mya Breitbart
- College of Marine Science, University of South Florida , St. Petersburg , FL , United States
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, United States; Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, United States
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85
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Rastrojo A, Alcamí A. Aquatic viral metagenomics: Lights and shadows. Virus Res 2016; 239:87-96. [PMID: 27889617 DOI: 10.1016/j.virusres.2016.11.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/18/2016] [Indexed: 01/02/2023]
Abstract
Viruses are the most abundant biological entities on Earth, exceeding bacteria in most of the ecosystems. Specially in oceans, viruses are thought to be the major planktonic predators shaping microorganism communities and controlling ocean biological capacity. Plankton lysis by viruses plays an important role in ocean nutrient and energy cycles. Viral metagenomics has emerged as a powerful tool to uncover viral diversity in aquatic ecosystems through the use of Next Generation Sequencing. However, many of the commonly used viral sample preparation steps have several important biases that must be considered to avoid a misinterpretation of the results. In addition to biases caused by the purification of virus particles, viral DNA/RNA amplification and the preparation of genomic libraries could also introduce biases, and a detailed knowledge about such protocols is required. In this review, the main steps in the viral metagenomic workflow are described paying special attention to the potential biases introduced by each one.
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Affiliation(s)
- Alberto Rastrojo
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas y Universidad Autónoma de Madrid), Madrid, Spain
| | - Antonio Alcamí
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas y Universidad Autónoma de Madrid), Madrid, Spain.
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86
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Deep sequencing for discovery and evolutionary analysis of plant viruses. Virus Res 2016; 239:82-86. [PMID: 27876625 DOI: 10.1016/j.virusres.2016.11.019] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/18/2016] [Indexed: 11/21/2022]
Abstract
The advent of next generation sequencing (NGS), or deep sequencing, has allowed great advances to be made in discovery, diagnostics, and evolutionary studies in plant viruses. Various methods have been used for enrichment for virus-specific nucleic acids, each of which have some drawbacks. Many novel viruses have been discovered in plants by NGS technologies, and there is a good deal of promise for more comprehensive studies in virus evolution. However, each aspect of using NGS has its caveats that need to be considered, and there is still a need for better tools of analysis, as well as method for validation of sequence variation.
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87
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Near Real-Time Flow Cytometry Monitoring of Bacterial and Viral Removal Efficiencies during Water Reclamation Processes. WATER 2016. [DOI: 10.3390/w8100464] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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88
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Pearson VM, Caudle SB, Rokyta DR. Viral recombination blurs taxonomic lines: examination of single-stranded DNA viruses in a wastewater treatment plant. PeerJ 2016; 4:e2585. [PMID: 27781171 PMCID: PMC5075696 DOI: 10.7717/peerj.2585] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 09/19/2016] [Indexed: 12/26/2022] Open
Abstract
Understanding the structure and dynamics of microbial communities, especially those of economic concern, is of paramount importance to maintaining healthy and efficient microbial communities at agricultural sites and large industrial cultures, including bioprocessors. Wastewater treatment plants are large bioprocessors which receive water from multiple sources, becoming reservoirs for the collection of many viral families that infect a broad range of hosts. To examine this complex collection of viruses, full-length genomes of circular ssDNA viruses were isolated from a wastewater treatment facility using a combination of sucrose-gradient size selection and rolling-circle amplification and sequenced on an Illumina MiSeq. Single-stranded DNA viruses are among the least understood groups of microbial pathogens due to genomic biases and culturing difficulties, particularly compared to the larger, more often studied dsDNA viruses. However, the group contains several notable well-studied examples, including agricultural pathogens which infect both livestock and crops (Circoviridae and Geminiviridae), and model organisms for genetics and evolution studies (Microviridae). Examination of the collected viral DNA provided evidence for 83 unique genotypic groupings, which were genetically dissimilar to known viral types and exhibited broad diversity within the community. Furthermore, although these genomes express similarities to known viral families, such as Circoviridae, Geminiviridae, and Microviridae, many are so divergent that they may represent new taxonomic groups. This study demonstrated the efficacy of the protocol for separating bacteria and large viruses from the sought after ssDNA viruses and the ability to use this protocol to obtain an in-depth analysis of the diversity within this group.
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Affiliation(s)
- Victoria M Pearson
- Department of Biological Science, Florida State University , Tallahassee , FL , USA
| | - S Brian Caudle
- Division of Food Safety, Florida Department of Agriculture and Consumer Services , Tallahassee , FL , USA
| | - Darin R Rokyta
- Department of Biological Science, Florida State University , Tallahassee , FL , USA
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89
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Uyaguari-Diaz MI, Chan M, Chaban BL, Croxen MA, Finke JF, Hill JE, Peabody MA, Van Rossum T, Suttle CA, Brinkman FSL, Isaac-Renton J, Prystajecky NA, Tang P. A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples. MICROBIOME 2016; 4:20. [PMID: 27391119 PMCID: PMC5011856 DOI: 10.1186/s40168-016-0166-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/04/2016] [Indexed: 05/16/2023]
Abstract
BACKGROUND Studies of environmental microbiota typically target only specific groups of microorganisms, with most focusing on bacteria through taxonomic classification of 16S rRNA gene sequences. For a more holistic understanding of a microbiome, a strategy to characterize the viral, bacterial, and eukaryotic components is necessary. RESULTS We developed a method for metagenomic and amplicon-based analysis of freshwater samples involving the concentration and size-based separation of eukaryotic, bacterial, and viral fractions. Next-generation sequencing and culture-independent approaches were used to describe and quantify microbial communities in watersheds with different land use in British Columbia. Deep amplicon sequencing was used to investigate the distribution of certain viruses (g23 and RdRp), bacteria (16S rRNA and cpn60), and eukaryotes (18S rRNA and ITS). Metagenomic sequencing was used to further characterize the gene content of the bacterial and viral fractions at both taxonomic and functional levels. CONCLUSION This study provides a systematic approach to separate and characterize eukaryotic-, bacterial-, and viral-sized particles. Methodologies described in this research have been applied in temporal and spatial studies to study the impact of land use on watershed microbiomes in British Columbia.
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Affiliation(s)
- Miguel I. Uyaguari-Diaz
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Michael Chan
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
| | - Bonnie L. Chaban
- South Kensington Campus, Imperial College London, Sir Ernst Chain Building, London, SW7 2AZ UK
| | - Matthew A. Croxen
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
| | - Jan F. Finke
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Janet E. Hill
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4 Canada
| | - Michael A. Peabody
- Department of Molecular Biology and Biochemistry, South Science Building, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Thea Van Rossum
- Department of Molecular Biology and Biochemistry, South Science Building, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Curtis A. Suttle
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1Z8 Canada
| | - Fiona S. L. Brinkman
- Department of Molecular Biology and Biochemistry, South Science Building, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Judith Isaac-Renton
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Natalie A. Prystajecky
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Patrick Tang
- Department of Pathology, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
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90
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Bruder K, Malki K, Cooper A, Sible E, Shapiro JW, Watkins SC, Putonti C. Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges. Evol Bioinform Online 2016; 12:25-33. [PMID: 27375355 PMCID: PMC4915788 DOI: 10.4137/ebo.s38549] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/03/2016] [Accepted: 04/10/2016] [Indexed: 12/30/2022] Open
Abstract
Advances in bioinformatics and sequencing technologies have allowed for the analysis of complex microbial communities at an unprecedented rate. While much focus is often placed on the cellular members of these communities, viruses play a pivotal role, particularly bacteria-infecting viruses (bacteriophages); phages mediate global biogeochemical processes and drive microbial evolution through bacterial grazing and horizontal gene transfer. Despite their importance and ubiquity in nature, very little is known about the diversity and structure of viral communities. Though the need for culture-based methods for viral identification has been somewhat circumvented through metagenomic techniques, the analysis of metaviromic data is marred with many unique issues. In this review, we examine the current bioinformatic approaches for metavirome analyses and the inherent challenges facing the field as illustrated by the ongoing efforts in the exploration of freshwater phage populations.
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Affiliation(s)
- Katherine Bruder
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - Kema Malki
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | | | - Emily Sible
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - Jason W Shapiro
- Department of Biology, Loyola University Chicago, Chicago, IL, USA.; Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA
| | | | - Catherine Putonti
- Department of Biology, Loyola University Chicago, Chicago, IL, USA.; Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA.; Department of Computer Science, Loyola University Chicago, Chicago, IL, USA
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91
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Miranda JA, Culley AI, Schvarcz CR, Steward GF. RNA viruses as major contributors to Antarctic virioplankton. Environ Microbiol 2016; 18:3714-3727. [PMID: 26950773 DOI: 10.1111/1462-2920.13291] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 03/05/2016] [Indexed: 11/28/2022]
Abstract
Early work on marine algal viruses focused exclusively on those having DNA genomes, but recent studies suggest that RNA viruses, especially those with positive-sense, single-stranded RNA (+ssRNA) genomes, are abundant in tropical and temperate coastal seawater. To test whether this was also true of polar waters, we estimated the relative abundances of RNA and DNA viruses using a mass ratio approach and conducted shotgun metagenomics on purified viral samples collected from a coastal site near Palmer Station, Antarctica on six occasions throughout a summer phytoplankton bloom (November-March). Our data suggest that RNA viruses contributed up to 65% of the total virioplankton (8-65%), and that, as observed previously in warmer waters, the majority of RNA viruses in these Antarctic RNA virus metagenomes had +ssRNA genomes most closely related to viruses in the order Picornavirales. Assembly of the metagenomic reads resulted in five novel, nearly complete genomes, three of which had features similar to diatom-infecting viruses. Our data are consistent with the hypothesis that RNA viruses influence diatom bloom dynamics in Antarctic waters.
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Affiliation(s)
- Jaclyn A Miranda
- Department of Oceanography, Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, 1950 East-West Road, Honolulu, HI, 96822, USA
| | - Alexander I Culley
- Department of Oceanography, Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, 1950 East-West Road, Honolulu, HI, 96822, USA
| | - Christopher R Schvarcz
- Department of Oceanography, Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, 1950 East-West Road, Honolulu, HI, 96822, USA
| | - Grieg F Steward
- Department of Oceanography, Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, 1950 East-West Road, Honolulu, HI, 96822, USA
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92
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Aguirre de Cárcer D, López-Bueno A, Alonso-Lobo JM, Quesada A, Alcamí A. Metagenomic analysis of lacustrine viral diversity along a latitudinal transect of the Antarctic Peninsula. FEMS Microbiol Ecol 2016; 92:fiw074. [PMID: 27059864 DOI: 10.1093/femsec/fiw074] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2016] [Indexed: 01/21/2023] Open
Abstract
Environmental viruses constitute the most abundant biological entities on earth, and harbor an enormous genetic diversity. While their strong influence on the ecosystem is widely acknowledged, current knowledge about their diversity and distribution remains limited. Here we present the metagenomic study of viral communities from freshwater bodies located along a transect of the Antarctic Peninsula. These ecosystems were chosen on the basis of environmental and biogeographical variation. The results obtained indicate that the virus assemblages were diverse, and that the larger fraction represented viruses with no close relatives in the databases. Comparisons to existing metaviromes showed that the communities studied were dissimilar to other freshwater viromes including those from the Arctic. Finally, we observed no indication of there being a reduction in either viral richness or diversity estimates with increasing latitude along the studied transect, further adding to the controversy regarding the possible existence of latitudinal gradients of diversity in the microbial world.
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Affiliation(s)
- Daniel Aguirre de Cárcer
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Alberto López-Bueno
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Juan M Alonso-Lobo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Antonio Quesada
- Departamento de Biología, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Antonio Alcamí
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid, 28049 Madrid, Spain
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93
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Hause BM, Palinski R, Hesse R, Anderson G. Highly diverse posaviruses in swine faeces are aquatic in origin. J Gen Virol 2016; 97:1362-1367. [PMID: 27002315 DOI: 10.1099/jgv.0.000461] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Posaviruses are a group of highly divergent viruses identified in swine faeces that are distantly related to other members of the order Picornavirales. Eighteen posavirus genomes were assembled from 10 out of 25 (40 %) faecal-swab pools collected from healthy adult swine. Phylogenetic analysis of the conserved RNA-dependent RNA polymerase (Pol) domain found that posaviruses form a large, highly diverse, monophyletic clade, which includes similar viruses identified in human (husavirus) and fish (fisavirus) faeces or intestinal contents, respectively. Quantitative reverse transcription PCR analysis of water samples collected from commercial swine barns identified four out of 19 (21 %) samples were positive using a 5'-nuclease assay targeting the Pol region of posavirus 1. ICPD (immunoprecipitation coupled to PCR detection) assays to explore serological evidence of posavirus infection found only a single positive sample, suggesting posaviruses do not commonly infect swine, and together these results suggests a likely aquatic host.
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Affiliation(s)
- Ben M Hause
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Rachel Palinski
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Richard Hesse
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS 66506, USA
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA
| | - Gary Anderson
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS 66506, USA
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA
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94
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Diverse circular replication-associated protein encoding viruses circulating in invertebrates within a lake ecosystem. INFECTION GENETICS AND EVOLUTION 2016; 39:304-316. [PMID: 26873065 DOI: 10.1016/j.meegid.2016.02.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/30/2016] [Accepted: 02/07/2016] [Indexed: 11/24/2022]
Abstract
Over the last five years next-generation sequencing has become a cost effective and efficient method for identifying known and unknown microorganisms. Access to this technique has dramatically changed the field of virology, enabling a wide range of environmental viral metagenome studies to be undertaken of organisms and environmental samples from polar to tropical regions. These studies have led to the discovery of hundreds of highly divergent single stranded DNA (ssDNA) virus-like sequences encoding replication-associated proteins. Yet, few studies have explored how viruses might be shared in an ecosystem through feeding relationships. Here we identify 169 circular molecules (160 CRESS DNA molecules, nine circular molecules) recovered from a New Zealand freshwater lake, that we have tentatively classified into 51 putatively novel species and five previously described species (DflaCV-3, -5, -6, -8, -10). The CRESS DNA viruses identified in this study were recovered from molluscs (Echyridella menzeisii, Musculium novaezelandiae, Potamopyrgus antipodarum and Physella acuta) and insect larvae (Procordulia grayi, Xanthocnemis zealandica, and Chironomus zealandicus) collected from Lake Sarah, as well as from the lake water and benthic sediments. Extensive diversity was observed across most CRESS DNA molecules recovered. The putative capsid protein of one viral species was found to be most similar to those of members of the Tombusviridae family, thus expanding the number of known RNA-DNA hybrid viruses in nature. We noted a strong association between the CRESS DNA viruses and circular molecules identified in the water and browser organisms (C. zealandicus, P. antipodarum and P. acuta), and between water sediments and undefended prey species (C. zealandicus). However, we were unable to find any significant correlation of viral assemblages to the potential feeding relationships of the host aquatic invertebrates.
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95
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Székely AJ, Breitbart M. Single-stranded DNA phages: from early molecular biology tools to recent revolutions in environmental microbiology. FEMS Microbiol Lett 2016; 363:fnw027. [DOI: 10.1093/femsle/fnw027] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2016] [Indexed: 01/22/2023] Open
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96
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Colombo S, Arioli S, Guglielmetti S, Lunelli F, Mora D. Virome-associated antibiotic-resistance genes in an experimental aquaculture facility. FEMS Microbiol Ecol 2016; 92:fiw003. [DOI: 10.1093/femsec/fiw003] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2015] [Indexed: 12/28/2022] Open
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97
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Lin J, Singh A. Detection of human enteric viruses in Umgeni River, Durban, South Africa. JOURNAL OF WATER AND HEALTH 2015; 13:1098-112. [PMID: 26608771 DOI: 10.2166/wh.2015.238] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The prevalence of adenovirus (AdV), rotaviruses (RV) and enteroviruses (EV) in Umgeni River waters of Durban, South Africa was assessed qualitatively and quantitatively during April 2011 to January 2012 using polymerase chain reaction (PCR)/reverse transcription-polymerase chain reaction (RT-PCR), nested PCR and quantitative PCR (qPCR), as well as nested integrated cell culture PCR (nested ICC-PCR). The phylogenetic analysis of the adenovirus and enterovirus amplicons was also performed. The nested PCR results effectively detected the presence of AdV and EV in all water samples. The results of qPCR demonstrated that higher populations of EV and of AdV were widely found in the Umgeni River. Rotavirus could only be detected in the upper Umgeni River, mainly during drier seasons. Nested ICC-PCR further confirmed the presence of infectious AdV and EV particles in 100% of water samples using various cell lines. The present study identifies potential viral hazards of Umgeni River water for domestic water supply and recreational activities.
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Affiliation(s)
- Johnson Lin
- Discipline of Microbiology, School of Life Sciences, University of KwaZulu-Natal (Westville), Private Bag X54001, Durban, South Africa E-mail:
| | - Atheesha Singh
- Discipline of Microbiology, School of Life Sciences, University of KwaZulu-Natal (Westville), Private Bag X54001, Durban, South Africa E-mail:
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98
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Santiago-Rodriguez TM, Fornaciari G, Luciani S, Dowd SE, Toranzos GA, Marota I, Cano RJ. Natural mummification of the human gut preserves bacteriophage DNA. FEMS Microbiol Lett 2015; 363:fnv219. [PMID: 26564967 DOI: 10.1093/femsle/fnv219] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2015] [Indexed: 12/23/2022] Open
Abstract
The natural mummification process of the human gut represents a unique opportunity to study the resulting microbial community structure and composition. While results are providing insights into the preservation of bacteria, fungi, pathogenic eukaryotes and eukaryotic viruses, no studies have demonstrated that the process of natural mummification also results in the preservation of bacteriophage DNA. We characterized the gut microbiome of three pre-Columbian Andean mummies, namely FI3, FI9 and FI12, and found sequences homologous to viruses. From the sequences attributable to viruses, 50.4% (mummy FI3), 1.0% (mummy FI9) and 84.4% (mummy FI12) were homologous to bacteriophages. Sequences corresponding to the Siphoviridae, Myoviridae, Podoviridae and Microviridae families were identified. Predicted putative bacterial hosts corresponded mainly to the Firmicutes and Proteobacteria, and included Bacillus, Staphylococcus, Clostridium, Escherichia, Vibrio, Klebsiella, Pseudomonas and Yersinia. Predicted functional categories associated with bacteriophages showed a representation of structural, replication, integration and entry and lysis genes. The present study suggests that the natural mummification of the human gut results in the preservation of bacteriophage DNA, representing an opportunity to elucidate the ancient phageome and to hypothesize possible mechanisms of preservation.
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Affiliation(s)
- Tasha M Santiago-Rodriguez
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA Department of Biology, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Gino Fornaciari
- Department of Translational Research on New Technologies in Medicine and Surgery, Division of Paleopathology, University of Pisa, Pisa 56126, Italy Center for Anthropological, Paleopathological and Historical Studies of the Sardinian and Mediterranean Populations, Department of Biomedical Sciences, University of Sassari, Sassari 07100, Italy
| | - Stefania Luciani
- Laboratory of Molecular Archaeo-Anthropology/ancient DNA, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino 62032, Italy
| | - Scot E Dowd
- Molecular Research LP (MR DNA), Shallowater, TX 79363, USA
| | - Gary A Toranzos
- Department of Biology, University of Puerto Rico, San Juan 00932, Puerto Rico
| | - Isolina Marota
- Laboratory of Molecular Archaeo-Anthropology/ancient DNA, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino 62032, Italy
| | - Raul J Cano
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA Department of Biology, California Polytechnic State University, San Luis Obispo, CA 93407, USA
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99
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Li B, Ju F, Cai L, Zhang T. Profile and Fate of Bacterial Pathogens in Sewage Treatment Plants Revealed by High-Throughput Metagenomic Approach. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:10492-502. [PMID: 26252189 DOI: 10.1021/acs.est.5b02345] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The broad-spectrum profile of bacterial pathogens and their fate in sewage treatment plants (STPs) were investigated using high-throughput sequencing based metagenomic approach. This novel approach could provide a united platform to standardize bacterial pathogen detection and realize direct comparison among different samples. Totally, 113 bacterial pathogen species were detected in eight samples including influent, effluent, activated sludge (AS), biofilm, and anaerobic digestion sludge with the abundances ranging from 0.000095% to 4.89%. Among these 113 bacterial pathogens, 79 species were reported in STPs for the first time. Specially, compared to AS in bulk mixed liquor, more pathogen species and higher total abundance were detected in upper foaming layer of AS. This suggests that the foaming layer of AS might impose more threat to onsite workers and citizens in the surrounding areas of STPs because pathogens in foaming layer are easily transferred into air and cause possible infections. The high removal efficiency (98.0%) of total bacterial pathogens suggests that AS treatment process is effective to remove most bacterial pathogens. Remarkable similarities of bacterial pathogen compositions between influent and human gut indicated that bacterial pathogen profiles in influents could well reflect the average bacterial pathogen communities of urban resident guts within the STP catchment area.
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Affiliation(s)
- Bing Li
- Key Laboratory of Microorganism Application and Risk Control of Shenzhen, Graduate School at Shenzhen, Tsinghua University , Shenzhen 518055, China
| | - Feng Ju
- Environmental Biotechnology Lab, The University of Hong Kong , Hong Kong SAR, China
| | - Lin Cai
- Environmental Biotechnology Lab, The University of Hong Kong , Hong Kong SAR, China
| | - Tong Zhang
- Environmental Biotechnology Lab, The University of Hong Kong , Hong Kong SAR, China
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100
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Kuo HW, Chen LZ, Shih MH. High prevalence of type 41 and high sequence diversity of partial hexon gene of human adenoviruses in municipal raw sewage and activated sludge. J Appl Microbiol 2015; 119:1181-95. [PMID: 26189615 DOI: 10.1111/jam.12907] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/24/2015] [Accepted: 07/04/2015] [Indexed: 11/29/2022]
Abstract
AIM This study was aimed to assess seasonal/geographical distribution and sequence diversity of partial hexon gene for human adenoviruses (HAdVs) within raw sewages (RS) and activated sludges (AS). METHODS AND RESULTS Assessments were based on high-throughput sequencing (HTS) for polymerase chain reaction (PCR)-amplified 128-bp partial hexon gene fragments and followed by principal coordinate analyses (PCoA) for revealed sequences. Sequencing results showed that the majority of sequences (>90%) for the RS or AS samples were identical to HAdV type 41 of species F, while rest of few sequences belonged to HAdV species-D and -C were only occurred rarely without significant seasonal/geographical variation. The partial hexon genes were highly diverse as many sequence types and operational taxonomic unit groups were noticed among the matched sequences. CONCLUSIONS This study demonstrated that HAdV-41 was constantly appeared in the RS and AS samples from Taiwan throughout the year without significant seasonal or geographical variations; but, had high sequence diverse noticed for the 128-bp partial hexon gene fragments. SIGNIFICANCE AND IMPACT OF THE STUDY High-throughput-sequencing results provided better insights of HAdV distribution and genetic diversity for raw sewage and AS samples allowing some probable biases for cloning-sequencing approach to be defeated and further providing public health awareness regarding viral-contaminated sewages or sludges.
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Affiliation(s)
- H-W Kuo
- Department of Environmental Science and Engineering, Tunghai University, Taichung, Taiwan
| | - L-Z Chen
- Department of Environmental Science and Engineering, Tunghai University, Taichung, Taiwan
| | - M-H Shih
- Department of Environmental Science and Engineering, Tunghai University, Taichung, Taiwan
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