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Wu LY, Wijesekara Y, Piedade GJ, Pappas N, Brussaard CPD, Dutilh BE. Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes. Genome Biol 2024; 25:97. [PMID: 38622738 PMCID: PMC11020464 DOI: 10.1186/s13059-024-03236-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinformatic virus identification tools have been developed for this task, making it challenging to choose the right tools, parameters, and cutoffs. As all these tools measure different biological signals, and use different algorithms and training and reference databases, it is imperative to conduct an independent benchmarking to give users objective guidance. RESULTS We compare the performance of nine state-of-the-art virus identification tools in thirteen modes on eight paired viral and microbial datasets from three distinct biomes, including a new complex dataset from Antarctic coastal waters. The tools have highly variable true positive rates (0-97%) and false positive rates (0-30%). PPR-Meta best distinguishes viral from microbial contigs, followed by DeepVirFinder, VirSorter2, and VIBRANT. Different tools identify different subsets of the benchmarking data and all tools, except for Sourmash, find unique viral contigs. Performance of tools improved with adjusted parameter cutoffs, indicating that adjustment of parameter cutoffs before usage should be considered. CONCLUSIONS Together, our independent benchmarking facilitates selecting choices of bioinformatic virus identification tools and gives suggestions for parameter adjustments to viromics researchers.
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Affiliation(s)
- Ling-Yi Wu
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Yasas Wijesekara
- Institute of Bioinformatics, University Medicine Greifswald, Felix Hausdorff Str. 8, 17475, Greifswald, Germany
| | - Gonçalo J Piedade
- Department Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, PO Box 59, Texel, 1790 AB, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Nikolaos Pappas
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Corina P D Brussaard
- Department Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, PO Box 59, Texel, 1790 AB, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743, Jena, Germany.
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Zheng Y, Gao Z, Wu S, Ruan A. Community Structure, Drivers, and Potential Functions of Different Lifestyle Viruses in Chaohu Lake. Viruses 2024; 16:590. [PMID: 38675931 PMCID: PMC11053968 DOI: 10.3390/v16040590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/06/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Viruses, as the most prolific entities on Earth, constitute significant ecological groups within freshwater lakes, exerting pivotal ecological roles. In this study, we selected Chaohu Lake, a representative eutrophic freshwater lake in China, as our research site to explore the community distribution, driving mechanisms, and potential ecological functions of diverse viral communities, the intricate virus-host interaction systems, and the overarching influence of viruses on global biogeochemical cycling.
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Affiliation(s)
- Yu Zheng
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210024, China; (Y.Z.); (Z.G.); (S.W.)
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Zihao Gao
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210024, China; (Y.Z.); (Z.G.); (S.W.)
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Shuai Wu
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210024, China; (Y.Z.); (Z.G.); (S.W.)
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Aidong Ruan
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210024, China; (Y.Z.); (Z.G.); (S.W.)
- College of Geography and Remote Sensing, Hohai University, Nanjing 210098, China
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Kosmopoulos JC, Klier KM, Langwig MV, Tran PQ, Anantharaman K. Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.15.562385. [PMID: 37904928 PMCID: PMC10614762 DOI: 10.1101/2023.10.15.562385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Background Viruses, the majority of which are uncultivated, are among the most abundant biological entities on Earth. From altering microbial physiology to driving community dynamics, viruses are fundamental members of microbiomes. While the number of studies leveraging viral metagenomics (viromics) for studying uncultivated viruses is growing, standards for viromics research are lacking. Viromics can utilize computational discovery of viruses from total metagenomes of all community members (hereafter metagenomes) or use physical separation of virus-specific fractions (hereafter viromes). However, differences in the recovery and interpretation of viruses from metagenomes and viromes obtained from the same samples remain understudied. Results Here, we compare viral communities from paired viromes and metagenomes obtained from 60 diverse samples across human gut, soil, freshwater, and marine ecosystems. Overall, viral communities obtained from viromes were more abundant and species rich than those obtained from metagenomes, although there were some exceptions. Despite this, metagenomes still contained many viral genomes not detected in viromes. We also found notable differences in the predicted lytic state of viruses detected in viromes vs metagenomes at the time of sequencing. Other forms of variation observed include genome presence/absence, genome quality, and encoded protein content between viromes and metagenomes, but the magnitude of these differences varied by environment. Conclusions Overall, our results show that the choice of method can lead to differing interpretations of viral community ecology. We suggest that the choice of whether to target a metagenome or virome to study viral communities should be dependent on the environmental context and ecological questions being asked. However, our overall recommendation to researchers investigating viral ecology and evolution is to pair both approaches to maximize their respective benefits.
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Affiliation(s)
- James C. Kosmopoulos
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Katherine M. Klier
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Freshwater and Marine Sciences Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Marguerite V. Langwig
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Freshwater and Marine Sciences Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Patricia Q. Tran
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Muscatt G, Cook R, Millard A, Bending GD, Jameson E. Viral metagenomics reveals diverse virus-host interactions throughout the soil depth profile. mBio 2023; 14:e0224623. [PMID: 38032184 PMCID: PMC10746233 DOI: 10.1128/mbio.02246-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Soil viruses can moderate the roles that their host microbes play in global carbon cycling. However, given that most studies investigate the surface layer (i.e., top 20 cm) of soil, the extent to which this occurs in subsurface soil (i.e., below 20 cm) is unknown. Here, we leveraged public sequencing data to investigate the interactions between viruses and their hosts at soil depth intervals, down to 115 cm. While most viruses were detected throughout the soil depth profile, their adaptation to host microbes varied. Nonetheless, we uncovered evidence for the potential of soil viruses to encourage their hosts to recycle plant-derived carbon in both surface and subsurface soils. This work reasons that our understanding of soil viral functions requires us to continue to dig deeper and compare viruses existing throughout soil ecosystems.
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Affiliation(s)
- George Muscatt
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Ryan Cook
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, United Kingdom
| | - Andrew Millard
- Department of Genetics and Genome Biology, Leicester Centre for Phage Research, University of Leicester, Leicester, United Kingdom
| | - Gary D. Bending
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
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Cao MM, Liu SY, Bi L, Chen SJ, Wu HY, Ge Y, Han B, Zhang LM, He JZ, Han LL. Distribution Characteristics of Soil Viruses Under Different Precipitation Gradients on the Qinghai-Tibet Plateau. Front Microbiol 2022; 13:848305. [PMID: 35464951 PMCID: PMC9022101 DOI: 10.3389/fmicb.2022.848305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
Viruses are extremely abundant in the soil environment and have potential roles in impacting on microbial population, evolution, and nutrient biogeochemical cycles. However, how environment and climate changes affect soil viruses is still poorly understood. Here, a metagenomic approach was used to investigate the distribution, diversity, and potential biogeochemical impacts of DNA viruses in 12 grassland soils under three precipitation gradients on the Qinghai-Tibet Plateau, which is one of the most sensitive areas to climate change. A total of 557 viral operational taxonomic units were obtained, spanning 152 viral families from the 30 metagenomes. Both virus-like particles (VLPs) and microbial abundance increased with average annual precipitation. A significant positive correlation of VLP counts was observed with soil water content, total carbon, total nitrogen, soil organic matter, and total phosphorus. Among these biological and abiotic factors, SWC mainly contributed to the variability in VLP abundance. The order Caudovirales (70.1% of the identified viral order) was the predominant viral type in soils from the Qinghai-Tibet Plateau, with the Siphoviridae family being the most abundant. Remarkably, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes represented by glycoside hydrolases were identified, indicating that soil viruses may play a potential role in the carbon cycle on the Qinghai-Tibet Plateau. There were more diverse hosts and abundant CAZyme genes in soil with moderate precipitation. Our study provides a strong evidence that changes in precipitation impact not only viral abundance and virus–host interactions in soil but also the viral functional potential, especially carbon cycling.
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Affiliation(s)
- Miao-Miao Cao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Si-Yi Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,The Zhongke-Ji'an Institute for Eco-Environmental Sciences, Ji'an, China
| | - Li Bi
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Shu-Jun Chen
- Information Technology Center, Tsinghua University, Beijing, China
| | - Hua-Yong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Bing Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ji-Zheng He
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.,Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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