Complementary insights into gut viral genomes: a comparative benchmark of short- and long-read metagenomes using diverse assemblers and binners
Abstract Background Metagenome-assembled viral genomes have significantly advanced the discovery and characterization of the human gut virome. However, we lack a comparative assessment of assembly tools on the efficacy of viral genome identification, particularly across next-generation sequencing (N...
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BMC
2024-12-01
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| Series: | Microbiome |
| Online Access: | https://doi.org/10.1186/s40168-024-01981-z |
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| author | Huarui Wang Chuqing Sun Yun Li Jingchao Chen Xing-Ming Zhao Wei-Hua Chen |
| author_facet | Huarui Wang Chuqing Sun Yun Li Jingchao Chen Xing-Ming Zhao Wei-Hua Chen |
| author_sort | Huarui Wang |
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| description | Abstract Background Metagenome-assembled viral genomes have significantly advanced the discovery and characterization of the human gut virome. However, we lack a comparative assessment of assembly tools on the efficacy of viral genome identification, particularly across next-generation sequencing (NGS) and third-generation sequencing (TGS) data. Results We evaluated the efficiency of NGS, TGS, and hybrid assemblers for viral genome discovery using 95 viral-like particle (VLP)-enriched fecal samples sequenced on both Illumina and PacBio platforms. MEGAHIT, metaFlye, and hybridSPAdes emerged as the optimal choices for NGS, TGS, and hybrid datasets, respectively. Notably, these assemblers recovered distinct viral genomes, demonstrating a remarkable degree of complementarity. By combining individual assembler results, we expanded the total number of nonredundant high-quality viral genomes by 4.83 ~ 21.7-fold compared to individual assemblers. Among them, viral genomes from NGS and TGS data have the least overlap, indicating the impact of data type on viral genome recovery. We also evaluated four binning methods, finding that CONCOCT incorporated more unrelated contigs into the same bins, while MetaBAT2, AVAMB, and vRhyme balanced inclusiveness and taxonomic consistency within bins. Conclusions Our findings highlight the challenges in metagenome-driven viral discovery, underscoring tool limitations. We advocate for combined use of multiple assemblers and sequencing technologies when feasible and highlight the urgent need for specialized tools tailored to gut virome assembly. This study contributes essential insights for advancing viral genome research in the context of gut metagenomics. Video Abstract |
| format | Article |
| id | doaj-art-43149ed026b74696a9e404ea43da1c7e |
| institution | OA Journals |
| issn | 2049-2618 |
| language | English |
| publishDate | 2024-12-01 |
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| series | Microbiome |
| spelling | doaj-art-43149ed026b74696a9e404ea43da1c7e2025-08-20T02:31:44ZengBMCMicrobiome2049-26182024-12-0112111410.1186/s40168-024-01981-zComplementary insights into gut viral genomes: a comparative benchmark of short- and long-read metagenomes using diverse assemblers and binnersHuarui Wang0Chuqing Sun1Yun Li2Jingchao Chen3Xing-Ming Zhao4Wei-Hua Chen5Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and TechnologyKey Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and TechnologyKey Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and TechnologyKey Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and TechnologyDepartment of Neurology, Institute of Science and Technology for Brain-Inspired Intelligence, Zhongshan Hospitaland, Fudan University Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and TechnologyAbstract Background Metagenome-assembled viral genomes have significantly advanced the discovery and characterization of the human gut virome. However, we lack a comparative assessment of assembly tools on the efficacy of viral genome identification, particularly across next-generation sequencing (NGS) and third-generation sequencing (TGS) data. Results We evaluated the efficiency of NGS, TGS, and hybrid assemblers for viral genome discovery using 95 viral-like particle (VLP)-enriched fecal samples sequenced on both Illumina and PacBio platforms. MEGAHIT, metaFlye, and hybridSPAdes emerged as the optimal choices for NGS, TGS, and hybrid datasets, respectively. Notably, these assemblers recovered distinct viral genomes, demonstrating a remarkable degree of complementarity. By combining individual assembler results, we expanded the total number of nonredundant high-quality viral genomes by 4.83 ~ 21.7-fold compared to individual assemblers. Among them, viral genomes from NGS and TGS data have the least overlap, indicating the impact of data type on viral genome recovery. We also evaluated four binning methods, finding that CONCOCT incorporated more unrelated contigs into the same bins, while MetaBAT2, AVAMB, and vRhyme balanced inclusiveness and taxonomic consistency within bins. Conclusions Our findings highlight the challenges in metagenome-driven viral discovery, underscoring tool limitations. We advocate for combined use of multiple assemblers and sequencing technologies when feasible and highlight the urgent need for specialized tools tailored to gut virome assembly. This study contributes essential insights for advancing viral genome research in the context of gut metagenomics. Video Abstracthttps://doi.org/10.1186/s40168-024-01981-z |
| spellingShingle | Huarui Wang Chuqing Sun Yun Li Jingchao Chen Xing-Ming Zhao Wei-Hua Chen Complementary insights into gut viral genomes: a comparative benchmark of short- and long-read metagenomes using diverse assemblers and binners Microbiome |
| title | Complementary insights into gut viral genomes: a comparative benchmark of short- and long-read metagenomes using diverse assemblers and binners |
| title_full | Complementary insights into gut viral genomes: a comparative benchmark of short- and long-read metagenomes using diverse assemblers and binners |
| title_fullStr | Complementary insights into gut viral genomes: a comparative benchmark of short- and long-read metagenomes using diverse assemblers and binners |
| title_full_unstemmed | Complementary insights into gut viral genomes: a comparative benchmark of short- and long-read metagenomes using diverse assemblers and binners |
| title_short | Complementary insights into gut viral genomes: a comparative benchmark of short- and long-read metagenomes using diverse assemblers and binners |
| title_sort | complementary insights into gut viral genomes a comparative benchmark of short and long read metagenomes using diverse assemblers and binners |
| url | https://doi.org/10.1186/s40168-024-01981-z |
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