1
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Huss P, Kieft K, Meger A, Nishikawa K, Anantharaman K, Raman S. Engineering bacteriophages through deep mining of metagenomic motifs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.07.527309. [PMID: 36798209 PMCID: PMC9934549 DOI: 10.1101/2023.02.07.527309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Bacteriophages can adapt to new hosts by altering sequence motifs through recombination or convergent evolution. Where such motifs exist and what fitness advantage they confer remains largely unknown. We report a new method, Metagenomic Sequence Informed Functional Scoring (Meta-SIFT), to discover sequence motifs in metagenomic datasets that can be used to engineer phage activity. Meta-SIFT uses experimental deep mutational scanning data to create sequence profiles to enable deep mining of metagenomes for functional motifs which are otherwise invisible to searches. We experimentally tested over 17,000 Meta-SIFT derived sequence motifs in the receptor-binding protein of the T7 phage. The screen revealed thousands of T7 variants with novel host specificity with functional motifs sourced from distant families. Position, substitution and location preferences dictated specificity across a panel of 20 hosts and conditions. To demonstrate therapeutic utility, we engineered active T7 variants against foodborne pathogen E. coli O121. Meta-SIFT is a powerful tool to unlock the functional potential encoded in phage metagenomes to engineer bacteriophages.
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2
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Liu Y, Zhu C, Liang Y, McMinn A, Zheng K, Wang Z, Wang H, Ren L, Shao H, Sung YY, Mok WJ, Wong LL, Wang M. Genome analysis of vB_SupP_AX, a novel N4-like phage infecting Sulfitobacter. Int Microbiol 2024; 27:1297-1306. [PMID: 38190086 DOI: 10.1007/s10123-023-00476-5] [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: 10/10/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/09/2024]
Abstract
Sulfitobacter is a bacterium recognized for its production of AMP-independent sulfite oxidase, which is instrumental in the creation of sulfite biosensors. This capability underscores its ecological and economic relevance. In this study, we present a newly discovered phage, Sulfitobacter phage vB_SupP_AX, which was isolated from Maidao of Qingdao, China. The vB_SupP_AX genome is linear and double-stranded and measures 75,445 bp with a GC content of 49%. It encompasses four transfer RNA (tRNA) sequences and 79 open reading frames (ORFs), one of which is an auxiliary metabolic gene encoding thioredoxin. Consistent with other N4-like phages, vB_SupP_AX possesses three distinct RNA polymerases and is characterized by the presence of four tRNA molecules. Comparative genomic and phylogenetic analyses position vB_SupP_AX and three other viral genomes from the Integrated Microbial Genomes/Virus v4 database within the Rhodovirinae virus subfamily. The identification of vB_SupP_AX enhances our understanding of virus-host interactions within marine ecosystems.
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Affiliation(s)
- Yundan Liu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Chengrui Zhu
- Haide College, Ocean University of China, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China.
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China.
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Kaiyang Zheng
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Ziyue Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hongmin Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Linyi Ren
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Yeong Yik Sung
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), Kuala Nerus, Malaysia
| | - Wen Jye Mok
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), Kuala Nerus, Malaysia
| | - Li Lian Wong
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), Kuala Nerus, Malaysia
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China.
- Haide College, Ocean University of China, Qingdao, China.
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China.
- The Affiliated Hospital of Qingdao University, Qingdao, China.
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3
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Yu M, Zhang M, Zeng R, Cheng R, Zhang R, Hou Y, Kuang F, Feng X, Dong X, Li Y, Shao Z, Jin M. Diversity and potential host-interactions of viruses inhabiting deep-sea seamount sediments. Nat Commun 2024; 15:3228. [PMID: 38622147 PMCID: PMC11018836 DOI: 10.1038/s41467-024-47600-1] [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: 10/18/2023] [Accepted: 04/04/2024] [Indexed: 04/17/2024] Open
Abstract
Seamounts are globally distributed across the oceans and form one of the major oceanic biomes. Here, we utilized combined analyses of bulk metagenome and virome to study viral communities in seamount sediments in the western Pacific Ocean. Phylogenetic analyses and the protein-sharing network demonstrate extensive diversity and previously unknown viral clades. Inference of virus-host linkages uncovers extensive interactions between viruses and dominant prokaryote lineages, and suggests that viruses play significant roles in carbon, sulfur, and nitrogen cycling by compensating or augmenting host metabolisms. Moreover, temperate viruses are predicted to be prevalent in seamount sediments, which tend to carry auxiliary metabolic genes for host survivability. Intriguingly, the geographical features of seamounts likely compromise the connectivity of viral communities and thus contribute to the high divergence of viral genetic spaces and populations across seamounts. Altogether, these findings provides knowledge essential for understanding the biogeography and ecological roles of viruses in globally widespread seamounts.
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Affiliation(s)
- Meishun Yu
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Menghui Zhang
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Runying Zeng
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Ruolin Cheng
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Yanping Hou
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Fangfang Kuang
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Xuejin Feng
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Xiyang Dong
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Yinfang Li
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China.
| | - Min Jin
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China.
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4
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Pinto Y, Chakraborty M, Jain N, Bhatt AS. Phage-inclusive profiling of human gut microbiomes with Phanta. Nat Biotechnol 2024; 42:651-662. [PMID: 37231259 DOI: 10.1038/s41587-023-01799-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 04/20/2023] [Indexed: 05/27/2023]
Abstract
Due to technical limitations, most gut microbiome studies have focused on prokaryotes, overlooking viruses. Phanta, a virome-inclusive gut microbiome profiling tool, overcomes the limitations of assembly-based viral profiling methods by using customized k-mer-based classification tools and incorporating recently published catalogs of gut viral genomes. Phanta's optimizations consider the small genome size of viruses, sequence homology with prokaryotes and interactions with other gut microbes. Extensive testing of Phanta on simulated data demonstrates that it quickly and accurately quantifies prokaryotes and viruses. When applied to 245 fecal metagenomes from healthy adults, Phanta identifies ~200 viral species per sample, ~5× more than standard assembly-based methods. We observe a ~2:1 ratio between DNA viruses and bacteria, with higher interindividual variability of the gut virome compared to the gut bacteriome. In another cohort, we observe that Phanta performs equally well on bulk versus virus-enriched metagenomes, making it possible to study prokaryotes and viruses in a single experiment, with a single analysis.
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Affiliation(s)
- Yishay Pinto
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine, Divisions of Hematology and Blood & Marrow Transplantation, Stanford University, Stanford, CA, USA
| | | | - Navami Jain
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine, Divisions of Hematology and Blood & Marrow Transplantation, Stanford University, Stanford, CA, USA
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Medicine, Divisions of Hematology and Blood & Marrow Transplantation, Stanford University, Stanford, CA, USA.
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5
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Ma B, Wang Y, Zhao K, Stirling E, Lv X, Yu Y, Hu L, Tang C, Wu C, Dong B, Xue R, Dahlgren RA, Tan X, Dai H, Zhu YG, Chu H, Xu J. Biogeographic patterns and drivers of soil viromes. Nat Ecol Evol 2024; 8:717-728. [PMID: 38383853 DOI: 10.1038/s41559-024-02347-2] [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: 04/26/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024]
Abstract
Viruses are crucial in shaping soil microbial functions and ecosystems. However, studies on soil viromes have been limited in both spatial scale and biome coverage. Here we present a comprehensive synthesis of soil virome biogeographic patterns using the Global Soil Virome dataset (GSV) wherein we analysed 1,824 soil metagenomes worldwide, uncovering 80,750 partial genomes of DNA viruses, 96.7% of which are taxonomically unassigned. The biogeography of soil viral diversity and community structure varies across different biomes. Interestingly, the diversity of viruses does not align with microbial diversity and contrasts with it by showing low diversity in forest and shrubland soils. Soil texture and moisture conditions are further corroborated as key factors affecting diversity by our predicted soil viral diversity atlas, revealing higher diversity in humid and subhumid regions. In addition, the binomial degree distribution pattern suggests a random co-occurrence pattern of soil viruses. These findings are essential for elucidating soil viral ecology and for the comprehensive incorporation of viruses into soil ecosystem models.
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Affiliation(s)
- Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Yiling Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Kankan Zhao
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Erinne Stirling
- Agriculture and Food, CSIRO, Adelaide, South Australia, Australia
- Acid Sulfate Soils Centre, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Xiaofei Lv
- Department of Environmental Engineering, China Jiliang University, Hangzhou, China
| | - Yijun Yu
- Arable Soil Quality and Fertilizer Administration Bureau of Zhejiang Province, Hangzhou, China
| | - Lingfei Hu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Chao Tang
- Institute of Applied Remote Sensing and Information Technology, Zhejiang University, Hangzhou, China
| | - Chuyi Wu
- School of Earth Sciences, Zhejiang University, Hangzhou, China
| | - Baiyu Dong
- Institute of Applied Remote Sensing and Information Technology, Zhejiang University, Hangzhou, China
| | - Ran Xue
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Randy A Dahlgren
- Department of Land, Air and Water Resources, University of California, Davis, CA, USA
| | - Xiangfeng Tan
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hengyi Dai
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Yong-Guan Zhu
- Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China.
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6
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Chen L, Banfield JF. COBRA improves the completeness and contiguity of viral genomes assembled from metagenomes. Nat Microbiol 2024; 9:737-750. [PMID: 38321183 PMCID: PMC10914622 DOI: 10.1038/s41564-023-01598-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 12/19/2023] [Indexed: 02/08/2024]
Abstract
Viruses are often studied using metagenome-assembled sequences, but genome incompleteness hampers comprehensive and accurate analyses. Contig Overlap Based Re-Assembly (COBRA) resolves assembly breakpoints based on the de Bruijn graph and joins contigs. Here we benchmarked COBRA using ocean and soil viral datasets. COBRA accurately joined the assembled sequences and achieved notably higher genome accuracy than binning tools. From 231 published freshwater metagenomes, we obtained 7,334 bacteriophage clusters, ~83% of which represent new phage species. Notably, ~70% of these were circular, compared with 34% before COBRA analyses. We expanded sampling of huge phages (≥200 kbp), the largest of which was curated to completion (717 kbp). Improved phage genomes from Rotsee Lake provided context for metatranscriptomic data and indicated the in situ activity of huge phages, whiB-encoding phages and cysC- and cysH-encoding phages. COBRA improves viral genome assembly contiguity and completeness, thus the accuracy and reliability of analyses of gene content, diversity and evolution.
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Affiliation(s)
- LinXing Chen
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
- Department of Environmental Science Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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7
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Zolfo M, Silverj A, Blanco-Míguez A, Manghi P, Rota-Stabelli O, Heidrich V, Jensen J, Maharjan S, Franzosa E, Menni C, Visconti A, Pinto F, Ciciani M, Huttenhower C, Cereseto A, Asnicar F, Kitano H, Yamada T, Segata N. Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.19.580813. [PMID: 38464031 PMCID: PMC10925137 DOI: 10.1101/2024.02.19.580813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Viruses are an abundant and crucial component of the human microbiome, but accurately discovering them via metagenomics is still challenging. Currently, the available viral reference genomes poorly represent the diversity in microbiome samples, and expanding such a set of viral references is difficult. As a result, many viruses are still undetectable through metagenomics even when considering the power of de novo metagenomic assembly and binning, as viruses lack universal markers. Here, we describe a novel approach to catalog new viral members of the human gut microbiome and show how the resulting resource improves metagenomic analyses. We retrieved >3,000 viral-like particles (VLP) enriched metagenomic samples (viromes), evaluated the efficiency of the enrichment in each sample to leverage the viromes of highest purity, and applied multiple analysis steps involving assembly and comparison with hundreds of thousands of metagenome-assembled genomes to discover new viral genomes. We reported over 162,000 viral sequences passing quality control from thousands of gut metagenomes and viromes. The great majority of the retrieved viral sequences (~94.4%) were of unknown origin, most had a CRISPR spacer matching host bacteria, and four of them could be detected in >50% of a set of 18,756 gut metagenomes we surveyed. We included the obtained collection of sequences in a new MetaPhlAn 4.1 release, which can quantify reads within a metagenome matching the known and newly uncovered viral diversity. Additionally, we released the viral database for further virome and metagenomic studies of the human microbiome.
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Affiliation(s)
- Moreno Zolfo
- Department CIBIO, University of Trento, Italy
- Integrated Open Systems Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
| | - Andrea Silverj
- Department CIBIO, University of Trento, Italy
- Center Agriculture Food Environment (C3A), University of Trento, Italy
- Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | | | | | - Omar Rota-Stabelli
- Department CIBIO, University of Trento, Italy
- Center Agriculture Food Environment (C3A), University of Trento, Italy
- Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | | | - Jordan Jensen
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Sagun Maharjan
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Eric Franzosa
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Cristina Menni
- Department of Twin Research & Genetic Epidemiology, King’s College London, London, UK
| | - Alessia Visconti
- Center for Biostatistics, Epidemiology and Public Health, Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | | | | | - Curtis Huttenhower
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | | | - Hiroaki Kitano
- Integrated Open Systems Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
- The Systems Biology Institute (SBI), Tokyo, Japan
- IOM Bioworks Pvt. Ltd., Centre for Cellular and Molecular Platforms (C-CAMP), GKVK Post, Bellary Rd, Bengaluru, Karnataka-560065, India
| | - Takuji Yamada
- Integrated Open Systems Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
- Metagen, Inc., Yamagata, Japan
- Metagen Therapeutics, Inc., Yamagata, Japan
- digzyme, Inc., Tokyo, Japan
| | - Nicola Segata
- Department CIBIO, University of Trento, Italy
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
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8
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Flamholz ZN, Biller SJ, Kelly L. Large language models improve annotation of prokaryotic viral proteins. Nat Microbiol 2024; 9:537-549. [PMID: 38287147 PMCID: PMC11311208 DOI: 10.1038/s41564-023-01584-8] [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: 04/23/2023] [Accepted: 12/08/2023] [Indexed: 01/31/2024]
Abstract
Viral genomes are poorly annotated in metagenomic samples, representing an obstacle to understanding viral diversity and function. Current annotation approaches rely on alignment-based sequence homology methods, which are limited by the paucity of characterized viral proteins and divergence among viral sequences. Here we show that protein language models can capture prokaryotic viral protein function, enabling new portions of viral sequence space to be assigned biologically meaningful labels. When applied to global ocean virome data, our classifier expanded the annotated fraction of viral protein families by 29%. Among previously unannotated sequences, we highlight the identification of an integrase defining a mobile element in marine picocyanobacteria and a capsid protein that anchors globally widespread viral elements. Furthermore, improved high-level functional annotation provides a means to characterize similarities in genomic organization among diverse viral sequences. Protein language models thus enhance remote homology detection of viral proteins, serving as a useful complement to existing approaches.
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Affiliation(s)
- Zachary N Flamholz
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Steven J Biller
- Department of Biological Sciences, Wellesley College, Wellesley, MA, USA
| | - Libusha Kelly
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA.
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9
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Zhang T, Zhou K, Wang Y, Xu J, Zheng Q, Luo T, Jiao N. Genomic insights into the adaptation of Synechococcus to the coastal environment on Xiamen. Front Microbiol 2023; 14:1292150. [PMID: 38059125 PMCID: PMC10696648 DOI: 10.3389/fmicb.2023.1292150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/01/2023] [Indexed: 12/08/2023] Open
Abstract
Synechococcus are widely distributed in the global ocean, from the pelagic zone to coastal waters. However, little is known about Synechococcus in coastal seawater due to limitations in isolation and culture conditions. In this study, a combination of metagenomic sequencing technology, flow cytometry sorting, and multiple displacement amplification was used to investigate Synechococcus in the coastal seawater of Xiamen Island. The results revealed 18 clades of Synechococcus and diverse metabolic genes that appear to contribute to their adaptation to the coastal environment. Intriguingly, some metabolic genes related to the metabolism of carbohydrates, energy, nucleotides, and amino acids were found in 89 prophage regions that were detected in 16,258 Synechococcus sequences. The detected metabolic genes can enable prophages to contribute to the adaptation of Synechococcus hosts to the coastal marine environment. The detection of prophages also suggests that the cyanophages have infected Synechococcus. On the other hand, the identification of 773 genes associated with antiviral defense systems indicates that Synechococcus in Xiamen have evolved genetic traits in response to cyanophage infection. Studying the community diversity and functional genes of Synechococcus provides insights into their role in environmental adaptation and marine ecosystems.
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Affiliation(s)
- Ting Zhang
- Fujian Key Laboratory of Marine Carbon Sequestration, Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, Fujian, China
| | - Kun Zhou
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | - Yanhui Wang
- Fujian Key Laboratory of Marine Carbon Sequestration, Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, Fujian, China
| | - Jinxin Xu
- Fujian Key Laboratory of Marine Carbon Sequestration, Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, Fujian, China
| | - Qiang Zheng
- Fujian Key Laboratory of Marine Carbon Sequestration, Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, Fujian, China
| | - Tingwei Luo
- Fujian Key Laboratory of Marine Carbon Sequestration, Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, Fujian, China
| | - Nianzhi Jiao
- Fujian Key Laboratory of Marine Carbon Sequestration, Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, Fujian, China
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10
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Chen Y, Guo R, Liang Y, Luo L, Han Y, Wang H, Zhang H, Liu Y, Zheng K, Shao H, Sung YY, Mok WJ, Wong LL, McMinn A, Wang M. Characterization and genomic analysis of a novel lytic phage vB_PstM_ZRG1 infecting Stutzerimonas stutzeri, representing a new viral genus, Elithevirus. Virus Res 2023; 334:199183. [PMID: 37499764 PMCID: PMC10404802 DOI: 10.1016/j.virusres.2023.199183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
Abstract
Stutzerimonas stutzeri is an opportunistic pathogen widely distributed in the environment and displays diverse metabolic capabilities. In this study, a novel lytic S. stutzeri phage, named vB_PstM_ZRG1, was isolated from the seawater in the East China Sea (29°09'N, 123°39'E). vB_PstM_ZRG1 was stable at temperatures ranging from -20°C to 65°C and across a wide range of pH values from 3 to 10. The genome of vB_PstM_ZRG1 was determined to be a double-stranded DNA with a genome size of 52,767 bp, containing 78 putative open reading frames (ORFs). Three auxiliary metabolic genes encoded by phage vB_PstM_ZRG1 were predicted, including Toll/interleukin-1 receptor (TIR) domain, proline-alanine-alanine-arginine (PAAR) protein and SGNH (Ser-Gly-Asn-His) family hydrolase, especially TIR domain is not common in isolated phages. Phylogenic and network analysis showed that vB_PstM_ZRG1 has low similarity to other phage genomes in the GenBank and IMG/VR database, and might represent a novel viral genus, named Elithevirus. Additionally, the distribution map results indicated that vB_PstM_ZRG1 could infect both extreme colds- and warm-type hosts in the marine environment. In summary, our finding provided basic information for further research on the relationship between S. stutzeri and their phages, and expanded our understanding of genomic characteristics, phylogenetic diversity and distribution of Elithevirus.
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Affiliation(s)
- Ying Chen
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Ruizhe Guo
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China.
| | - Lin Luo
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Ying Han
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hongmin Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hong Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yundan Liu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Kaiyang Zheng
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China
| | - Yeong Yik Sung
- UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China; Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Wen Jye Mok
- UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China; Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Li Lian Wong
- UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China; Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China; Haide College, Ocean University of China, Qingdao, China; The Affiliated Hospital of Qingdao University, Qingdao 266000, China.
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11
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Vik D, Bolduc B, Roux S, Sun CL, Pratama AA, Krupovic M, Sullivan MB. MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets. ISME COMMUNICATIONS 2023; 3:87. [PMID: 37620369 PMCID: PMC10449787 DOI: 10.1038/s43705-023-00295-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/04/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023]
Abstract
Our knowledge of viral sequence space has exploded with advancing sequencing technologies and large-scale sampling and analytical efforts. Though archaea are important and abundant prokaryotes in many systems, our knowledge of archaeal viruses outside of extreme environments is limited. This largely stems from the lack of a robust, high-throughput, and systematic way to distinguish between bacterial and archaeal viruses in datasets of curated viruses. Here we upgrade our prior text-based tool (MArVD) via training and testing a random forest machine learning algorithm against a newly curated dataset of archaeal viruses. After optimization, MArVD2 presented a significant improvement over its predecessor in terms of scalability, usability, and flexibility, and will allow user-defined custom training datasets as archaeal virus discovery progresses. Benchmarking showed that a model trained with viral sequences from the hypersaline, marine, and hot spring environments correctly classified 85% of the archaeal viruses with a false detection rate below 2% using a random forest prediction threshold of 80% in a separate benchmarking dataset from the same habitats.
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Affiliation(s)
- Dean Vik
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA.
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA.
| | - Benjamin Bolduc
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christine L Sun
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Akbar Adjie Pratama
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université Paris Cité, CNRS UMR6047, Paris, France
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA.
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA.
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA.
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12
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Zhang M, Hao Y, Yi Y, Liu S, Sun Q, Tan X, Tang S, Xiao X, Jian H. Unexplored diversity and ecological functions of transposable phages. THE ISME JOURNAL 2023; 17:1015-1028. [PMID: 37069234 PMCID: PMC10284936 DOI: 10.1038/s41396-023-01414-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 04/02/2023] [Accepted: 04/05/2023] [Indexed: 04/19/2023]
Abstract
Phages are prevalent in diverse environments and play major ecological roles attributed to their tremendous diversity and abundance. Among these viruses, transposable phages (TBPs) are exceptional in terms of their unique lifestyle, especially their replicative transposition. Although several TBPs have been isolated and the life cycle of the representative phage Mu has been extensively studied, the diversity distribution and ecological functions of TBPs on the global scale remain unknown. Here, by mining TBPs from enormous microbial genomes and viromes, we established a TBP genome dataset (TBPGD), that expands the number of accessible TBP genomes 384-fold. TBPs are prevalent in diverse biomes and show great genetic diversity. Based on taxonomic evaluations, we propose the categorization of TBPs into four viral groups, including 11 candidate subfamilies. TBPs infect multiple bacterial phyla, and seem to infect a wider range of hosts than non-TBPs. Diverse auxiliary metabolic genes (AMGs) are identified in the TBP genomes, and genes related to glycoside hydrolases and pyrimidine deoxyribonucleotide biosynthesis are highly enriched. Finally, the influences of TBPs on their hosts are experimentally examined by using the marine bacterium Shewanella psychrophila WP2 and its infecting transposable phage SP2. Collectively, our findings greatly expand the genetic diversity of TBPs, and comprehensively reveal their potential influences in various ecosystems.
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Affiliation(s)
- Mujie Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yali Hao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Yi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shunzhang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qingyang Sun
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoli Tan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shan Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China.
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13
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Miao Y, Bian J, Dong G, Dai T. DETIRE: a hybrid deep learning model for identifying viral sequences from metagenomes. Front Microbiol 2023; 14:1169791. [PMID: 37396369 PMCID: PMC10313334 DOI: 10.3389/fmicb.2023.1169791] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/18/2023] [Indexed: 07/04/2023] Open
Abstract
A metagenome contains all DNA sequences from an environmental sample, including viruses, bacteria, archaea, and eukaryotes. Since viruses are of huge abundance and have caused vast mortality and morbidity to human society in history as a type of major pathogens, detecting viruses from metagenomes plays a crucial role in analyzing the viral component of samples and is the very first step for clinical diagnosis. However, detecting viral fragments directly from the metagenomes is still a tough issue because of the existence of a huge number of short sequences. In this study a hybrid Deep lEarning model for idenTifying vIral sequences fRom mEtagenomes (DETIRE) is proposed to solve the problem. First, the graph-based nucleotide sequence embedding strategy is utilized to enrich the expression of DNA sequences by training an embedding matrix. Then, the spatial and sequential features are extracted by trained CNN and BiLSTM networks, respectively, to enrich the features of short sequences. Finally, the two sets of features are weighted combined for the final decision. Trained by 220,000 sequences of 500 bp subsampled from the Virus and Host RefSeq genomes, DETIRE identifies more short viral sequences (<1,000 bp) than the three latest methods, such as DeepVirFinder, PPR-Meta, and CHEER. DETIRE is freely available at Github (https://github.com/crazyinter/DETIRE).
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14
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Guajardo-Leiva S, Mendez KN, Meneses C, Díez B, Castro-Nallar E. A First Insight into the Microbial and Viral Communities of Comau Fjord—A Unique Human-Impacted Ecosystem in Patagonia (42∘ S). Microorganisms 2023; 11:microorganisms11040904. [PMID: 37110327 PMCID: PMC10143455 DOI: 10.3390/microorganisms11040904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/17/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023] Open
Abstract
While progress has been made in surveying the oceans to understand microbial and viral communities, the coastal ocean and, specifically, estuarine waters, where the effects of anthropogenic activity are greatest, remain partially understudied. The coastal waters of Northern Patagonia are of interest since this region experiences high-density salmon farming as well as other disturbances such as maritime transport of humans and cargo. Here, we hypothesized that viral and microbial communities from the Comau Fjord would be distinct from those collected in global surveys yet would have the distinctive features of microbes from coastal and temperate regions. We further hypothesized that microbial communities will be functionally enriched in antibiotic resistance genes (ARGs) in general and in those related to salmon farming in particular. Here, the analysis of metagenomes and viromes obtained for three surface water sites showed that the structure of the microbial communities was distinct in comparison to global surveys such as the Tara Ocean, though their composition converges with that of cosmopolitan marine microbes belonging to Proteobacteria, Bacteroidetes, and Actinobacteria. Similarly, viral communities were also divergent in structure and composition but matched known viral members from North America and the southern oceans. Microbial communities were functionally enriched in ARGs dominated by beta-lactams and tetracyclines, bacitracin, and the group macrolide–lincosamide–streptogramin (MLS) but were not different from other communities from the South Atlantic, South Pacific, and Southern Oceans. Similarly, viral communities were characterized by exhibiting protein clusters similar to those described globally (Tara Oceans Virome); however, Comau Fjord viromes displayed up to 50% uniqueness in their protein content. Altogether, our results indicate that microbial and viral communities from the Comau Fjord are a reservoir of untapped diversity and that, given the increasing anthropogenic impacts in the region, they warrant further study, specifically regarding resilience and resistance against antimicrobials and hydrocarbons.
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Affiliation(s)
- Sergio Guajardo-Leiva
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Campus Talca, Universidad de Talca, Avda. Lircay s/n, Talca 3465548, Chile
- Centro de Ecología Integrativa, Campus Talca, Universidad de Talca, Avda. Lircay s/n, Talca 3465548, Chile
| | - Katterinne N. Mendez
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile
| | - Claudio Meneses
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- ANID—Millennium Science Initiative Program—Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago 8370186, Chile
| | - Beatriz Díez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Center for Climate and Resilience Research (CR)2, Santiago 8370449, Chile
- Millennium Institute Center for Genome Regulation (CGR), Santiago 7800003, Chile
| | - Eduardo Castro-Nallar
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Campus Talca, Universidad de Talca, Avda. Lircay s/n, Talca 3465548, Chile
- Centro de Ecología Integrativa, Campus Talca, Universidad de Talca, Avda. Lircay s/n, Talca 3465548, Chile
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15
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Wang Z, Li J, Ma L, Liu X, Wei H, Xiao Y, Tao S. Metagenomic Sequencing Identified Specific Bacteriophage Signature Discriminating between Healthy and Diarrheal Neonatal Piglets. Nutrients 2023; 15:nu15071616. [PMID: 37049457 PMCID: PMC10097093 DOI: 10.3390/nu15071616] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Neonatal diarrhea is one of the most severe diseases in human beings and pigs, leading to high mortality and growth faltering. Gut microbiome-related studies mostly focus on the relationship between bacteria and neonatal diarrhea onset, and no research study has investigated the role of the gut virome in neonatal diarrhea. Here, using metagenomic sequencing, we characterized the fecal viral community of diarrheal and healthy neonatal piglets. We found that the viral community of diarrheal piglets showed higher individual heterogeneity and elevated abundance of Myoviridae. By predicting the bacterial host of the identified viral genomes, phages infecting Proteobacteria, especially E. coli, were the dominant taxa in neonatal diarrheal piglets. Consistent with this, the antibiotic resistance gene of E. coli origin was also enriched in neonatal diarrheal piglets. Finally, we established a random forest model to accurately discriminate between neonatal diarrheal piglets and healthy controls and identified genus E. coli- and genus listeria-infecting bacteriophages, including psa and C5 viruses, as key biomarkers. In conclusion, we provide the first glance of viral community and function characteristics in diarrheal and healthy neonatal piglets. These findings expand our understanding of the relationship among phages, bacteria and diarrhea, and may facilitate the development of therapeutics for the prevention and treatment of neonatal diarrhea.
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16
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Viruses Regulate Microbial Community Assembly Together with Environmental Factors in Acid Mine Drainage. Appl Environ Microbiol 2023; 89:e0197322. [PMID: 36656039 PMCID: PMC9973029 DOI: 10.1128/aem.01973-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Viruses are widespread in various ecosystems, and they play important roles in regulating the microbial community via host-virus interactions. Recently, metagenomic studies showed that there are extremely diverse viruses in different environments from the ocean to the human gut, but the influences of viral communities on microbial communities are poorly understood, especially in extreme environments. Here, we used metagenomics to characterize microbial communities and viral communities in acid mine drainage (AMD) and evaluated how viruses shape microbial community constrained by the harsh environments. Our results showed that AMD viral communities are significantly associated with the microbial communities, and viral diversity has positive correlations with microbial diversity. Viral community explained more variations of microbial community composition than environmental factors in AMD of a polymetallic mine. Moreover, we found that viruses harboring adaptive genes regulate a relative abundance of hosts under the modulation of environmental factors, such as pH. We also observed that viral diversity has significant correlations with the global properties of microbial cooccurrence networks, such as modularity. In addition, the results of null modeling analyses revealed that viruses significantly affect microbial community phylogeny and play important roles in regulating ecological processes of community assembly, such as dispersal limitation and homogenous dispersal. Together, these results revealed that AMD viruses are critical forces driving microbial network and community assembly via host-virus interactions. IMPORTANCE Viruses as mobile genetic elements play critical roles in the adaptive evolution of their hosts in extreme environments. However, how viruses further influence microbial community structure and assembly is still unclear. A recent metagenomic study observed diverse viruses unexplored in acid mine drainage, revealing the associations between the viral community and environmental factors. Here, we showed that viruses together with environmental factors can constrain the relative abundance of host and microbial community assembly in AMD of copper mines and polymetallic mines. Our results highlight the importance of viruses in shaping the microbial community from the individual host level to the community level.
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17
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Camargo AP, Nayfach S, Chen IMA, Palaniappan K, Ratner A, Chu K, Ritter S, Reddy TBK, Mukherjee S, Schulz F, Call L, Neches R, Woyke T, Ivanova N, Eloe-Fadrosh E, Kyrpides N, Roux S. IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata. Nucleic Acids Res 2023; 51:D733-D743. [PMID: 36399502 PMCID: PMC9825611 DOI: 10.1093/nar/gkac1037] [Citation(s) in RCA: 77] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/15/2022] [Accepted: 10/25/2022] [Indexed: 11/19/2022] Open
Abstract
Viruses are widely recognized as critical members of all microbiomes. Metagenomics enables large-scale exploration of the global virosphere, progressively revealing the extensive genomic diversity of viruses on Earth and highlighting the myriad of ways by which viruses impact biological processes. IMG/VR provides access to the largest collection of viral sequences obtained from (meta)genomes, along with functional annotation and rich metadata. A web interface enables users to efficiently browse and search viruses based on genome features and/or sequence similarity. Here, we present the fourth version of IMG/VR, composed of >15 million virus genomes and genome fragments, a ≈6-fold increase in size compared to the previous version. These clustered into 8.7 million viral operational taxonomic units, including 231 408 with at least one high-quality representative. Viral sequences in IMG/VR are now systematically identified from genomes, metagenomes, and metatranscriptomes using a new detection approach (geNomad), and IMG standard annotation are complemented with genome quality estimation using CheckV, taxonomic classification reflecting the latest taxonomic standards, and microbial host taxonomy prediction. IMG/VR v4 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.
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Affiliation(s)
- Antonio Pedro Camargo
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Stephen Nayfach
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - I-Min A Chen
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Anna Ratner
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ken Chu
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Stephan J Ritter
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - T B K Reddy
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Supratim Mukherjee
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lee Call
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Russell Y Neches
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Natalia N Ivanova
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Emiley A Eloe-Fadrosh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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18
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Seong HJ, Roux S, Hwang CY, Sul WJ. Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics. MICROBIOME 2022; 10:157. [PMID: 36167684 PMCID: PMC9516812 DOI: 10.1186/s40168-022-01340-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 07/28/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND DNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in culturable microorganisms, resulting in a limited understanding of DNA methylation from a microbial ecology perspective. Here, we analyze the distribution patterns of several microbial epigenetics marks in the ocean microbiome through genome-centric metagenomics across all domains of life. RESULTS We reconstructed 15,056 viral, 252 prokaryotic, 56 giant viral, and 6 eukaryotic metagenome-assembled genomes from northwest Pacific Ocean seawater samples using short- and long-read sequencing approaches. These metagenome-derived genomes mostly represented novel taxa, and recruited a majority of reads. Thanks to single-molecule real-time (SMRT) sequencing technology, base modification could also be detected for these genomes. This showed that DNA methylation can readily be detected across dominant oceanic bacterial, archaeal, and viral populations, and microbial epigenetic changes correlate with population differentiation. Furthermore, our genome-wide epigenetic analysis of Pelagibacter suggests that GANTC, a DNA methyltransferase target motif, is related to the cell cycle and is affected by environmental conditions. Yet, the presence of this motif also partitions the phylogeny of the Pelagibacter phages, possibly hinting at a competitive co-evolutionary history and multiple effects of a single methylation mark. CONCLUSIONS Overall, this study elucidates that DNA methylation patterns are associated with ecological changes and virus-host dynamics in the ocean microbiome. Video Abstract.
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Affiliation(s)
- Hoon Je Seong
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Chung Yeon Hwang
- School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul, Republic of Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
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19
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Elbehery AHA, Deng L. Insights into the global freshwater virome. Front Microbiol 2022; 13:953500. [PMID: 36246212 PMCID: PMC9554406 DOI: 10.3389/fmicb.2022.953500] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/11/2022] [Indexed: 11/29/2022] Open
Abstract
Viruses are by far the most abundant life forms on this planet. Yet, the full viral diversity remains mostly unknown, especially in environments like freshwater. Therefore, we aimed to study freshwater viruses in a global context. To this end, we downloaded 380 publicly available viral metagenomes (>1 TB). More than 60% of these metagenomes were discarded based on their levels of cellular contamination assessed by ribosomal DNA content. For the remaining metagenomes, assembled contigs were decontaminated using two consecutive steps, eventually yielding 273,365 viral contigs longer than 1,000 bp. Long enough contigs (≥ 10 kb) were clustered to identify novel genomes/genome fragments. We could recover 549 complete circular and high-quality draft genomes, out of which 10 were recognized as being novel. Functional annotation of these genomes showed that most of the annotated coding sequences are DNA metabolic genes or phage structural genes. On the other hand, taxonomic analysis of viral contigs showed that most of the assigned contigs belonged to the order Caudovirales, particularly the families of Siphoviridae, Myoviridae, and Podoviridae. The recovered viral contigs contained several auxiliary metabolic genes belonging to several metabolic pathways, especially carbohydrate and amino acid metabolism in addition to photosynthesis as well as hydrocarbon degradation and antibiotic resistance. Overall, we present here a set of prudently chosen viral contigs, which should not only help better understanding of freshwater viruses but also be a valuable resource for future virome studies.
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Affiliation(s)
- Ali H. A. Elbehery
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City, Egypt
- *Correspondence: Ali H. A. Elbehery,
| | - Li Deng
- Helmholtz Centre Munich – German Research Centre for Environmental Health, Institute of Virology, Neuherberg, Germany
- Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, Freising, Germany
- Li Deng,
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20
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Nishijima S, Nagata N, Kiguchi Y, Kojima Y, Miyoshi-Akiyama T, Kimura M, Ohsugi M, Ueki K, Oka S, Mizokami M, Itoi T, Kawai T, Uemura N, Hattori M. Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort. Nat Commun 2022; 13:5252. [PMID: 36068216 PMCID: PMC9448778 DOI: 10.1038/s41467-022-32832-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 08/17/2022] [Indexed: 11/19/2022] Open
Abstract
Indigenous bacteriophage communities (virome) in the human gut have a huge impact on the structure and function of gut bacterial communities (bacteriome), but virome variation at a population scale is not fully investigated yet. Here, we analyse the gut dsDNA virome in the Japanese 4D cohort of 4198 deeply phenotyped individuals. By assembling metagenomic reads, we discover thousands of high-quality phage genomes including previously uncharacterised phage clades with different bacterial hosts than known major ones. The distribution of host bacteria is a strong determinant for the distribution of phages in the gut, and virome diversity is highly correlated with anti-viral defence mechanisms of the bacteriome, such as CRISPR-Cas and restriction-modification systems. We identify 97 various intrinsic/extrinsic factors that significantly affect the virome structure, including age, sex, lifestyle, and diet, most of which showed consistent associations with both phages and their predicted bacterial hosts. Among the metadata categories, disease and medication have the strongest effects on the virome structure. Overall, these results present a basis to understand the symbiotic communities of bacteria and their viruses in the human gut, which will facilitate the medical and industrial applications of indigenous viruses.
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Affiliation(s)
- Suguru Nishijima
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.
- Computational Bio Big Data Open Innovation Lab., National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Naoyoshi Nagata
- Department of Gastroenterological Endoscopy, Tokyo Medical University, Tokyo, Japan.
- Department of Gastroenterology and Hepatology, National Center for Global Health and Medicine, Tokyo, Japan.
| | - Yuya Kiguchi
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yasushi Kojima
- Department of Gastroenterology and Hepatology, National Center for Global Health and Medicine, Tokyo, Japan
| | - Tohru Miyoshi-Akiyama
- Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Moto Kimura
- Department of Clinical Research Strategic Planning Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan
| | - Mitsuru Ohsugi
- Department of Diabetes, Endocrinology, and Metabolism, Center Hospital, National Center for Global Health and Medicine, Tokyo, Japan
- Diabetes and Metabolism Information Center, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kohjiro Ueki
- Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shinichi Oka
- AIDS Clinical Center, National Center for Global Health and Medicine Hospital, Tokyo, Japan
| | - Masashi Mizokami
- Genome Medical Sciences Project, Research Institute, National Center for Global Health and Medicine, Chiba, Japan
| | - Takao Itoi
- Department of Gastroenterology and Hepatology, Tokyo Medical University, Tokyo, Japan
| | - Takashi Kawai
- Department of Gastroenterological Endoscopy, Tokyo Medical University, Tokyo, Japan
| | - Naomi Uemura
- Department of Gastroenterology and Hepatology, National Center for Global Health and Medicine, Kohnodai Hospital, Tokyo, Japan
| | - Masahira Hattori
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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21
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Gao C, Liang Y, Jiang Y, Paez-Espino D, Han M, Gu C, Wang M, Yang Y, Liu F, Yang Q, Gong Z, Zhang X, Luo Z, He H, Guo C, Shao H, Zhou C, Shi Y, Xin Y, Xing J, Tang X, Qin Q, Zhang YZ, He J, Jiao N, McMinn A, Tian J, Suttle CA, Wang M. Virioplankton assemblages from challenger deep, the deepest place in the oceans. iScience 2022; 25:104680. [PMID: 35942087 PMCID: PMC9356048 DOI: 10.1016/j.isci.2022.104680] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/25/2022] [Accepted: 06/23/2022] [Indexed: 11/26/2022] Open
Abstract
Hadal ocean biosphere, that is, the deepest part of the world's oceans, harbors a unique microbial community, suggesting a potential uncovered co-occurring virioplankton assemblage. Herein, we reveal the unique virioplankton assemblages of the Challenger Deep, comprising 95,813 non-redundant viral contigs from the surface to the hadal zone. Almost all of the dominant viral contigs in the hadal zone were unclassified, potentially related to Alteromonadales and Oceanospirillales. 2,586 viral auxiliary metabolic genes from 132 different KEGG orthologous groups were mainly related to the carbon, nitrogen, sulfur, and arsenic metabolism. Lysogenic viral production and integrase genes were augmented in the hadal zone, suggesting the prevalence of viral lysogenic life strategy. Abundant rve genes in the hadal zone, which function as transposase in the caudoviruses, further suggest the prevalence of viral-mediated horizontal gene transfer. This study provides fundamental insights into the virioplankton assemblages of the hadal zone, reinforcing the necessity of incorporating virioplankton into the hadal biogeochemical cycles.
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Affiliation(s)
- Chen Gao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Yong Jiang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - David Paez-Espino
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Mammoth Biosciences, Inc., South San Francisco, CA, USA
| | - Meiaoxue Han
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Chengxiang Gu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Meiwen Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Yumei Yang
- Inquire Life Diagnostics, Inc, Xi’an 710100, China
| | - Fengjiao Liu
- The Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - Qingwei Yang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Zheng Gong
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Xinran Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Zhixiang Luo
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Hui He
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Cui Guo
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Chun Zhou
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Yang Shi
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Yu Xin
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Institute for Advanced Ocean Study, Ocean University of China, Qingdao 266100, China
| | - Jinyan Xing
- The Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - Xuexi Tang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
| | - Qilong Qin
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, China
| | - Jianfeng He
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, China
| | - Nianzhi Jiao
- Institute of Marine Microbes and Ecospheres, State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, Fujian 361005, China
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7001, Australia
| | - Jiwei Tian
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao 266100, China
- Laboratory for Ocean and Climate Dynamics, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Curtis A. Suttle
- Departments of Earth, Ocean and Atmospheric Sciences, Microbiology and Immunology and Botany and Institute for the Oceans and Fisheries, the University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
- The Affiliated Hospital of Qingdao University, Qingdao 266000, China
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22
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Kumar S, Kumar GS, Maitra SS, Malý P, Bharadwaj S, Sharma P, Dwivedi VD. Viral informatics: bioinformatics-based solution for managing viral infections. Brief Bioinform 2022; 23:6659740. [PMID: 35947964 DOI: 10.1093/bib/bbac326] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 06/26/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Several new viral infections have emerged in the human population and establishing as global pandemics. With advancements in translation research, the scientific community has developed potential therapeutics to eradicate or control certain viral infections, such as smallpox and polio, responsible for billions of disabilities and deaths in the past. Unfortunately, some viral infections, such as dengue virus (DENV) and human immunodeficiency virus-1 (HIV-1), are still prevailing due to a lack of specific therapeutics, while new pathogenic viral strains or variants are emerging because of high genetic recombination or cross-species transmission. Consequently, to combat the emerging viral infections, bioinformatics-based potential strategies have been developed for viral characterization and developing new effective therapeutics for their eradication or management. This review attempts to provide a single platform for the available wide range of bioinformatics-based approaches, including bioinformatics methods for the identification and management of emerging or evolved viral strains, genome analysis concerning the pathogenicity and epidemiological analysis, computational methods for designing the viral therapeutics, and consolidated information in the form of databases against the known pathogenic viruses. This enriched review of the generally applicable viral informatics approaches aims to provide an overview of available resources capable of carrying out the desired task and may be utilized to expand additional strategies to improve the quality of translation viral informatics research.
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Affiliation(s)
- Sanjay Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | - Geethu S Kumar
- Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | | | - Petr Malý
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Shiv Bharadwaj
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Vivek Dhar Dwivedi
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India.,Institute of Advanced Materials, IAAM, 59053 Ulrika, Sweden
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23
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Bhardwaj K, Garg A, Pandey AD, Sharma H, Kumar M, Vrati S. Insights into the human gut virome by sampling a population from the Indian subcontinent. J Gen Virol 2022; 103. [PMID: 35951476 DOI: 10.1099/jgv.0.001774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gut virome plays an important role in human physiology but remains poorly understood. This study reports an investigation of the human gut DNA-virome of a previously unexplored ethnic population through metagenomics of faecal samples collected from individuals residing in Northern India. Analysis shows that, similar to the populations investigated earlier, majority of the identified virome belongs to bacteriophages and a smaller fraction (<20 %) consists of viruses that infect animals, archaea, protists, multiple domains or plants. However, crAss-like phages, in this population, are dominated by the genera VI, VII and VIII. Interestingly, it also reveals the presence of a virus family, Sphaerolipoviridae, which has not been detected in the human gut earlier. Viral families, Siphoviridae, Myoviridae, Podoviridae, Microviridae, Herelleviridae and Phycodnaviridae are detected in all of the analysed individuals, which supports the existence of a core virome. Lysogeny-associated genes were found in less than 10 % of the assembled genomes and a negative correlation was observed in the richness of bacterial and free-viral species, suggesting that the dominant lifestyle of gut phage is not lysogenic. This is in contrast to some of the earlier studies. Further, several hundred high-quality viral genomes were recovered. Detailed characterization of these genomes would be useful for understanding the biology of these viruses and their significance in human physiology.
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Affiliation(s)
- Kanchan Bhardwaj
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad-Gurugram Expressway, Faridabad-121 001, Haryana, India.,Manav Rachna International Institute of Research and Studies, Sector-43, Aravali hills, Faridabad-121 004, Haryana, India
| | - Anjali Garg
- Department of Biophysics, University of Delhi, South Campus, New Delhi-110021, India
| | - Abhay Deep Pandey
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad-Gurugram Expressway, Faridabad-121 001, Haryana, India
| | - Himani Sharma
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad-Gurugram Expressway, Faridabad-121 001, Haryana, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi, South Campus, New Delhi-110021, India
| | - Sudhanshu Vrati
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad-Gurugram Expressway, Faridabad-121 001, Haryana, India
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24
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Chitcharoen S, Sivapornnukul P, Payungporn S. Revolutionized virome research using systems microbiology approaches. Exp Biol Med (Maywood) 2022; 247:1135-1147. [PMID: 35723062 PMCID: PMC9335507 DOI: 10.1177/15353702221102895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Currently, both pathogenic and commensal viruses are continuously being discovered and acknowledged as ubiquitous components of microbial communities. The advancements of systems microbiological approaches have changed the face of virome research. Here, we focus on viral metagenomic approach to study virus community and their interactions with other microbial members as well as their hosts. This review also summarizes challenges, limitations, and benefits of the current virome approaches. Potentially, the studies of virome can be further applied in various biological and clinical fields.
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Affiliation(s)
- Suwalak Chitcharoen
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand,Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pavaret Sivapornnukul
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Sunchai Payungporn.
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25
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Zuo W, Michail S, Sun F. Metagenomic Analyses of Multiple Gut Datasets Revealed the Association of Phage Signatures in Colorectal Cancer. Front Cell Infect Microbiol 2022; 12:918010. [PMID: 35782128 PMCID: PMC9240273 DOI: 10.3389/fcimb.2022.918010] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/12/2022] [Indexed: 12/24/2022] Open
Abstract
The association of colorectal cancer (CRC) and the human gut microbiome dysbiosis has been the focus of several studies in the past. Many bacterial taxa have been shown to have differential abundance among CRC patients compared to healthy controls. However, the relationship between CRC and non-bacterial gut microbiome such as the gut virome is under-studied and not well understood. In this study we conducted a comprehensive analysis of the association of viral abundances with CRC using metagenomic shotgun sequencing data of 462 CRC subjects and 449 healthy controls from 7 studies performed in 8 different countries. Despite the high heterogeneity, our results showed that the virome alpha diversity was consistently higher in CRC patients than in healthy controls (p-value <0.001). This finding is in sharp contrast to previous reports of low alpha diversity of prokaryotes in CRC compared to healthy controls. In addition to the previously known association of Podoviridae, Siphoviridae and Myoviridae with CRC, we further demonstrate that Herelleviridae, a newly constructed viral family, is significantly depleted in CRC subjects. Our interkingdom association analysis reveals a less intertwined correlation between the gut virome and bacteriome in CRC compared to healthy controls. Furthermore, we show that the viral abundance profiles can be used to accurately predict CRC disease status (AUROC >0.8) in both within-study and cross-study settings. The combination of training sets resulted in rather generalized and accurate prediction models. Our study clearly shows that subjects with colorectal cancer harbor a distinct human gut virome profile which may have an important role in this disease.
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Affiliation(s)
- Wenxuan Zuo
- Quantitative and Computational Biology Department, University of Southern California, Los Angeles, CA, United States
| | - Sonia Michail
- Department of Pediatrics, Keck School of Medicine of the University of Southern California, Los Angeles, CA, United States
| | - Fengzhu Sun
- Quantitative and Computational Biology Department, University of Southern California, Los Angeles, CA, United States
- *Correspondence: Fengzhu Sun,
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26
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Liang G, Gao H, Bushman FD. The pediatric virome in health and disease. Cell Host Microbe 2022; 30:639-649. [PMID: 35550667 DOI: 10.1016/j.chom.2022.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/22/2022] [Accepted: 04/11/2022] [Indexed: 11/03/2022]
Abstract
Associations between the global microbiome and diseases of children have been studied extensively; however, research on the viral component of the microbiome, the "virome," is less advanced. The analysis of disease associations with the virome is often technically challenging, requiring a close examination of the "virome dark matter." The gut is a particularly rich source of viral particles, and now multiple studies have reported intriguing associations of the virome with childhood diseases. For example, virome studies have elucidated new lineages of gut viruses that appear to be tightly associated with childhood diarrhea, and consistent patterns are starting to emerge from virome studies in pediatric IBD. In this review, we summarize the methods for studying the virome and recent research on the nature of the virome during childhood, focusing on specific studies of the intestinal virome in pediatric diseases.
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Affiliation(s)
- Guanxiang Liang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
| | - Hongyan Gao
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6076, USA.
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27
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Host-Associated Phages Disperse across the Extraterrestrial Analogue Antarctica. Appl Environ Microbiol 2022; 88:e0031522. [PMID: 35499326 DOI: 10.1128/aem.00315-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Extreme Antarctic conditions provide one of the closest analogues of extraterrestrial environments. Since air and snow samples, especially from polar regions, yield DNA amounts in the lower picogram range, binning of prokaryotic genomes is challenging and renders studying the dispersal of biological entities across these environments difficult. Here, we hypothesized that dispersal of host-associated bacteriophages (adsorbed, replicating, or prophages) across the Antarctic continent can be tracked via their genetic signatures, aiding our understanding of virus and host dispersal across long distances. Phage genome fragments (PGFs) reconstructed from surface snow metagenomes of three Antarctic stations were assigned to four host genomes, mainly Betaproteobacteria, including Ralstonia spp. We reconstructed the complete genome of a temperate phage with nearly complete alignment to a prophage in the reference genome of Ralstonia pickettii 12D. PGFs from different stations were related to each other at the genus level and matched similar hosts. Metagenomic read mapping and nucleotide polymorphism analysis revealed a wide dispersal of highly identical PGFs, 13 of which were detected in seawater from the Western Antarctic Peninsula at a distance of 5,338 km from the snow sampling stations. Our results suggest that host-associated phages, especially of Ralstonia sp., disperse over long distances despite the harsh conditions of the Antarctic continent. Given that 14 phages associated with two R. pickettii draft genomes isolated from space equipment were identified, we conclude that Ralstonia phages are ideal mobile genetic elements to track dispersal and contamination in ecosystems relevant for astrobiology. IMPORTANCE Host-associated phages of the bacterium Ralstonia identified in snow samples can be used to track microbial dispersal over thousands of kilometers across the Antarctic continent, which functions as an extraterrestrial analogue because of its harsh environmental conditions. Due to the presence of these bacteria carrying genome-integrated prophages on space-related equipment and the potential for dispersal of host-associated phages demonstrated here, our work has implications for planetary protection, a discipline in astrobiology interested in preventing contamination of celestial bodies with alien biomolecules or forms of life.
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Quantifying and Cataloguing Unknown Sequences within Human Microbiomes. mSystems 2022; 7:e0146821. [PMID: 35258340 PMCID: PMC9052204 DOI: 10.1128/msystems.01468-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Advances in genome sequencing technologies and lower costs have enabled the exploration of a multitude of known and novel environments and microbiomes. This has led to an exponential growth in the raw sequence data that are deposited in online repositories. Metagenomic and metatranscriptomic data sets are typically analysed with regard to a specific biological question. However, it is widely acknowledged that these data sets are comprised of a proportion of sequences that bear no similarity to any currently known biological sequence, and this so-called "dark matter" is often excluded from downstream analyses. In this study, a systematic framework was developed to assemble, identify, and measure the proportion of unknown sequences present in distinct human microbiomes. This framework was applied to 40 distinct studies, comprising 963 samples, and covering 10 different human microbiomes including fecal, oral, lung, skin, and circulatory system microbiomes. We found that while the human microbiome is one of the most extensively studied, on average 2% of assembled sequences have not yet been taxonomically defined. However, this proportion varied extensively among different microbiomes and was as high as 25% for skin and oral microbiomes that have more interactions with the environment. A rate of taxonomic characterization of 1.64% of unknown sequences being characterized per month was calculated from these taxonomically unknown sequences discovered in this study. A cross-study comparison led to the identification of similar unknown sequences in different samples and/or microbiomes. Both our computational framework and the novel unknown sequences produced are publicly available for future cross-referencing. Our approach led to the discovery of several novel viral genomes that bear no similarity to sequences in the public databases. Some of these are widespread as they have been found in different microbiomes and studies. Hence, our study illustrates how the systematic characterization of unknown sequences can help the discovery of novel microbes, and we call on the research community to systematically collate and share the unknown sequences from metagenomic studies to increase the rate at which the unknown sequence space can be classified.
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Martinez-Hernandez F, Diop A, Garcia-Heredia I, Bobay LM, Martinez-Garcia M. Unexpected myriad of co-occurring viral strains and species in one of the most abundant and microdiverse viruses on Earth. THE ISME JOURNAL 2022; 16:1025-1035. [PMID: 34775488 PMCID: PMC8940918 DOI: 10.1038/s41396-021-01150-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/15/2021] [Accepted: 10/28/2021] [Indexed: 11/09/2022]
Abstract
Viral genetic microdiversity drives adaptation, pathogenicity, and speciation and has critical consequences for the viral-host arms race occurring at the strain and species levels, which ultimately impact microbial community structure and biogeochemical cycles. Despite the fact that most efforts have focused on viral macrodiversity, little is known about the microdiversity of ecologically important viruses on Earth. Recently, single-virus genomics discovered the putatively most abundant ocean virus in temperate and tropical waters: the uncultured dsDNA virus vSAG 37-F6 infecting Pelagibacter, the most abundant marine bacteria. In this study, we report the cooccurrence of up to ≈1,500 different viral strains (>95% nucleotide identity) and ≈30 related species (80-95% nucleotide identity) in a single oceanic sample. Viral microdiversity was maintained over space and time, and most alleles were the result of synonymous mutations without any apparent adaptive benefits to cope with host translation codon bias and efficiency. Gene flow analysis used to delimitate species according to the biological species concept (BSC) revealed the impact of recombination in shaping vSAG 37-F6 virus and Pelagibacter speciation. Data demonstrated that this large viral microdiversity somehow mirrors the host species diversity since ≈50% of the 926 analyzed Pelagibacter genomes were found to belong to independent BSC species that do not significantly engage in gene flow with one another. The host range of this evolutionarily successful virus revealed that a single viral species can infect multiple Pelagibacter BSC species, indicating that this virus crosses not only formal BSC barriers but also biomes since viral ancestors are found in freshwater.
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Affiliation(s)
| | - Awa Diop
- Department of Biology, University of North Carolina at Greensboro, Greensboro, USA
| | | | - Louis-Marie Bobay
- Department of Biology, University of North Carolina at Greensboro, Greensboro, USA
| | - Manuel Martinez-Garcia
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain.
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Chen LX, Jaffe AL, Borges AL, Penev PI, Nelson TC, Warren LA, Banfield JF. Phage-encoded ribosomal protein S21 expression is linked to late-stage phage replication. ISME COMMUNICATIONS 2022; 2:31. [PMID: 37938675 PMCID: PMC9723584 DOI: 10.1038/s43705-022-00111-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/31/2022] [Accepted: 02/03/2022] [Indexed: 06/16/2023]
Abstract
The ribosomal protein S21 (bS21) gene has been detected in diverse viruses with a large range of genome sizes, yet its in situ expression and potential significance have not been investigated. Here, we report five closely related clades of bacteriophages (phages) represented by 47 genomes (8 curated to completion and up to 331 kbp in length) that encode a bS21 gene. The bS21 gene is on the reverse strand within a conserved region that encodes the large terminase, major capsid protein, prohead protease, portal vertex proteins, and some hypothetical proteins. Based on CRISPR spacer targeting, the predominance of bacterial taxonomic affiliations of phage genes with those from Bacteroidetes, and the high sequence similarity of the phage bS21 genes and those from Bacteroidetes classes of Flavobacteriia, Cytophagia and Saprospiria, these phages are predicted to infect diverse Bacteroidetes species that inhabit a range of depths in freshwater lakes. Thus, bS21 phages have the potential to impact microbial community composition and carbon turnover in lake ecosystems. The transcriptionally active bS21-encoding phages were likely in the late stage of replication when collected, as core structural genes and bS21 were highly expressed. Thus, our analyses suggest that the phage bS21, which is involved in translation initiation, substitutes into the Bacteroidetes ribosomes and selects preferentially for phage transcripts during the late-stage replication when large-scale phage protein production is required for assembly of phage particles.
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Affiliation(s)
- Lin-Xing Chen
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Alexander L Jaffe
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Adair L Borges
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Petar I Penev
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | | | - Lesley A Warren
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, ON, Canada
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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31
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Bartlau N, Wichels A, Krohne G, Adriaenssens EM, Heins A, Fuchs BM, Amann R, Moraru C. Highly diverse flavobacterial phages isolated from North Sea spring blooms. THE ISME JOURNAL 2022; 16:555-568. [PMID: 34475519 PMCID: PMC8776804 DOI: 10.1038/s41396-021-01097-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 08/17/2021] [Indexed: 11/24/2022]
Abstract
It is generally recognized that phages are a mortality factor for their bacterial hosts. This could be particularly true in spring phytoplankton blooms, which are known to be closely followed by a highly specialized bacterial community. We hypothesized that phages modulate these dense heterotrophic bacteria successions following phytoplankton blooms. In this study, we focused on Flavobacteriia, because they are main responders during these blooms and have an important role in the degradation of polysaccharides. A cultivation-based approach was used, obtaining 44 lytic flavobacterial phages (flavophages), representing twelve new species from two viral realms. Taxonomic analysis allowed us to delineate ten new phage genera and ten new families, from which nine and four, respectively, had no previously cultivated representatives. Genomic analysis predicted various life styles and genomic replication strategies. A likely eukaryote-associated host habitat was reflected in the gene content of some of the flavophages. Detection in cellular metagenomes and by direct-plating showed that part of these phages were actively replicating in the environment during the 2018 spring bloom. Furthermore, CRISPR/Cas spacers and re-isolation during two consecutive years suggested that, at least part of the new flavophages are stable components of the microbial community in the North Sea. Together, our results indicate that these diverse flavophages have the potential to modulate their respective host populations.
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Affiliation(s)
- Nina Bartlau
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Antje Wichels
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Biologische Anstalt Helgoland, Heligoland, Germany
| | - Georg Krohne
- Imaging Core Facility, Biocenter, University of Würzburg, Würzburg, Germany
| | | | - Anneke Heins
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
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Yahara K. バクテリオファージのビッグデータ解析. Uirusu 2022; 72:63-66. [PMID: 37899231 DOI: 10.2222/jsv.72.63] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
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Panwar P, Allen MA, Williams TJ, Haque S, Brazendale S, Hancock AM, Paez-Espino D, Cavicchioli R. Remarkably coherent population structure for a dominant Antarctic Chlorobium species. MICROBIOME 2021; 9:231. [PMID: 34823595 PMCID: PMC8620254 DOI: 10.1186/s40168-021-01173-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 10/09/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND In Antarctica, summer sunlight enables phototrophic microorganisms to drive primary production, thereby "feeding" ecosystems to enable their persistence through the long, dark winter months. In Ace Lake, a stratified marine-derived system in the Vestfold Hills of East Antarctica, a Chlorobium species of green sulphur bacteria (GSB) is the dominant phototroph, although its seasonal abundance changes more than 100-fold. Here, we analysed 413 Gb of Antarctic metagenome data including 59 Chlorobium metagenome-assembled genomes (MAGs) from Ace Lake and nearby stratified marine basins to determine how genome variation and population structure across a 7-year period impacted ecosystem function. RESULTS A single species, Candidatus Chlorobium antarcticum (most similar to Chlorobium phaeovibrioides DSM265) prevails in all three aquatic systems and harbours very little genomic variation (≥ 99% average nucleotide identity). A notable feature of variation that did exist related to the genomic capacity to biosynthesize cobalamin. The abundance of phylotypes with this capacity changed seasonally ~ 2-fold, consistent with the population balancing the value of a bolstered photosynthetic capacity in summer against an energetic cost in winter. The very high GSB concentration (> 108 cells ml-1 in Ace Lake) and seasonal cycle of cell lysis likely make Ca. Chlorobium antarcticum a major provider of cobalamin to the food web. Analysis of Ca. Chlorobium antarcticum viruses revealed the species to be infected by generalist (rather than specialist) viruses with a broad host range (e.g., infecting Gammaproteobacteria) that were present in diverse Antarctic lakes. The marked seasonal decrease in Ca. Chlorobium antarcticum abundance may restrict specialist viruses from establishing effective lifecycles, whereas generalist viruses may augment their proliferation using other hosts. CONCLUSION The factors shaping Antarctic microbial communities are gradually being defined. In addition to the cold, the annual variation in sunlight hours dictates which phototrophic species can grow and the extent to which they contribute to ecosystem processes. The Chlorobium population studied was inferred to provide cobalamin, in addition to carbon, nitrogen, hydrogen, and sulphur cycling, as critical ecosystem services. The specific Antarctic environmental factors and major ecosystem benefits afforded by this GSB likely explain why such a coherent population structure has developed in this Chlorobium species. Video abstract.
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Affiliation(s)
- Pratibha Panwar
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Michelle A Allen
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Sabrina Haque
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- Present address: Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, 2109, Australia
| | - Sarah Brazendale
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- , Present address: Pegarah, Australia
| | - Alyce M Hancock
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- Present address: Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Battery Point, Tasmania, Australia
| | - David Paez-Espino
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Present address: Mammoth Biosciences, Inc., 1000 Marina Blvd. Suite 600, Brisbane, CA, USA
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia.
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Happel AU, Balle C, Maust BS, Konstantinus IN, Gill K, Bekker LG, Froissart R, Passmore JA, Karaoz U, Varsani A, Jaspan H. Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents. Viruses 2021; 13:2341. [PMID: 34960611 PMCID: PMC8708031 DOI: 10.3390/v13122341] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/18/2021] [Accepted: 11/18/2021] [Indexed: 12/11/2022] Open
Abstract
The interaction between gut bacterial and viral microbiota is thought to be important in human health. While fluctuations in female genital tract (FGT) bacterial microbiota similarly determine sexual health, little is known about the presence, persistence, and function of vaginal bacteriophages. We conducted shotgun metagenome sequencing of cervicovaginal samples from South African adolescents collected longitudinally, who received no antibiotics. We annotated viral reads and circular bacteriophages, identified CRISPR loci and putative prophages, and assessed their diversity, persistence, and associations with bacterial microbiota composition. Siphoviridae was the most prevalent bacteriophage family, followed by Myoviridae, Podoviridae, Herelleviridae, and Inoviridae. Full-length siphoviruses targeting bacterial vaginosis (BV)-associated bacteria were identified, suggesting their presence in vivo. CRISPR loci and prophage-like elements were common, and genomic analysis suggested higher diversity among Gardnerella than Lactobacillus prophages. We found that some prophages were highly persistent within participants, and identical prophages were present in cervicovaginal secretions of multiple participants, suggesting that prophages, and thus bacterial strains, are shared between adolescents. The number of CRISPR loci and prophages were associated with vaginal microbiota stability and absence of BV. Our analysis suggests that (pro)phages are common in the FGT and vaginal bacteria and (pro)phages may interact.
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Affiliation(s)
- Anna-Ursula Happel
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (A.-U.H.); (C.B.); (I.N.K.); (J.-A.P.)
| | - Christina Balle
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (A.-U.H.); (C.B.); (I.N.K.); (J.-A.P.)
| | - Brandon S. Maust
- Seattle Children’s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109, USA;
- Department of Pediatrics, University of Washington School of Medicine, 1959 NE Pacific St., Seattle, WA 98195, USA
| | - Iyaloo N. Konstantinus
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (A.-U.H.); (C.B.); (I.N.K.); (J.-A.P.)
- Namibia Institute of Pathology, Hosea Kutako, Windhoek 10005, Namibia
| | - Katherine Gill
- Desmond Tutu HIV Centre, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (K.G.); (L.-G.B.)
- NRF-DST CAPRISA Centre of Excellence in HIV Prevention, 719 Umbilo Road, Congella, Durban 4013, South Africa
| | - Linda-Gail Bekker
- Desmond Tutu HIV Centre, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (K.G.); (L.-G.B.)
- NRF-DST CAPRISA Centre of Excellence in HIV Prevention, 719 Umbilo Road, Congella, Durban 4013, South Africa
| | - Rémy Froissart
- CNRS, IRD, Université Montpellier, UMR 5290, MIVEGEC, 34394 Montpellier, France;
| | - Jo-Ann Passmore
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (A.-U.H.); (C.B.); (I.N.K.); (J.-A.P.)
- Desmond Tutu HIV Centre, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (K.G.); (L.-G.B.)
- NRF-DST CAPRISA Centre of Excellence in HIV Prevention, 719 Umbilo Road, Congella, Durban 4013, South Africa
- National Health Laboratory Service, Anzio Road, Cape Town 7925, South Africa
| | - Ulas Karaoz
- Earth and Environmental Science, Lawrence Berkeley National Laboratories, 1 Cyclotron Rd., Berkeley, CA 94720, USA;
| | - Arvind Varsani
- The Biodesign Center of Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa
| | - Heather Jaspan
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (A.-U.H.); (C.B.); (I.N.K.); (J.-A.P.)
- Seattle Children’s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109, USA;
- Department of Pediatrics, University of Washington School of Medicine, 1959 NE Pacific St., Seattle, WA 98195, USA
- Department of Global Health, University of Washington School of Public Health, 1510 San Juan Road NE, Seattle, WA 98195, USA
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Unveiling Ecological and Genetic Novelty within Lytic and Lysogenic Viral Communities of Hot Spring Phototrophic Microbial Mats. Microbiol Spectr 2021; 9:e0069421. [PMID: 34787442 PMCID: PMC8597652 DOI: 10.1128/spectrum.00694-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Viruses exert diverse ecosystem impacts by controlling their host community through lytic predator-prey dynamics. However, the mechanisms by which lysogenic viruses influence their host-microbial community are less clear. In hot springs, lysogeny is considered an active lifestyle, yet it has not been systematically studied in all habitats, with phototrophic microbial mats (PMMs) being particularly not studied. We carried out viral metagenomics following in situ mitomycin C induction experiments in PMMs from Porcelana hot spring (Northern Patagonia, Chile). The compositional changes of viral communities at two different sites were analyzed at the genomic and gene levels. Furthermore, the presence of integrated prophage sequences in environmental metagenome-assembled genomes from published Porcelana PMM metagenomes was analyzed. Our results suggest that virus-specific replicative cycles (lytic and lysogenic) were associated with specific host taxa with different metabolic capacities. One of the most abundant lytic viral groups corresponded to cyanophages, which would infect the cyanobacteria Fischerella, the most active and dominant primary producer in thermophilic PMMs. Likewise, lysogenic viruses were related exclusively to chemoheterotrophic bacteria from the phyla Proteobacteria, Firmicutes, and Actinobacteria. These temperate viruses possess accessory genes to sense or control stress-related processes in their hosts, such as sporulation and biofilm formation. Taken together, these observations suggest a nexus between the ecological role of the host (metabolism) and the type of viral lifestyle in thermophilic PMMs. This has direct implications in viral ecology, where the lysogenic-lytic switch is determined by nutrient abundance and microbial density but also by the metabolism type that prevails in the host community. IMPORTANCE Hot springs harbor microbial communities dominated by a limited variety of microorganisms and, as such, have become a model for studying community ecology and understanding how biotic and abiotic interactions shape their structure. Viruses in hot springs are shown to be ubiquitous, numerous, and active components of these communities. However, lytic and lysogenic viral communities of thermophilic phototrophic microbial mats (PMMs) remain largely unexplored. In this work, we use the power of viral metagenomics to reveal changes in the viral community following a mitomycin C induction experiment in PMMs. The importance of our research is that it will improve our understanding of viral lifestyles in PMMs via exploring the differences in the composition of natural and induced viral communities at the genome and gene levels. This novel information will contribute to deciphering which biotic and abiotic factors may control the transitions between lytic and lysogenic cycles in these extreme environments.
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Dutilh BE, Varsani A, Tong Y, Simmonds P, Sabanadzovic S, Rubino L, Roux S, Muñoz AR, Lood C, Lefkowitz EJ, Kuhn JH, Krupovic M, Edwards RA, Brister JR, Adriaenssens EM, Sullivan MB. Perspective on taxonomic classification of uncultivated viruses. Curr Opin Virol 2021; 51:207-215. [PMID: 34781105 DOI: 10.1016/j.coviro.2021.10.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 12/19/2022]
Abstract
Historically, virus taxonomy has been limited to describing viruses that were readily cultivated in the laboratory or emerging in natural biomes. Metagenomic analyses, single-particle sequencing, and database mining efforts have yielded new sequence data on an astounding number of previously unknown viruses. As metagenomes are relatively free of biases, these data provide an unprecedented insight into the vastness of the virosphere, but to properly value the extent of this diversity it is critical that the viruses are taxonomically classified. Inclusion of uncultivated viruses has already improved the process as well as the understanding of the taxa, viruses, and their evolutionary relationships. The continuous development and testing of computational tools will be required to maintain a dynamic virus taxonomy that can accommodate the new discoveries.
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Affiliation(s)
- Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands; Institute of Bioloversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, 07743, Jena, Germany.
| | - Arvind Varsani
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, 7925, Cape Town, South Africa
| | - Yigang Tong
- Beijing Advanced Innovation Centre for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, MS 39762, USA
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alejandro Reyes Muñoz
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Cédric Lood
- Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 23, 3001, Leuven, Belgium; Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Mart Krupovic
- Institut Pasteur, Université de Paris, Archaeal Virology Unit, F-75015, Paris, France
| | - Robert A Edwards
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD 20894, USA
| | | | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH, USA
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DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes. mBio 2021; 12:e0259521. [PMID: 34724822 PMCID: PMC8567247 DOI: 10.1128/mbio.02595-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Soil viruses are abundant, but the influence of the environment and climate on soil viruses remains poorly understood. Here, we addressed this gap by comparing the diversity, abundance, lifestyle, and metabolic potential of DNA viruses in three grassland soils with historical differences in average annual precipitation, low in eastern Washington (WA), high in Iowa (IA), and intermediate in Kansas (KS). Bioinformatics analyses were applied to identify a total of 2,631 viral contigs, including 14 complete viral genomes from three deep metagenomes (1 terabase [Tb] each) that were sequenced from bulk soil DNA. An additional three replicate metagenomes (∼0.5 Tb each) were obtained from each location for statistical comparisons. Identified viruses were primarily bacteriophages targeting dominant bacterial taxa. Both viral and host diversity were higher in soil with lower precipitation. Viral abundance was also significantly higher in the arid WA location than in IA and KS. More lysogenic markers and fewer clustered regularly interspaced short palindromic repeats (CRISPR) spacer hits were found in WA, reflecting more lysogeny in historically drier soil. More putative auxiliary metabolic genes (AMGs) were also detected in WA than in the historically wetter locations. The AMGs occurring in 18 pathways could potentially contribute to carbon metabolism and energy acquisition in their hosts. Structural equation modeling (SEM) suggested that historical precipitation influenced viral life cycle and selection of AMGs. The observed and predicted relationships between soil viruses and various biotic and abiotic variables have value for predicting viral responses to environmental change.
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Genome and Ecology of a Novel Alteromonas Podovirus, ZP6, Representing a New Viral Genus, Mareflavirus. Microbiol Spectr 2021; 9:e0046321. [PMID: 34643440 PMCID: PMC8515928 DOI: 10.1128/spectrum.00463-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Alteromonas is a ubiquitous, abundant, copiotrophic and phytoplankton-associated marine member of the Gammaproteobacteria with a range extending from tropical waters to polar regions and including hadal zones. Here, we describe a novel Alteromonas phage, ZP6, that was isolated from surface coastal waters of Qingdao, China. ZP6 contains a linear, double-stranded, 38,080-bp DNA molecule with 50.1% G+C content and 47 putative open reading frames (ORFs). Three auxiliary metabolic genes were identified, encoding metal-dependent phosphohydrolase, diaminopurine synthetase, and nucleotide pyrophosphohydrolase. The first two ORFs facilitate the replacement of adenine (A) by diaminopurine (Z) in phage genomes and help phages to evade attack from host restriction enzymes. The nucleotide pyrophosphohydrolase enables the host cells to stop programmed cell death and improves the survival rate of the host in a nutrient-depleted environment. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analysis revealed that ZP6 is most closely related to Enhodamvirus but with low similarity (shared genes, <30%, and average nucleotide sequence identity, <65%); it is distinct from other bacteriophages. Together, these results suggest that ZP6 could represent a novel viral genus, here named Mareflavirus. Combining its ability to infect Alteromonas, its harboring of a diaminopurine genome-biosynthetic system, and its representativeness of an understudied viral group, ZP6 could be an important and novel model system for marine virus research. IMPORTANCEAlteromonas is an important symbiotic bacterium of phytoplankton, but research on its bacteriophages is still at an elementary level. Our isolation and genome characterization of a novel Alteromonas podovirus, ZP6, identified a new viral genus of podovirus, namely, Mareflavirus. The ZP6 genome, with a diaminopurine genome-biosynthetic system, is different from those of other isolated Alteromonas phages and will bring new impetus to the development of virus classification and provide important insights into novel viral sequences from metagenomic data sets.
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Tang Z, Fan W, Li Q, Wang D, Wen M, Wang J, Li X, Zhou Y. MVIP: multi-omics portal of viral infection. Nucleic Acids Res 2021; 50:D817-D827. [PMID: 34718748 PMCID: PMC8689837 DOI: 10.1093/nar/gkab958] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/30/2021] [Accepted: 10/05/2021] [Indexed: 12/13/2022] Open
Abstract
Virus infections are huge threats to living organisms and cause many diseases, such as COVID-19 caused by SARS-CoV-2, which has led to millions of deaths. To develop effective strategies to control viral infection, we need to understand its molecular events in host cells. Virus related functional genomic datasets are growing rapidly, however, an integrative platform for systematically investigating host responses to viruses is missing. Here, we developed a user-friendly multi-omics portal of viral infection named as MVIP (https://mvip.whu.edu.cn/). We manually collected available high-throughput sequencing data under viral infection, and unified their detailed metadata including virus, host species, infection time, assay, and target, etc. We processed multi-layered omics data of more than 4900 viral infected samples from 77 viruses and 33 host species with standard pipelines, including RNA-seq, ChIP-seq, and CLIP-seq, etc. In addition, we integrated these genome-wide signals into customized genome browsers, and developed multiple dynamic charts to exhibit the information, such as time-course dynamic and differential gene expression profiles, alternative splicing changes and enriched GO/KEGG terms. Furthermore, we implemented several tools for efficiently mining the virus-host interactions by virus, host and genes. MVIP would help users to retrieve large-scale functional information and promote the understanding of virus-host interactions.
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Affiliation(s)
- Zhidong Tang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Weiliang Fan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Qiming Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Dehe Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Miaomiao Wen
- Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Junhao Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xingqiao Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yu Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China.,Institute for Advanced Studies, Wuhan University, Wuhan 430072, China.,RNA Institute, Wuhan University, Wuhan 430072, China.,Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430072, China
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Viral Characteristics of the Warm Atlantic and Cold Arctic Water Masses in the Nordic Seas. Appl Environ Microbiol 2021; 87:e0116021. [PMID: 34469192 DOI: 10.1128/aem.01160-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nordic Seas are the subarctic seas connecting the Arctic Ocean and North Atlantic Ocean with complex water masses, experiencing an abrupt climate change. Though knowledge of the marine virosphere has expanded rapidly, the diversity of viruses and their relationships with host cells and water masses in the Nordic Seas remain to be fully revealed. Here, we establish the Nordic Sea DNA virome (NSV) data set of 55,315 viral contigs including 1,478 unique viral populations from seven stations influenced by both the warm Atlantic and cold Arctic water masses. Caudovirales dominated in the seven NSVs, especially in the warm Atlantic waters. The major giant nucleocytoplasmic large DNA viruses (NCLDVs) contributed a significant proportion of the classified viral contigs in the NSVs (32.2%), especially in the cold Arctic waters (44.9%). The distribution patterns of Caudovirales and NCLDVs were a reflection of the community structure of their hosts in the corresponding water masses and currents. Latitude, pH, and flow speed were found to be key factors influencing the microbial communities and coinfluencing the variation of viral communities. Network analysis illustrated the tight coupling between the variation of viral communities and microbial communities in the Nordic Seas. This study suggests a probable linkage between viromes, host cells, and surface water masses from both the cool Arctic and warm Atlantic Oceans. IMPORTANCE This is a systematic study of Nordic Sea viromes using metagenomic analysis. The viral diversity, community structure, and their relationships with host cells and the complex water masses from both the cool Arctic and the warm Atlantic oceans were illustrated. The NCLDVs and Caudovirales are proposed as the viral characteristics of the cold Arctic and warm Atlantic waters, respectively. This study provides an important background for the viromes in the subarctic seas connecting the Arctic Ocean and North Atlantic Ocean and sheds light on their responses to abrupt climate change in the future.
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Van Espen L, Bak EG, Beller L, Close L, Deboutte W, Juel HB, Nielsen T, Sinar D, De Coninck L, Frithioff-Bøjsøe C, Fonvig CE, Jacobsen S, Kjærgaard M, Thiele M, Fullam A, Kuhn M, Holm JC, Bork P, Krag A, Hansen T, Arumugam M, Matthijnssens J. A Previously Undescribed Highly Prevalent Phage Identified in a Danish Enteric Virome Catalog. mSystems 2021; 6:e0038221. [PMID: 34665009 PMCID: PMC8525569 DOI: 10.1128/msystems.00382-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 09/02/2021] [Indexed: 01/06/2023] Open
Abstract
Gut viruses are important, yet often neglected, players in the complex human gut microbial ecosystem. Recently, the number of human gut virome studies has been increasing; however, we are still only scratching the surface of the immense viral diversity. In this study, 254 virus-enriched fecal metagenomes from 204 Danish subjects were used to generate the Danish Enteric Virome Catalog (DEVoC) containing 12,986 nonredundant viral scaffolds, of which the majority was previously undescribed, encoding 190,029 viral genes. The DEVoC was used to compare 91 healthy DEVoC gut viromes from children, adolescents, and adults that were used to create the DEVoC. Gut viromes of healthy Danish subjects were dominated by phages. While most phage genomes (PGs) only occurred in a single subject, indicating large virome individuality, 39 PGs were present in more than 10 healthy subjects. Among these 39 PGs, the prevalences of three PGs were associated with age. To further study the prevalence of these 39 prevalent PGs, 1,880 gut virome data sets of 27 studies from across the world were screened, revealing several age-, geography-, and disease-related prevalence patterns. Two PGs also showed a remarkably high prevalence worldwide-a crAss-like phage (20.6% prevalence), belonging to the tentative AlphacrAssvirinae subfamily, and a previously undescribed circular temperate phage infecting Bacteroides dorei (14.4% prevalence), called LoVEphage because it encodes lots of viral elements. Due to the LoVEphage's high prevalence and novelty, public data sets in which the LoVEphage was detected were de novo assembled, resulting in an additional 18 circular LoVEphage-like genomes (67.9 to 72.4 kb). IMPORTANCE Through generation of the DEVoC, we added numerous previously uncharacterized viral genomes and genes to the ever-increasing worldwide pool of human gut viromes. The DEVoC, the largest human gut virome catalog generated from consistently processed fecal samples, facilitated the analysis of the 91 healthy Danish gut viromes. Characterizing the biggest cohort of healthy gut viromes from children, adolescents, and adults to date confirmed the previously established high interindividual variation in human gut viromes and demonstrated that the effect of age on the gut virome composition was limited to the prevalence of specific phage (groups). The identification of a previously undescribed prevalent phage illustrates the usefulness of developing virome catalogs, and we foresee that the DEVoC will benefit future analysis of the roles of gut viruses in human health and disease.
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Affiliation(s)
- Lore Van Espen
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Emilie Glad Bak
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leen Beller
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Lila Close
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Ward Deboutte
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Helene Bæk Juel
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Trine Nielsen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Deniz Sinar
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Lander De Coninck
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Christine Frithioff-Bøjsøe
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Children’s Obesity Clinic, accredited European Centre for Obesity Management, Department of Paediatrics, Copenhagen University Hospital Holbaek, Holbaek, Denmark
| | - Cilius Esmann Fonvig
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Children’s Obesity Clinic, accredited European Centre for Obesity Management, Department of Paediatrics, Copenhagen University Hospital Holbaek, Holbaek, Denmark
| | - Suganya Jacobsen
- Department of Gastroenterology and Hepatology, Centre for Liver Research, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Maria Kjærgaard
- Department of Gastroenterology and Hepatology, Centre for Liver Research, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Maja Thiele
- Department of Gastroenterology and Hepatology, Centre for Liver Research, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Anthony Fullam
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Michael Kuhn
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jens-Christian Holm
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Children’s Obesity Clinic, accredited European Centre for Obesity Management, Department of Paediatrics, Copenhagen University Hospital Holbaek, Holbaek, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany
- Yonsei Frontier Lab (YFL), Yonsei University, Seoul, South Korea
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Aleksander Krag
- Department of Gastroenterology and Hepatology, Centre for Liver Research, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manimozhiyan Arumugam
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jelle Matthijnssens
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
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Sugimoto R, Nishimura L, Nguyen PT, Ito J, Parrish NF, Mori H, Kurokawa K, Nakaoka H, Inoue I. Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: Viruses, plasmids, and more. PLoS Comput Biol 2021; 17:e1009428. [PMID: 34673779 PMCID: PMC8530359 DOI: 10.1371/journal.pcbi.1009428] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 09/07/2021] [Indexed: 12/12/2022] Open
Abstract
Viruses are the most numerous biological entity, existing in all environments and infecting all cellular organisms. Compared with cellular life, the evolution and origin of viruses are poorly understood; viruses are enormously diverse, and most lack sequence similarity to cellular genes. To uncover viral sequences without relying on either reference viral sequences from databases or marker genes that characterize specific viral taxa, we developed an analysis pipeline for virus inference based on clustered regularly interspaced short palindromic repeats (CRISPR). CRISPR is a prokaryotic nucleic acid restriction system that stores the memory of previous exposure. Our protocol can infer CRISPR-targeted sequences, including viruses, plasmids, and previously uncharacterized elements, and predict their hosts using unassembled short-read metagenomic sequencing data. By analyzing human gut metagenomic data, we extracted 11,391 terminally redundant CRISPR-targeted sequences, which are likely complete circular genomes. The sequences included 2,154 tailed-phage genomes, together with 257 complete crAssphage genomes, 11 genomes larger than 200 kilobases, 766 genomes of Microviridae species, 56 genomes of Inoviridae species, and 95 previously uncharacterized circular small genomes that have no reliably predicted protein-coding gene. We predicted the host(s) of approximately 70% of the discovered genomes at the taxonomic level of phylum by linking protospacers to taxonomically assigned CRISPR direct repeats. These results demonstrate that our protocol is efficient for de novo inference of CRISPR-targeted sequences and their host prediction. The evolution and origins of viruses are long-standing questions in the field of biology. Viral genomes provide fundamental information to infer the evolution and origin of viruses. However, viruses are extraordinarily diverse, and there are no single genes shared across entire species. Several methods were developed to collect viral genomes from metagenome. To infer viral genomes from metagenome, previous approaches relied on reference viral genomes. We thought that such reference-based methods may not be sufficient to uncover diverse viral genomes; therefore, we developed a pipeline that utilizes CRISPR, a prokaryotic adaptive immunological memory. Using this pipeline, we discovered more than 10,000 positively complete CRISPR-targeted genomes from human gut metagenome datasets. A substantial portion of the discovered genomes encoded various types of capsid proteins, supporting the contention that these sequences are viral. Although the majority of these capsid-protein-coding sequences were previously characterized, we notably discovered Inoviridae genomes that were previously difficult to infer as being viral. Furthermore, some of the remaining unclassified sequences without a detectable capsid-protein-encoding gene had a notably low protein-coding ratio. Overall, our pipeline successfully discovered viruses and previously uncharacterized presumably mobile genetic elements targeted by CRISPR.
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Affiliation(s)
- Ryota Sugimoto
- Human Genetics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
| | - Luca Nishimura
- Human Genetics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
- The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Phuong Thanh Nguyen
- Human Genetics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
- The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Nicholas F. Parrish
- Genome Immunobiology RIKEN Hakubi Research Team, Center for Integrative Medical Sciences, RIKEN, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Hiroshi Mori
- Genome Diversity Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
| | - Ken Kurokawa
- Genome Evolution Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
| | - Hirofumi Nakaoka
- Department of Cancer Genome Research, Sasaki Institute, Chiyoda-ku, Tokyo, Japan
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
- * E-mail:
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Song L, Zhang L, Fang X. Characterizing Enterotypes in Human Metagenomics: A Viral Perspective. Front Microbiol 2021; 12:740990. [PMID: 34659174 PMCID: PMC8511818 DOI: 10.3389/fmicb.2021.740990] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/09/2021] [Indexed: 11/13/2022] Open
Abstract
The diversity and high genomic mutation rates of viral species hinder our understanding of viruses and their contributions to human health. Viral enterotypes as a description of the gut virome, its characteristics have not been thoroughly studied. Here we investigated the human gut virome composition using previously published sequencing data of 2,690 metagenomes from seven countries with various phenotypes. We found that the virome was dominated by double-stranded DNA viruses in our data, and young children and adults showed different stages in their fecal enterovirus composition. Beta diversity showed there were significantly less homogeneous in individuals with severe disorders of bile acid secretion, such as cirrhosis. In contrast, there were no significant differences in distances to centroids or viral components between patients with phenotypes unrelated to bile acid, such as hypertension. Enterotypes determined independently from various projects showed similar specific viruses and enrichment direction. Confounding factors, such as different sequencing platforms and library construction, did not confuse enterotyping. The gut virome composition pattern could be described by two viral enterotypes, which supported a discrete, rather than a gradient, distribution. Three main components, enterotype 1 and 2 specific viruses and the other, comprise the total viral variation in these sets. Compared with enterotype 2, enterotype 1 had a higher viral count, Shannon index, and similarity between samples. The relative abundance of enterotype-specific viruses is a crucial determinant of enterotype assignment. Samples not matching any of the defined enterotypes in the database did not necessarily correlate to sickness. Therefore, the background context must be carefully considered when using a viral enterotype as a feature for disease prediction. Our results highlight important insights into the human gut virome composition by exploring two-main viral enterotypes in population and providing an alternate covariate for early disease screening.
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Affiliation(s)
- Li Song
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lu Zhang
- Department of Computer Science, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Xiaodong Fang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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Bhattarai B, Bhattacharjee AS, Coutinho FH, Goel RK. Viruses and Their Interactions With Bacteria and Archaea of Hypersaline Great Salt Lake. Front Microbiol 2021; 12:701414. [PMID: 34650523 PMCID: PMC8506154 DOI: 10.3389/fmicb.2021.701414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/06/2021] [Indexed: 01/15/2023] Open
Abstract
Viruses play vital biogeochemical and ecological roles by (a) expressing auxiliary metabolic genes during infection, (b) enhancing the lateral transfer of host genes, and (c) inducing host mortality. Even in harsh and extreme environments, viruses are major players in carbon and nutrient recycling from organic matter. However, there is much that we do not yet understand about viruses and the processes mediated by them in the extreme environments such as hypersaline habitats. The Great Salt Lake (GSL) in Utah, United States is a hypersaline ecosystem where the biogeochemical role of viruses is poorly understood. This study elucidates the diversity of viruses and describes virus–host interactions in GSL sediments along a salinity gradient. The GSL sediment virosphere consisted of Haloviruses (32.07 ± 19.33%) and members of families Siphoviridae (39.12 ± 19.8%), Myoviridae (13.7 ± 6.6%), and Podoviridae (5.43 ± 0.64%). Our results demonstrate that salinity alongside the concentration of organic carbon and inorganic nutrients (nitrogen and phosphorus) governs the viral, bacteria, and archaeal diversity in this habitat. Computational host predictions for the GSL viruses revealed a wide host range with a dominance of viruses that infect Proteobacteria, Actinobacteria, and Firmicutes. Identification of auxiliary metabolic genes for photosynthesis (psbA), carbon fixation (rbcL, cbbL), formaldehyde assimilation (SHMT), and nitric oxide reduction (NorQ) shed light on the roles played by GSL viruses in biogeochemical cycles of global relevance.
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Affiliation(s)
- Bishav Bhattarai
- Department of Civil and Environmental Engineering, The University of Utah, Salt Lake City, UT, United States
| | - Ananda S Bhattacharjee
- Carl R. Woese Institute for Genomic Biology, The University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Felipe H Coutinho
- Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Ramesh K Goel
- Department of Civil and Environmental Engineering, The University of Utah, Salt Lake City, UT, United States
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Forsberg KJ, Schmidtke DT, Werther R, Uribe RV, Hausman D, Sommer MOA, Stoddard BL, Kaiser BK, Malik HS. The novel anti-CRISPR AcrIIA22 relieves DNA torsion in target plasmids and impairs SpyCas9 activity. PLoS Biol 2021; 19:e3001428. [PMID: 34644300 PMCID: PMC8545432 DOI: 10.1371/journal.pbio.3001428] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 10/25/2021] [Accepted: 09/28/2021] [Indexed: 11/18/2022] Open
Abstract
To overcome CRISPR-Cas defense systems, many phages and mobile genetic elements (MGEs) encode CRISPR-Cas inhibitors called anti-CRISPRs (Acrs). Nearly all characterized Acrs directly bind Cas proteins to inactivate CRISPR immunity. Here, using functional metagenomic selection, we describe AcrIIA22, an unconventional Acr found in hypervariable genomic regions of clostridial bacteria and their prophages from human gut microbiomes. AcrIIA22 does not bind strongly to SpyCas9 but nonetheless potently inhibits its activity against plasmids. To gain insight into its mechanism, we obtained an X-ray crystal structure of AcrIIA22, which revealed homology to PC4-like nucleic acid-binding proteins. Based on mutational analyses and functional assays, we deduced that acrIIA22 encodes a DNA nickase that relieves torsional stress in supercoiled plasmids. This may render them less susceptible to SpyCas9, which uses free energy from negative supercoils to form stable R-loops. Modifying DNA topology may provide an additional route to CRISPR-Cas resistance in phages and MGEs.
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Affiliation(s)
- Kevin J. Forsberg
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
| | - Danica T. Schmidtke
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Rachel Werther
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Ruben V. Uribe
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Deanna Hausman
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Morten O. A. Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Barry L. Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Brett K. Kaiser
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Biology, Seattle University, Seattle, Washington, United States of America
| | - Harmit S. Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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Kiguchi Y, Nishijima S, Kumar N, Hattori M, Suda W. Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA pre-processing chimeric reads. DNA Res 2021; 28:6377780. [PMID: 34586399 DOI: 10.1093/dnares/dsab019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Indexed: 01/21/2023] Open
Abstract
The human gut bacteriophage community (phageome) plays an important role in the host's health and disease; however, the entire structure is poorly understood, partly owing to the generation of many incomplete genomes in conventional short-read metagenomics. Here, we show long-read metagenomics of amplified DNA of low-biomass phageomes with multiple displacement amplification (MDA), involving the development of a novel bioinformatics tool, split amplified chimeric read algorithm (SACRA), that efficiently pre-processed numerous chimeric reads generated through MDA. Using five samples, SACRA markedly reduced the average chimera ratio from 72% to 1.5% in PacBio reads with an average length of 1.8 kb. De novo assembly of chimera-less PacBio long reads reconstructed contigs of ≥5 kb with an average proportion of 27%, which was 1% in contigs from MiSeq short reads, thereby dramatically improving contig length and genome completeness. Comparison of PacBio and MiSeq contigs found MiSeq contig fragmentations frequently near local repeats and hypervariable regions in the phage genomes, and those caused by multiple homologous phage genomes coexisting in the community. We also developed a reference-independent method to assess the completeness of the linear phage genomes. Overall, we established a SACRA-coupled long-read metagenomics robust to highly diverse gut phageomes, identifying high-quality circular and linear phage genomes with adequate sequence quantity.
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Affiliation(s)
- Yuya Kiguchi
- Cooperative Major in Advanced Health Science, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo 169-8555, Japan
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Suguru Nishijima
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo 169-8555, Japan
- Integrated Institute for Regulatory Science, Waseda University, Tokyo 169-8555, Japan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Naveen Kumar
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Masahira Hattori
- Cooperative Major in Advanced Health Science, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Wataru Suda
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
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Zielezinski A, Barylski J, Karlowski WM. Taxonomy-aware, sequence similarity ranking reliably predicts phage-host relationships. BMC Biol 2021; 19:223. [PMID: 34625070 PMCID: PMC8501573 DOI: 10.1186/s12915-021-01146-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/06/2021] [Indexed: 12/02/2022] Open
Abstract
Background Characterizing phage–host interactions is critical to understanding the ecological role of both partners and effective isolation of phage therapeuticals. Unfortunately, experimental methods for studying these interactions are markedly slow, low-throughput, and unsuitable for phages or hosts difficult to maintain in laboratory conditions. Therefore, a number of in silico methods emerged to predict prokaryotic hosts based on viral sequences. One of the leading approaches is the application of the BLAST tool that searches for local similarities between viral and microbial genomes. However, this prediction method has three major limitations: (i) top-scoring sequences do not always point to the actual host; (ii) mosaic virus genomes may match to many, typically related, bacteria; and (iii) viral and host sequences may diverge beyond the point where their relationship can be detected by a BLAST alignment. Results We created an extension to BLAST, named Phirbo, that improves host prediction quality beyond what is obtainable from standard BLAST searches. The tool harnesses information concerning sequence similarity and bacteria relatedness to predict phage–host interactions. Phirbo was evaluated on three benchmark sets of known virus–host pairs, and it improved precision and recall by 11–40 percentage points over currently available, state-of-the-art, alignment-based, alignment-free, and machine-learning host prediction tools. Moreover, the discriminatory power of Phirbo for the recognition of virus–host relationships surpassed the results of other tools by at least 10 percentage points (area under the curve = 0.95), yielding a mean host prediction accuracy of 57% and 68% at the genus and family levels, respectively, and drops by 12 percentage points when using only a fraction of viral genome sequences (3 kb). Finally, we provide insights into a repertoire of protein and ncRNA genes that are shared between phages and hosts and may be prone to horizontal transfer during infection. Conclusions Our results suggest that Phirbo is a simple and effective tool for predicting phage–host relationships. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01146-6.
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Affiliation(s)
- Andrzej Zielezinski
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University Poznan, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
| | - Jakub Barylski
- Molecular Virology Research Unit, Faculty of Biology, Adam Mickiewicz University Poznan, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Wojciech M Karlowski
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University Poznan, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
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Diversity and distribution of viruses inhabiting the deepest ocean on Earth. THE ISME JOURNAL 2021; 15:3094-3110. [PMID: 33972725 PMCID: PMC8443753 DOI: 10.1038/s41396-021-00994-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 04/08/2021] [Accepted: 04/20/2021] [Indexed: 02/01/2023]
Abstract
As the most abundant biological entities on the planet, viruses significantly influence the overall functioning of marine ecosystems. The abundance, distribution, and biodiversity of viral communities in the upper ocean have been relatively well studied, but our understanding of viruses in the hadal biosphere remains poor. Here, we established the oceanic trench viral genome dataset (OTVGD) by analysing 19 microbial metagenomes derived from seawater and sediment samples of the Mariana, Yap, and Kermadec Trenches. The trench viral communities harbored remarkably high novelty, and they were predicted to infect ecologically important microbial clades, including Thaumarchaeota and Oleibacter. Significant inter-trench and intra-trench exchange of viral communities was proposed. Moreover, viral communities in different habitats (seawater/sediment and depth-stratified ocean zones) exhibited distinct niche-dependent distribution patterns and genomic properties. Notably, microbes and viruses in the hadopelagic seawater seemed to preferably adopt lysogenic lifestyles compared to those in the upper ocean. Furthermore, niche-specific auxiliary metabolic genes were identified in the hadal viral genomes, and a novel viral D-amino acid oxidase was functionally and phylogenetically characterized, suggesting the contribution of these genes in the utilization of refractory organic matter. Together, these findings highlight the genomic novelty, dynamic movement, and environment-driven diversification of viral communities in oceanic trenches, and suggest that viruses may influence the hadal ecosystem by reprogramming the metabolism of their hosts and modulating the community of keystone microbes.
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49
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Mechanism for Cas4-assisted directional spacer acquisition in CRISPR-Cas. Nature 2021; 598:515-520. [PMID: 34588691 PMCID: PMC9164213 DOI: 10.1038/s41586-021-03951-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 08/25/2021] [Indexed: 02/08/2023]
Abstract
Prokaryotes adapt to challenges from mobile genetic elements by integrating spacers derived from foreign DNA in the CRISPR array1. Spacer insertion is carried out by the Cas1-Cas2 integrase complex2-4. A substantial fraction of CRISPR-Cas systems use a Fe-S cluster containing Cas4 nuclease to ensure that spacers are acquired from DNA flanked by a protospacer adjacent motif (PAM)5,6 and inserted into the CRISPR array unidirectionally, so that the transcribed CRISPR RNA can guide target searching in a PAM-dependent manner. Here we provide a high-resolution mechanistic explanation for the Cas4-assisted PAM selection, spacer biogenesis and directional integration by type I-G CRISPR in Geobacter sulfurreducens, in which Cas4 is naturally fused with Cas1, forming Cas4/Cas1. During biogenesis, only DNA duplexes possessing a PAM-embedded 3'-overhang trigger Cas4/Cas1-Cas2 assembly. During this process, the PAM overhang is specifically recognized and sequestered, but is not cleaved by Cas4. This 'molecular constipation' prevents the PAM-side prespacer from participating in integration. Lacking such sequestration, the non-PAM overhang is trimmed by host nucleases and integrated to the leader-side CRISPR repeat. Half-integration subsequently triggers PAM cleavage and Cas4 dissociation, allowing spacer-side integration. Overall, the intricate molecular interaction between Cas4 and Cas1-Cas2 selects PAM-containing prespacers for integration and couples the timing of PAM processing with the stepwise integration to establish directionality.
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50
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Vink JNA, Baijens JHL, Brouns SJJ. PAM-repeat associations and spacer selection preferences in single and co-occurring CRISPR-Cas systems. Genome Biol 2021; 22:281. [PMID: 34593010 PMCID: PMC8482600 DOI: 10.1186/s13059-021-02495-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/09/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The adaptive CRISPR-Cas immune system stores sequences from past invaders as spacers in CRISPR arrays and thereby provides direct evidence that links invaders to hosts. Mapping CRISPR spacers has revealed many aspects of CRISPR-Cas biology, including target requirements such as the protospacer adjacent motif (PAM). However, studies have so far been limited by a low number of mapped spacers in the database. RESULTS By using vast metagenomic sequence databases, we map approximately one-third of more than 200,000 unique CRISPR spacers from a variety of microbes and derive a catalog of more than two hundred unique PAM sequences associated with specific CRISPR-Cas subtypes. These PAMs are further used to correctly assign the orientation of CRISPR arrays, revealing conserved patterns between the last nucleotides of the CRISPR repeat and PAM. We could also deduce CRISPR-Cas subtype-specific preferences for targeting either template or coding strand of open reading frames. While some DNA-targeting systems (type I-E and type II systems) prefer the template strand and avoid mRNA, other DNA- and RNA-targeting systems (types I-A and I-B and type III systems) prefer the coding strand and mRNA. In addition, we find large-scale evidence that both CRISPR-Cas adaptation machinery and CRISPR arrays are shared between different CRISPR-Cas systems. This could lead to simultaneous DNA and RNA targeting of invaders, which may be effective at combating mobile genetic invaders. CONCLUSIONS This study has broad implications for our understanding of how CRISPR-Cas systems work in a wide range of organisms for which only the genome sequence is known.
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Affiliation(s)
- Jochem N A Vink
- Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands
- Kavli Institute of Nanoscience, Delft, The Netherlands
| | - Jan H L Baijens
- Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands
- Kavli Institute of Nanoscience, Delft, The Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands.
- Kavli Institute of Nanoscience, Delft, The Netherlands.
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