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Remesh AT, Viswanathan R. CrAss-Like Phages: From Discovery in Human Fecal Metagenome to Application as a Microbial Source Tracking Marker. FOOD AND ENVIRONMENTAL VIROLOGY 2024:10.1007/s12560-024-09584-5. [PMID: 38413544 DOI: 10.1007/s12560-024-09584-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 01/24/2024] [Indexed: 02/29/2024]
Abstract
CrAss-like phages are a diverse group of bacteriophages genetically similar to the prototypical crAssphage (p-crAssphage), which was discovered in the human gut microbiome through a metagenomics approach. It was identified as a ubiquitous and highly abundant bacteriophage group in the gut microbiome. Initial co-occurrence analysis postulated Bacteroides spp. as the prospective bacterial host. Subsequent studies have confirmed multiple host species under Phylum Bacteroidetes and some Firmicutes. Detection of crAss-like phages in sewage-contaminated environmental water and robust correlation with enteric viruses and bacteria has culminated in their adoption as a microbial source tracking (MST) marker. Polymerase chain reaction (PCR) and real-time PCR assays have been developed utilizing the conserved genes in the p-crAssphage genome to detect human fecal contamination of different water sources, with high specificity. Numerous investigations have examined the implications of crAss-like phages in diverse disease conditions, including ulcerative colitis, obesity and metabolic syndrome, autism spectrum disorders, rheumatoid arthritis, atopic eczema, and other autoimmune disorders. These studies have unveiled associations between certain diseases and diminished abundance and diversity of crAss-like phages. This review offers insights into the diverse aspects of research on crAss-like phages, including their discovery, genomic characteristics, structure, taxonomy, isolation, molecular detection, application as an MST marker, and role as a gut microbiome modulator with consequential health implications.
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2
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Papudeshi B, Vega AA, Souza C, Giles SK, Mallawaarachchi V, Roach MJ, An M, Jacobson N, McNair K, Fernanda Mora M, Pastrana K, Boling L, Leigh C, Harker C, Plewa WS, Grigson SR, Bouras G, Decewicz P, Luque A, Droit L, Handley SA, Wang D, Segall AM, Dinsdale EA, Edwards RA. Host interactions of novel Crassvirales species belonging to multiple families infecting bacterial host, Bacteroides cellulosilyticus WH2. Microb Genom 2023; 9:001100. [PMID: 37665209 PMCID: PMC10569736 DOI: 10.1099/mgen.0.001100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/10/2023] [Indexed: 09/05/2023] Open
Abstract
Bacteroides, the prominent bacteria in the human gut, play a crucial role in degrading complex polysaccharides. Their abundance is influenced by phages belonging to the Crassvirales order. Despite identifying over 600 Crassvirales genomes computationally, only few have been successfully isolated. Continued efforts in isolation of more Crassvirales genomes can provide insights into phage-host-evolution and infection mechanisms. We focused on wastewater samples, as potential sources of phages infecting various Bacteroides hosts. Sequencing, assembly, and characterization of isolated phages revealed 14 complete genomes belonging to three novel Crassvirales species infecting Bacteroides cellulosilyticus WH2. These species, Kehishuvirus sp. 'tikkala' strain Bc01, Kolpuevirus sp. 'frurule' strain Bc03, and 'Rudgehvirus jaberico' strain Bc11, spanned two families, and three genera, displaying a broad range of virion productions. Upon testing all successfully cultured Crassvirales species and their respective bacterial hosts, we discovered that they do not exhibit co-evolutionary patterns with their bacterial hosts. Furthermore, we observed variations in gene similarity, with greater shared similarity observed within genera. However, despite belonging to different genera, the three novel species shared a unique structural gene that encodes the tail spike protein. When investigating the relationship between this gene and host interaction, we discovered evidence of purifying selection, indicating its functional importance. Moreover, our analysis demonstrated that this tail spike protein binds to the TonB-dependent receptors present on the bacterial host surface. Combining these observations, our findings provide insights into phage-host interactions and present three Crassvirales species as an ideal system for controlled infectivity experiments on one of the most dominant members of the human enteric virome.
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Affiliation(s)
- Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
| | - Alejandro A. Vega
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Cole Souza
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Sarah K. Giles
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
| | - Vijini Mallawaarachchi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
| | - Michael J. Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
| | - Michelle An
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Nicole Jacobson
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Katelyn McNair
- Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 992182, USA
| | - Maria Fernanda Mora
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Karina Pastrana
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Lance Boling
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Christopher Leigh
- Adelaide Microscopy, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Clarice Harker
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
| | - Will S. Plewa
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
| | - Susanna R. Grigson
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
| | - George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Przemysław Decewicz
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warsaw, 02-096, Poland
| | - Antoni Luque
- Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 992182, USA
- Department of Mathematics and Statistics, San Diego State University, 5500 Campanile Drive, San Diego, CA, 992182, USA
- Present address: Department of Biology, University of Miami, Coral Gables, Florida, USA
| | - Lindsay Droit
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Scott A. Handley
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - David Wang
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Anca M. Segall
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Elizabeth A. Dinsdale
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
| | - Robert A. Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
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Alotaibi R, Eifan S, Hanif A, Nour I, Alkathiri A. Prevalence and Genetic Diversity of Cross-Assembly Phages in Wastewater Treatment Plants in Riyadh, Saudi Arabia. Microorganisms 2023; 11:2167. [PMID: 37764011 PMCID: PMC10535421 DOI: 10.3390/microorganisms11092167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/20/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
The most common DNA virus found in wastewaters globally is the cross-assembly phage (crAssphage). King Saud University wastewater treatment plant (KSU-WWTP); Manfoha wastewater treatment plant (MN-WWTP); and the Embassy wastewater treatment plant (EMB-WWTP) in Riyadh, Saudi Arabia were selected, and 36 untreated sewage water samples during the year 2022 were used in the current study. The meteorological impact on crAssphage prevalence was investigated. CrAssphage prevalence was recorded using PCR and Sanger sequencing. The molecular diversity of crAssphage sequences was studied for viral gene segments from the major capsid protein (MCP) and membrane protein containing the peptidoglycan-binding domain (MP-PBD). KSU-WWTP and EMB-WWTP showed a higher prevalence of crAssphage (83.3%) than MN-WWTP (75%). Phylogenetic analysis of MCP and MP-PBD segments depicted a close relationship to the Japanese isolates. The MCP gene from the current study's isolate WW/2M/SA/2022 depicted zero evolutionary divergence from 3057_98020, 2683_104905, and 4238_99953 isolates (d = 0.000) from Japan. A significant influence of temporal variations on the prevalence of crAssphage was detected in the three WWTPs. CrAssphage displayed the highest prevalence at high temperatures (33-44 °C), low relative humidity (6-14%), and moderate wind speed (16-21 Km/h). The findings provided pioneering insights into crAssphage prevalence and its genetic diversity in WWTPs in Riyadh, Saudi Arabia.
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Affiliation(s)
| | | | - Atif Hanif
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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Papudeshi B, Vega AA, Souza C, Giles SK, Mallawaarachchi V, Roach MJ, An M, Jacobson N, McNair K, Mora MF, Pastrana K, Boling L, Leigh C, Harker C, Plewa WS, Grigson SR, Bouras G, Decewicz P, Luque A, Droit L, Handley SA, Wang D, Segall AM, Dinsdale EA, Edwards RA. Host interactions of novel Crassvirales species belonging to multiple families infecting bacterial host, Bacteroides cellulosilyticus WH2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.05.531146. [PMID: 36945541 PMCID: PMC10028833 DOI: 10.1101/2023.03.05.531146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Bacteroides, the prominent bacteria in the human gut, play a crucial role in degrading complex polysaccharides. Their abundance is influenced by phages belonging to the Crassvirales order. Despite identifying over 600 Crassvirales genomes computationally, only few have been successfully isolated. Continued efforts in isolation of more Crassvirales genomes can provide insights into phage-host-evolution and infection mechanisms. We focused on wastewater samples, as potential sources of phages infecting various Bacteroides hosts. Sequencing, assembly, and characterization of isolated phages revealed 14 complete genomes belonging to three novel Crassvirales species infecting Bacteroides cellulosilyticus WH2. These species, Kehishuvirus sp. 'tikkala' strain Bc01, Kolpuevirus sp. 'frurule' strain Bc03, and 'Rudgehvirus jaberico' strain Bc11, spanned two families, and three genera, displaying a broad range of virion productions. Upon testing all successfully cultured Crassvirales species and their respective bacterial hosts, we discovered that they do not exhibit co-evolutionary patterns with their bacterial hosts. Furthermore, we observed variations in gene similarity, with greater shared similarity observed within genera. However, despite belonging to different genera, the three novel species shared a unique structural gene that encodes the tail spike protein. When investigating the relationship between this gene and host interaction, we discovered evidence of purifying selection, indicating its functional importance. Moreover, our analysis demonstrated that this tail spike protein binds to the TonB-dependent receptors present on the bacterial host surface. Combining these observations, our findings provide insights into phage-host interactions and present three Crassvirales species as an ideal system for controlled infectivity experiments on one of the most dominant members of the human enteric virome. Impact statement Bacteriophages play a crucial role in shaping microbial communities within the human gut. Among the most dominant bacteriophages in the human gut microbiome are Crassvirales phages, which infect Bacteroides. Despite being widely distributed, only a few Crassvirales genomes have been isolated, leading to a limited understanding of their biology, ecology, and evolution. This study isolated and characterized three novel Crassvirales genomes belonging to two different families, and three genera, but infecting one bacterial host, Bacteroides cellulosilyticus WH2. Notably, the observation confirmed the phages are not co-evolving with their bacterial hosts, rather have a shared ability to exploit similar features in their bacterial host. Additionally, the identification of a critical viral protein undergoing purifying selection and interacting with the bacterial receptors opens doors to targeted therapies against bacterial infections. Given Bacteroides role in polysaccharide degradation in the human gut, our findings advance our understanding of the phage-host interactions and could have important implications for the development of phage-based therapies. These discoveries may hold implications for improving gut health and metabolism to support overall well-being. Data summary The genomes used in this research are available on Sequence Read Archive (SRA) within the project, PRJNA737576. Bacteroides cellulosilyticus WH2, Kehishuvirus sp. 'tikkala' strain Bc01, Kolpuevirus sp. ' frurule' strain Bc03, and 'Rudgehvirus jaberico' strain Bc11 are all available on GenBank with accessions NZ_CP072251.1 ( B. cellulosilyticus WH2), QQ198717 (Bc01), QQ198718 (Bc03), and QQ198719 (Bc11), and we are working on making the strains available through ATCC. The 3D protein structures for the three Crassvirales genomes are available to download at doi.org/10.25451/flinders.21946034.
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Affiliation(s)
- Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Alejandro A. Vega
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Cole Souza
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Sarah K. Giles
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Vijini Mallawaarachchi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Michael J. Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Michelle An
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Nicole Jacobson
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Katelyn McNair
- Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 992182, USA
| | - Maria Fernanda Mora
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Karina Pastrana
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Lance Boling
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Christopher Leigh
- Adelaide Microscopy, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Clarice Harker
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Will S. Plewa
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Susanna R. Grigson
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Przemysław Decewicz
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warsaw, 02-096, Poland
| | - Antoni Luque
- Department of Mathematics and Statistics, San Diego State University, 5500 Campanile Drive, San Diego, CA, 992182, USA
- Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 992182, USA
| | - Lindsay Droit
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Scott A. Handley
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - David Wang
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Anca M. Segall
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Elizabeth A. Dinsdale
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Robert A. Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
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Smith L, Goldobina E, Govi B, Shkoporov AN. Bacteriophages of the Order Crassvirales: What Do We Currently Know about This Keystone Component of the Human Gut Virome? Biomolecules 2023; 13:biom13040584. [PMID: 37189332 DOI: 10.3390/biom13040584] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 05/17/2023] Open
Abstract
The order Crassvirales comprises dsDNA bacteriophages infecting bacteria in the phylum Bacteroidetes that are found in a variety of environments but are especially prevalent in the mammalian gut. This review summarises available information on the genomics, diversity, taxonomy, and ecology of this largely uncultured viral taxon. With experimental data available from a handful of cultured representatives, the review highlights key properties of virion morphology, infection, gene expression and replication processes, and phage-host dynamics.
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Affiliation(s)
- Linda Smith
- APC Microbiome Ireland, Department of Medicine & School of Microbiology, University College Cork, T12 YT20 Cork, Ireland
| | - Ekaterina Goldobina
- APC Microbiome Ireland, Department of Medicine & School of Microbiology, University College Cork, T12 YT20 Cork, Ireland
| | - Bianca Govi
- APC Microbiome Ireland, Department of Medicine & School of Microbiology, University College Cork, T12 YT20 Cork, Ireland
| | - Andrey N Shkoporov
- APC Microbiome Ireland, Department of Medicine & School of Microbiology, University College Cork, T12 YT20 Cork, Ireland
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Cervantes-Echeverría M, Gallardo-Becerra L, Cornejo-Granados F, Ochoa-Leyva A. The Two-Faced Role of crAssphage Subfamilies in Obesity and Metabolic Syndrome: Between Good and Evil. Genes (Basel) 2023; 14:139. [PMID: 36672880 PMCID: PMC9858991 DOI: 10.3390/genes14010139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/27/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
Viral metagenomic studies of the human gut microbiota have unraveled the differences in phage populations between health and disease, stimulating interest in phages' role on bacterial ecosystem regulation. CrAssphage is a common and abundant family in the gut virome across human populations. Therefore, we explored its role in obesity (O) and obesity with metabolic syndrome (OMS) in a children's cohort. We found a significantly decreased prevalence, diversity, and richness of the crAssphage Alpha subfamily in OMS mainly driven by a decrease in the Alpha_1 and Alpha_4 genera. On the contrary, there was a significant increase in the Beta subfamily in OMS, mainly driven by an increase in Beta_6. Additionally, an overabundance of the Delta_8 genus was observed in OMS. Notably, a decreased abundance of crAssphages was significantly correlated with the overabundance of Bacilli in the same group. The Bacilli class is a robust taxonomical biomarker of O and was also significantly abundant in our OMS cohort. Our results suggest that a loss of stability in the Alpha subfamily of crAssphages is associated with O and OMS. Contrary, an overabundance of the Delta subfamily was found in OMS. Our study advises the importance of considering the dual role (good and evil) of crAssphage subfamilies and their participation in conditions such as O, where we suggest that Alpha loss and Delta gain are associated with obese individuals.
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Affiliation(s)
| | | | | | - Adrian Ochoa-Leyva
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico
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Rossi A, Morlino MS, Gaspari M, Basile A, Kougias P, Treu L, Campanaro S. Analysis of the anaerobic digestion metagenome under environmental stresses stimulating prophage induction. MICROBIOME 2022; 10:125. [PMID: 35965344 PMCID: PMC9377139 DOI: 10.1186/s40168-022-01316-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/25/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The viral community has the potential to influence the structure of the microbiome and thus the yield of the anaerobic digestion process. However, the virome composition in anaerobic digestion is still under-investigated. A viral induction experiment was conducted on separate batches undergoing a series of DNA-damaging stresses, in order to coerce temperate viruses to enter the lytic cycle. RESULTS The sequencing of the metagenome revealed a viral community almost entirely composed of tailed bacteriophages of the order Caudovirales. Following a binning procedure 1,092 viral and 120 prokaryotic genomes were reconstructed, 64 of which included an integrated prophage in their sequence. Clustering of coverage profiles revealed the presence of species, both viral and microbial, sharing similar reactions to shocks. A group of viral genomes, which increase under organic overload and decrease under basic pH, uniquely encode the yopX gene, which is involved in the induction of temperate prophages. Moreover, the in-silico functional analysis revealed an enrichment of sialidases in viral genomes. These genes are associated with tail proteins and, as such, are hypothesised to be involved in the interaction with the host. Archaea registered the most pronounced changes in relation to shocks and featured behaviours not shared with other species. Subsequently, data from 123 different samples of the global anaerobic digestion database was used to determine coverage profiles of host and viral genomes on a broader scale. CONCLUSIONS Viruses are key components in anaerobic digestion environments, shaping the microbial guilds which drive the methanogenesis process. In turn, environmental conditions are pivotal in shaping the viral community and the rate of induction of temperate viruses. This study provides an initial insight into the complexity of the anaerobic digestion virome and its relation with the microbial community and the diverse environmental parameters. Video Abstract.
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Affiliation(s)
- Alessandro Rossi
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
| | - Maria Silvia Morlino
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
| | - Maria Gaspari
- Department of Hydraulics, Soil Science and Agricultural Engineering, Faculty of Agriculture, Aristotle University of Thessaloniki, GR-54124, Thessaloniki, Greece
| | - Arianna Basile
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
| | - Panagiotis Kougias
- Soil and Water Resources Institute, Hellenic Agricultural Organisation Demeter, Thermi, 57001, Thessaloniki, Greece
| | - Laura Treu
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy.
| | - Stefano Campanaro
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
- CRIBI biotechnology center, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
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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: 22] [Impact Index Per Article: 7.3] [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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