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4. Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification

Author

Adriaenssens, Evelien M, Roux, Simon, Brister, J Rodney, Karsch-Mizrachi, Ilene, Kuhn, Jens H, Varsani, Arvind, Yigang, Tong, Reyes, Alejandro, Lood, Cédric, Lefkowitz, Elliot J, Sullivan, Matthew B, Edwards, Robert A, Simmonds, Peter, Rubino, Luisa, Sabanadzovic, Sead, Krupovic, Mart, and Dutilh, Bas E

Subjects
Microbiology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Genome, Viral, Phylogeny, Databases, Factual
Published
2023

5. iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria

Author

Roux, Simon, Camargo, Antonio Pedro, Coutinho, Felipe H, Dabdoub, Shareef M, Dutilh, Bas E, Nayfach, Stephen, and Tritt, Andrew

Subjects
Microbiology, Biological Sciences, Bioinformatics and Computational Biology, Networking and Information Technology R&D (NITRD), Bioengineering, Aetiology, 2.2 Factors relating to the physical environment, Infection, Archaea, Metagenome, Viruses, Bacteria, Metagenomics, Machine Learning, Genome, Viral, Agricultural and Veterinary Sciences, Medical and Health Sciences, Developmental Biology, Agricultural, veterinary and food sciences, Biological sciences, Biomedical and clinical sciences
Abstract

The extraordinary diversity of viruses infecting bacteria and archaea is now primarily studied through metagenomics. While metagenomes enable high-throughput exploration of the viral sequence space, metagenome-derived sequences lack key information compared to isolated viruses, in particular host association. Different computational approaches are available to predict the host(s) of uncultivated viruses based on their genome sequences, but thus far individual approaches are limited either in precision or in recall, i.e., for a number of viruses they yield erroneous predictions or no prediction at all. Here, we describe iPHoP, a two-step framework that integrates multiple methods to reliably predict host taxonomy at the genus rank for a broad range of viruses infecting bacteria and archaea, while retaining a low false discovery rate. Based on a large dataset of metagenome-derived virus genomes from the IMG/VR database, we illustrate how iPHoP can provide extensive host prediction and guide further characterization of uncultivated viruses.

Published
2023

6. Four principles to establish a universal virus taxonomy

Author

Simmonds, Peter, Adriaenssens, Evelien M, Zerbini, F Murilo, Abrescia, Nicola GA, Aiewsakun, Pakorn, Alfenas-Zerbini, Poliane, Bao, Yiming, Barylski, Jakub, Drosten, Christian, Duffy, Siobain, Duprex, W Paul, Dutilh, Bas E, Elena, Santiago F, García, Maria Laura, Junglen, Sandra, Katzourakis, Aris, Koonin, Eugene V, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Lefkowitz, Elliot J, Łobocka, Małgorzata, Lood, Cédric, Mahony, Jennifer, Meier-Kolthoff, Jan P, Mushegian, Arcady R, Oksanen, Hanna M, Poranen, Minna M, Reyes-Muñoz, Alejandro, Robertson, David L, Roux, Simon, Rubino, Luisa, Sabanadzovic, Sead, Siddell, Stuart, Skern, Tim, Smith, Donald B, Sullivan, Matthew B, Suzuki, Nobuhiro, Turner, Dann, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, and Vasilakis, Nikos

Subjects
Infectious Diseases, Infection, Humans, Bacteriophages, Metagenomics, Phylogeny, Viruses, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Developmental Biology
Abstract

A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., "arboviruses"), infecting a certain type of host (e.g., "mycoviruses," "bacteriophages") or displaying specific pathogenicity (e.g., "human immunodeficiency viruses"), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent.

Published
2023

9. Correction to: Changes to virus taxonomy and the ICTV Statutes ratifed by the International Committee on Taxonomy of Viruses (2023)

Author

Zerbini, Francisco Murilo, Siddell, Stuart G., Lefkowitz, Elliot J., Mushegian, Arcady R., Adriaenssens, Evelien M., Alfenas‑Zerbini, Poliane, Dempsey, Donald M., Dutilh, Bas E., García, María Laura, Hendrickson, R. Curtis, Junglen, Sandra, Krupovic, Mart, Kuhn, Jens H., Lambert, Amy J., Łobocka, Małgorzata, Oksanen, Hanna M., Robertson, David L., Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B., Suzuki, Nobuhiro, Van Doorslaer, Koenraad, Vandamme, Anne‑Mieke, and Varsani, Arvind

Published
2023
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11. Perspective on taxonomic classification of uncultivated viruses

Author

Dutilh, Bas E, Varsani, Arvind, Tong, Yigang, Simmonds, Peter, Sabanadzovic, Sead, Rubino, Luisa, Roux, Simon, Muñoz, Alejandro Reyes, Lood, Cédric, Lefkowitz, Elliot J, Kuhn, Jens H, Krupovic, Mart, Edwards, Robert A, Brister, J Rodney, Adriaenssens, Evelien M, and Sullivan, Matthew B

Subjects
Microbiology, Biological Sciences, Animals, Evolution, Molecular, Humans, Metagenomics, Phylogeny, Viruses, Medical Microbiology
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.

Published
2021

12. A Drug Recommendation System (Dr.S) for cancer cell lines

Author

Balvert, Marleen, Patoulidis, Georgios, Patti, Andrew, Deist, Timo M., Eyler, Christine, Dutilh, Bas E., Schönhuth, Alexander, and Craft, David

Subjects
Statistics - Machine Learning, Computer Science - Machine Learning, Quantitative Biology - Genomics, Quantitative Biology - Quantitative Methods
Abstract

Personalizing drug prescriptions in cancer care based on genomic information requires associating genomic markers with treatment effects. This is an unsolved challenge requiring genomic patient data in yet unavailable volumes as well as appropriate quantitative methods. We attempt to solve this challenge for an experimental proxy for which sufficient data is available: 42 drugs tested on 1018 cancer cell lines. Our goal is to develop a method to identify the drug that is most promising based on a cell line's genomic information. For this, we need to identify for each drug the machine learning method, choice of hyperparameters and genomic features for optimal predictive performance. We extensively compare combinations of gene sets (both curated and random), genetic features, and machine learning algorithms for all 42 drugs. For each drug, the best performing combination (considering only the curated gene sets) is selected. We use these top model parameters for each drug to build and demonstrate a Drug Recommendation System (Dr.S). Insights resulting from this analysis are formulated as best practices for developing drug recommendation systems. The complete software system, called the Cell Line Analyzer, is written in Python and available on github.

Published
2019

13. Recent changes to virus taxonomy ratified by the International Committee on Taxonomy of Viruses (2022)

Author

Walker, Peter J., Siddell, Stuart G., Lefkowitz, Elliot J., Mushegian, Arcady R., Adriaenssens, Evelien M., Alfenas-Zerbini, Poliane, Dempsey, Donald M., Dutilh, Bas E., García, María Laura, Curtis Hendrickson, R., Junglen, Sandra, Krupovic, Mart, Kuhn, Jens H., Lambert, Amy J., Łobocka, Małgorzata, Oksanen, Hanna M., Orton, Richard J., Robertson, David L., Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B., Suzuki, Nobuhiro, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, and Zerbini, Francisco Murilo

Published
2022
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14. Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2023)

Author

Zerbini, Francisco Murilo, Siddell, Stuart G., Lefkowitz, Elliot J., Mushegian, Arcady R., Adriaenssens, Evelien M., Alfenas‑Zerbini, Poliane, Dempsey, Donald M., Dutilh, Bas E., García, María Laura, Hendrickson, R. Curtis, Junglen, Sandra, Krupovic, Mart, Kuhn, Jens H., Lambert, Amy J., Łobocka, Małgorzata, Oksanen, Hanna M., Robertson, David L., Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B., Suzuki, Nobuhiro, Van Doorslaer, Koenraad, Vandamme, Anne‑Mieke, and Varsani, Arvind

Published
2023
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15. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

Author

Turner, Dann, Shkoporov, Andrey N., Lood, Cédric, Millard, Andrew D., Dutilh, Bas E., Alfenas-Zerbini, Poliane, van Zyl, Leonardo J., Aziz, Ramy K., Oksanen, Hanna M., Poranen, Minna M., Kropinski, Andrew M., Barylski, Jakub, Brister, J Rodney, Chanisvili, Nina, Edwards, Rob A., Enault, François, Gillis, Annika, Knezevic, Petar, Krupovic, Mart, Kurtböke, Ipek, Kushkina, Alla, Lavigne, Rob, Lehman, Susan, Lobocka, Malgorzata, Moraru, Cristina, Moreno Switt, Andrea, Morozova, Vera, Nakavuma, Jesca, Reyes Muñoz, Alejandro, Rūmnieks, Jānis, Sarkar, BL, Sullivan, Matthew B., Uchiyama, Jumpei, Wittmann, Johannes, Yigang, Tong, and Adriaenssens, Evelien M.

Published
2023
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18. Marine DNA Viral Macro- and Microdiversity from Pole to Pole

Author

Gregory, Ann C, Zayed, Ahmed A, Conceição-Neto, Nádia, Temperton, Ben, Bolduc, Ben, Alberti, Adriana, Ardyna, Mathieu, Arkhipova, Ksenia, Carmichael, Margaux, Cruaud, Corinne, Dimier, Céline, Domínguez-Huerta, Guillermo, Ferland, Joannie, Kandels, Stefanie, Liu, Yunxiao, Marec, Claudie, Pesant, Stéphane, Picheral, Marc, Pisarev, Sergey, Poulain, Julie, Tremblay, Jean-Éric, Vik, Dean, Coordinators, Tara Oceans, Acinas, Silvia G, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy, de Vargas, Colomban, Follows, Michael, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels-Lewis, Stefanie, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew B, Sunagawa, Shinichi, Wincker, Patrick, Culley, Alexander I, Dutilh, Bas E, and Roux, Simon

Subjects
Genetics, Infection, Life Below Water, Aquatic Organisms, Biodiversity, DNA Viruses, DNA, Viral, Metagenome, Water Microbiology, Tara Oceans Coordinators, community ecology, diversity gradients, marine biology, metagenomics, population ecology, species, viruses, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an ∼12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.

Published
2019

19. Minimum Information about an Uncultivated Virus Genome (MIUViG)

Author

Roux, Simon, Adriaenssens, Evelien M, Dutilh, Bas E, Koonin, Eugene V, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Brister, J Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K, Bordenstein, Seth R, Bork, Peer, Breitbart, Mya, Cochrane, Guy R, Daly, Rebecca A, Desnues, Christelle, Duhaime, Melissa B, Emerson, Joanne B, Enault, François, Fuhrman, Jed A, Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L, Ivanova, Natalia N, Labonté, Jessica M, Lee, Kyung-Bum, Malmstrom, Rex R, Martinez-Garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-Espino, David, Petit, Marie-Agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-Valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F, Sullivan, Matthew B, Sunagawa, Shinichi, Suttle, Curtis A, Temperton, Ben, Tringe, Susannah G, Thurber, Rebecca Vega, Webster, Nicole S, Whiteson, Katrine L, Wilhelm, Steven W, Wommack, K Eric, Woyke, Tanja, Wrighton, Kelly C, Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J, Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C, and Eloe-Fadrosh, Emiley A

Subjects
Microbiology, Biological Sciences, Genetics, Human Genome, Databases, Genetic, Genome, Viral, Genomics, Virus Cultivation, Viruses
Abstract

We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.

Published
2019

20. The human gut microbiome and health inequities

Author

Amato, Katherine R., Arrieta, Marie-Claire, Azad, Meghan B., Bailey, Michael T., Broussard, Josiane L., Bruggeling, Carlijn E., Claud, Erika C., Costello, Elizabeth K., Davenport, Emily R., Dutilh, Bas E., Ewald, Holly A. Swain, Ewald, Paul, Hanlon, Erin C., Julion, Wrenetha, Keshavarzian, Ali, Maurice, Corinne F., Miller, Gregory E., Preidis, Geoffrey A., Segurel, Laure, Singer, Burton, Subramanian, Sathish, Zhao, Liping, and Kuzawa, Christopher W.

Published
2021

22. Differentiating between viruses and virus species by writing their names correctly

Author

Zerbini, Francisco Murilo, Siddell, Stuart G., Mushegian, Arcady R., Walker, Peter J., Lefkowitz, Elliot J., Adriaenssens, Evelien M., Alfenas-Zerbini, Poliane, Dutilh, Bas E., García, María Laura, Junglen, Sandra, Krupovic, Mart, Kuhn, Jens H., Lambert, Amy J., Łobocka, Małgorzata, Oksanen, Hanna M., Robertson, David L., Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Suzuki, Nobuhiro, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, and Varsani, Arvind

Published
2022
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25. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021

Author

Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtböke, Ipek, Brister, J. Rodney, Lood, Cédric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Łobocka, Małgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, François, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, and Adriaenssens, Evelien M.

Published
2021
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26. Ecogenomics of the Marine Benthic Filamentous Cyanobacterium Adonisia

Author

Walter, Juline M., Coutinho, Felipe H., Leomil, Luciana, Hargreaves, Paulo I., Campeão, Mariana E., Vieira, Verônica V., Silva, Beatriz S., Fistarol, Giovana O., Salomon, Paulo S., Sawabe, Tomoo, Mino, Sayaka, Hosokawa, Masashi, Miyashita, Hideaki, Maruyama, Fumito, van Verk, Marcel C., Dutilh, Bas E., Thompson, Cristiane C., and Thompson, Fabiano L.

Published
2020

27. Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages

Author

Barylski, Jakub, Enault, François, Dutilh, Bas E., Schuller, Margo B.P., Edwards, Robert A., Gillis, Annika, Klumpp, Jochen, Knezevic, Petar, Krupovic, Mart, Kuhn, Jens H., Lavigne, Rob, Oksanen, Hanna M., Sullivan, Matthew B., Jang, Ho Bin, Simmonds, Peter, Aiewsakun, Pakorn, Wittmann, Johannes, Tolstoy, Igor, Brister, J. Rodney, Kropinski, Andrew M., and Adriaenssens, Evelien M.

Published
2020

28. Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021)

Author

Walker, Peter J., Siddell, Stuart G., Lefkowitz, Elliot J., Mushegian, Arcady R., Adriaenssens, Evelien M., Alfenas-Zerbini, Poliane, Davison, Andrew J., Dempsey, Donald M., Dutilh, Bas E., García, María Laura, Harrach, Balázs, Harrison, Robert L., Hendrickson, R. Curtis, Junglen, Sandra, Knowles, Nick J., Krupovic, Mart, Kuhn, Jens H., Lambert, Amy J., Łobocka, Małgorzata, Nibert, Max L., Oksanen, Hanna M., Orton, Richard J., Robertson, David L., Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B., Suzuki, Nobuhiro, Van Dooerslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, and Zerbini, Francisco Murilo

Published
2021
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30. Editorial: Virus Discovery by Metagenomics: The (Im)possibilities

Author

Dutilh, Bas E, Reyes, Alejandro, Hall, Richard J, and Whiteson, Katrine L

Subjects
Microbiology, Medical Microbiology, Biomedical and Clinical Sciences, Biological Sciences, metagenomics, virus discovery, virome, bacteriophages, phages, metagenome, bioinformatics, biological dark matter, Environmental Science and Management, Soil Sciences, Medical microbiology
Published
2017

33. Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes

Author

Theoretical Biology and Bioinformatics, Sub Bioinformatics, Hauptfeld, Ernestina, Pappas, Nikolaos, van Iwaarden, Sandra, Snoek, Basten L., Aldas-Vargas, Andrea, Dutilh, Bas E., von Meijenfeldt, F. A.Bastiaan, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Hauptfeld, Ernestina, Pappas, Nikolaos, van Iwaarden, Sandra, Snoek, Basten L., Aldas-Vargas, Andrea, Dutilh, Bas E., and von Meijenfeldt, F. A.Bastiaan

Published
2024

35. Phylogeny and disease associations of a widespread and ancient intestinal bacteriophage lineage.

Author

de Jonge, Patrick A., van den Born, Bert-Jan H., Zwinderman, Aeilko H., Nieuwdorp, Max, Dutilh, Bas E., and Herrema, Hilde

Subjects
INFLAMMATORY bowel diseases, PHYLOGENY, TYPE 2 diabetes, HUMAN microbiota, TYPE 1 diabetes, BACTERIOPHAGES
Abstract

Viruses are core components of the human microbiome, impacting health through interactions with gut bacteria and the immune system. Most human microbiome viruses are bacteriophages, which exclusively infect bacteria. Until recently, most gut virome studies focused on low taxonomic resolution (e.g., viral operational taxonomic units), hampering population-level analyses. We previously identified an expansive and widespread bacteriophage lineage in inhabitants of Amsterdam, the Netherlands. Here, we study their biodiversity and evolution in various human populations. Based on a phylogeny using sequences from six viral genome databases, we propose the Candidatus order Heliusvirales. We identify heliusviruses in 82% of 5441 individuals across 39 studies, and in nine metagenomes from humans that lived in Europe and North America between 1000 and 5000 years ago. We show that a large lineage started to diversify when Homo sapiens first appeared some 300,000 years ago. Ancient peoples and modern hunter-gatherers have distinct Ca. Heliusvirales populations with lower richness than modern urbanized people. Urbanized people suffering from type 1 and type 2 diabetes, as well as inflammatory bowel disease, have higher Ca. Heliusvirales richness than healthy controls. We thus conclude that these ancient core members of the human gut virome have thrived with increasingly westernized lifestyles. Here, based on phylogeny analyses using sequences from six viral genome databases, the authors study the biodiversity and evolution of a new bacteriophage lineage, Candidatus order Heliusvirales, and identify heliusviruses in 82% of 5,441 individuals across 39 studies, and in nine metagenomes from humans that lived in Europe and North America between 1,000 and 5,000 years ago, revealing associations with human diseases. [ABSTRACT FROM AUTHOR]

Published
2024
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36. Structural color in the bacterial domain: The ecogenomics of a 2-dimensional optical phenotype.

Author

Zomer, Aldert, Ingham, Colin J., von Meijenfeldt, F. A. Bastiaan, Doncel, Álvaro Escobar, van de Kerkhof, Gea T., Hamidjaja, Raditijo, Schouten, Sanne, Schertel, Lukas, Müller, Karin H., Catón, Laura, Hahnke, Richard L., Bolhuis, Henk, Vignolini, Silvia, and Dutilh, Bas E.

Subjects
STRUCTURAL colors, BACTERIAL genomes, NANOSTRUCTURED materials, MULTICELLULAR organisms, SEAWATER
Abstract

Structural color is an optical phenomenon resulting from light interacting with nanostructured materials. Although structural color (SC) is widespread in the tree of life, the underlying genetics and genomics are not well understood. Here, we collected and sequenced a set of 87 structurally colored bacterial isolates and 30 related strains lacking SC. Optical analysis of colonies indicated that diverse bacteria from at least two different phyla (Bacteroidetes and Proteobacteria) can create two-dimensional packing of cells capable of producing SC. A pan-genome-wide association approach was used to identify genes associated with SC. The biosynthesis of uroporphyrin and pterins, as well as carbohydrate utilization and metabolism, was found to be involved. Using this information, we constructed a classifier to predict SC directly from bacterial genome sequences and validated it by cultivating and scoring 100 strains that were not part of the training set. We predicted that SCr is widely distributed within gram-negative bacteria. Analysis of over 13,000 assembled metagenomes suggested that SC is nearly absent from most habitats associated with multicellular organisms except macroalgae and is abundant in marine waters and surface/air interfaces. This work provides a large-scale ecogenomics view of SC in bacteria and identifies microbial pathways and evolutionary relationships that underlie this optical phenomenon. [ABSTRACT FROM AUTHOR]

Published
2024
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40. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses.

Author

Roux, Simon, Brum, Jennifer R, Dutilh, Bas E, Sunagawa, Shinichi, Duhaime, Melissa B, Loy, Alexander, Poulos, Bonnie T, Solonenko, Natalie, Lara, Elena, Poulain, Julie, Pesant, Stéphane, Kandels-Lewis, Stefanie, Dimier, Céline, Picheral, Marc, Searson, Sarah, Cruaud, Corinne, Alberti, Adriana, Duarte, Carlos M, Gasol, Josep M, Vaqué, Dolors, Tara Oceans Coordinators, Bork, Peer, Acinas, Silvia G, Wincker, Patrick, and Sullivan, Matthew B

Subjects
Tara Oceans Coordinators, Viruses, Sulfur, DNA, Viral, Ecology, Ecosystem, Seawater, Genes, Viral, Genome, Viral, Expeditions, Oceans and Seas, Metagenome, Metagenomics, Nitrogen Cycle, Geographic Mapping, Datasets as Topic, General Science & Technology
Abstract

Ocean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting 'global ocean virome' dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups). This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks.

Published
2016

41. Changes to virus taxonomy and the Statutes ratified by the International Committee on Taxonomy of Viruses (2020)

Author

Walker, Peter J., Siddell, Stuart G., Lefkowitz, Elliot J., Mushegian, Arcady R., Adriaenssens, Evelien M., Dempsey, Donald M., Dutilh, Bas E., Harrach, Balázs, Harrison, Robert L., Hendrickson, R. Curtis, Junglen, Sandra, Knowles, Nick J., Kropinski, Andrew M., Krupovic, Mart, Kuhn, Jens H., Nibert, Max, Orton, Richard J., Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B., Varsani, Arvind, Zerbini, Francisco Murilo, and Davison, Andrew J.

Published
2020
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44. Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Author

Adriaenssens, Evelien M., Sullivan, Matthew B., Knezevic, Petar, van Zyl, Leonardo J., Sarkar, B. L., Dutilh, Bas E., Alfenas-Zerbini, Poliane, Łobocka, Małgorzata, Tong, Yigang, Brister, James Rodney, Moreno Switt, Andrea I., Klumpp, Jochen, Aziz, Ramy Karam, Barylski, Jakub, Uchiyama, Jumpei, Edwards, Rob A., Kropinski, Andrew M., Petty, Nicola K., Clokie, Martha R. J., Kushkina, Alla I., Morozova, Vera V., Duffy, Siobain, Gillis, Annika, Rumnieks, Janis, Kurtböke, İpek, Chanishvili, Nina, Goodridge, Lawrence, Wittmann, Johannes, Lavigne, Rob, Jang, Ho Bin, Prangishvili, David, Enault, Francois, Turner, Dann, Poranen, Minna M., Oksanen, Hanna M., and Krupovic, Mart

Published
2020
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45. Binomial nomenclature for virus species: a consultation

Author

Siddell, Stuart G., Walker, Peter J., Lefkowitz, Elliot J., Mushegian, Arcady R., Dutilh, Bas E., Harrach, Balázs, Harrison, Robert L., Junglen, Sandra, Knowles, Nick J., Kropinski, Andrew M., Krupovic, Mart, Kuhn, Jens H., Nibert, Max L., Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Varsani, Arvind, Zerbini, Francisco Murilo, and Davison, Andrew J.

Published
2020
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47. Virus Bioinformatics

Author

Pappas, Nikolaos, primary, Roux, Simon, additional, Hölzer, Martin, additional, Lamkiewicz, Kevin, additional, Mock, Florian, additional, Marz, Manja, additional, and Dutilh, Bas E., additional

Published
2021
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49. Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition

Author

Lim, Yan Wei, Cuevas, Daniel A, Silva, Genivaldo Gueiros Z, Aguinaldo, Kristen, Dinsdale, Elizabeth A, Haas, Andreas F, Hatay, Mark, Sanchez, Savannah E, Wegley-Kelly, Linda, Dutilh, Bas E, Harkins, Timothy T, Lee, Clarence C, Tom, Warren, Sandin, Stuart A, Smith, Jennifer E, Zgliczynski, Brian, Vermeij, Mark JA, Rohwer, Forest, and Edwards, Robert A

Subjects
Life Below Water, Genomics, Sequencing, Expeditions, Metagenomics, Environmental microbiology, Coral reef, Vibrio, Biological Sciences, Medical and Health Sciences
Abstract

Genomics and metagenomics have revolutionized our understanding of marine microbial ecology and the importance of microbes in global geochemical cycles. However, the process of DNA sequencing has always been an abstract extension of the research expedition, completed once the samples were returned to the laboratory. During the 2013 Southern Line Islands Research Expedition, we started the first effort to bring next generation sequencing to some of the most remote locations on our planet. We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the Ion Torrent PGM platform on the Merchant Yacht Hanse Explorer. Onboard sequence assembly, annotation, and analysis enabled us to investigate the role of the microbes in the coral reef ecology of these islands and atolls. This analysis identified phosphonate as an important phosphorous source for microbes growing in the Line Islands and reinforced the importance of L-serine in marine microbial ecosystems. Sequencing in the field allowed us to propose hypotheses and conduct experiments and further sampling based on the sequences generated. By eliminating the delay between sampling and sequencing, we enhanced the productivity of the research expedition. By overcoming the hurdles associated with sequencing on a boat in the middle of the Pacific Ocean we proved the flexibility of the sequencing, annotation, and analysis pipelines.

Published
2014

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