Despite large ongoing efforts to identify viruses in humans, animals and the environment, there are still multiple challenges remaining in the identification of novel viruses. These challenges remain both in the wet-lab as well as on the bioinformatical side. On the wet-lab side, divergent viruses can now be identified from an infected sample en masse, but different research groups use different protocols to analyse these samples and prepare them for sequencing. All the current approaches result in relative distributions, which lack (not only clinically important) absolute quantitation. Sample preparation, methods and standardisation are prerequisites for meaningful and comparable work. On the bioinformatical side, the most frequently used similarity-based virus identification approaches are largely limited by available databases, which are incomplete and often poorly annotated. VIROINF (together with the European Virus Bioinformatics Center) aims to set up a multiple-layer database for phages and their hosts (WP 1.2).
VIROINF aims to quantify viruses by four approaches (ESR 11):
- spiking in known amounts of selected viruses into a sample;
- developing qPCR assays for a selection of abundant viruses in particular sample sets;
- counting virus particles using flow cytometric approaches in collaboration with Corina Brussaard from the Netherlands Institute for Sea Research; and
- NGS-based quantification developed in collaboration with Baseclear.
The novel wet-lab approaches will be combined with newly developed advanced bioinformatical tools to identify viruses from metagenomic datasets (ESR 12), using sequence-dependent and -independent approaches. Motif searches, k-mer frequencies, and genome organisation are de novo approaches that will complement homology-based methods, allowing the detection of known and unknown viruses, yielding a comprehensive detection pipeline of all types of viruses ranging from well-studied human pathogens to completely novel bacteriophages. A range of available tools for taxonomic classification will be combined into a rapid pipeline.
PhD Projects
Main projects:
- ESR 11: Development of more quantitative viral metagenomics approaches to investigate the role of bacteriophages in the honey bee gut and their effects on health and development
- ESR 12: A machine learning pipeline to identify and characterise novel viruses in metagenome data
Side projects:
- ESR 5: Bacteriophage–host relationships prediction
- ESR 7: Generation of datasets for phage-bacterial interactions in complex communities and mutational spectra analysis following exposure to selective pressure
- ESR 13: Functional inferences from colinear crAssphage genomes
- ESR 14: Computational methods for the analysis of metagenomic datasets to extract viral sequences within the context of commercial data-mining
Journal Articles
Piedade, Gonçalo J.; Schön, Max E.; Lood, Cédric; Fofanov, Mikhail V.; Wesdorp, Ella M.; Biggs, Tristan E. G.; Wu, Lingyi; Bolhuis, Henk; Fischer, Matthias G.; Yutin, Natalya; Dutilh, Bas E.; Brussaard, Corina P. D.
Seasonal dynamics and diversity of Antarctic marine viruses reveal a novel viral seascape Journal Article
In: Nature Communications, vol. 15, pp. 9192, 2024.
@article{Piedade2024,
title = {Seasonal dynamics and diversity of Antarctic marine viruses reveal a novel viral seascape},
author = {Gonçalo J. Piedade and Max E. Schön and Cédric Lood and Mikhail V. Fofanov and Ella M. Wesdorp and Tristan E. G. Biggs and Lingyi Wu and Henk Bolhuis and Matthias G. Fischer and Natalya Yutin and Bas E. Dutilh and Corina P. D. Brussaard},
doi = {10.1038/s41467-024-53317-y},
year = {2024},
date = {2024-10-24},
urldate = {2024-10-24},
journal = {Nature Communications},
volume = {15},
pages = {9192},
abstract = {The Southern Ocean microbial ecosystem, with its pronounced seasonal shifts, is vulnerable to the impacts of climate change. Since viruses are key modulators of microbial abundance, diversity, and evolution, we need a better understanding of the effects of seasonality on the viruses in this region. Our comprehensive exploration of DNA viral diversity in the Southern Ocean reveals a unique and largely uncharted viral landscape, of which 75% was previously unidentified in other oceanic areas. We uncover novel viral taxa at high taxonomic ranks, expanding our understanding of crassphage, polinton-like virus, and virophage diversity. Nucleocytoviricota viruses represent an abundant and diverse group of Antarctic viruses, highlighting their potential as important regulators of phytoplankton population dynamics. Our temporal analysis reveals complex seasonal patterns in marine viral communities (bacteriophages, eukaryotic viruses) which underscores the apparent interactions with their microbial hosts, whilst deepening our understanding of their roles in the world’s most sensitive and rapidly changing ecosystem.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The Southern Ocean microbial ecosystem, with its pronounced seasonal shifts, is vulnerable to the impacts of climate change. Since viruses are key modulators of microbial abundance, diversity, and evolution, we need a better understanding of the effects of seasonality on the viruses in this region. Our comprehensive exploration of DNA viral diversity in the Southern Ocean reveals a unique and largely uncharted viral landscape, of which 75% was previously unidentified in other oceanic areas. We uncover novel viral taxa at high taxonomic ranks, expanding our understanding of crassphage, polinton-like virus, and virophage diversity. Nucleocytoviricota viruses represent an abundant and diverse group of Antarctic viruses, highlighting their potential as important regulators of phytoplankton population dynamics. Our temporal analysis reveals complex seasonal patterns in marine viral communities (bacteriophages, eukaryotic viruses) which underscores the apparent interactions with their microbial hosts, whilst deepening our understanding of their roles in the world’s most sensitive and rapidly changing ecosystem.
Wijesekara, Yasas; Wu, Ling-Yi; Beeloo, Rick; Rozwalak, Piotr; Hauptfeld, Ernestina; Doijad, Swapnil P.; Dutilh, Bas E.; Kaderali, Lars
Jaeger: an accurate and fast deep-learning tool to detect bacteriophage sequences Journal Article
In: bioRxiv, 2024.
@article{Wijesekara2024,
title = {Jaeger: an accurate and fast deep-learning tool to detect bacteriophage sequences},
author = {Yasas Wijesekara and Ling-Yi Wu and Rick Beeloo and Piotr Rozwalak and Ernestina Hauptfeld and Swapnil P. Doijad and Bas E. Dutilh and Lars Kaderali},
year = {2024},
date = {2024-09-24},
journal = {bioRxiv},
abstract = {Viruses are integral to every biome on Earth, yet we still need a more comprehensive picture of their identity and global distribution. Global metagenomics sequencing efforts revealed the genomic content of tens of thousands of environmental samples, however identifying the viral sequences in these datasets remains challenging due to their vast genomic diversity. Here, we address identifying bacteriophage sequences in unlabeled sequencing data. In a recent benchmarking paper, we observed that existing deep-learning tools show a high true positive rate, but may also produce many false positives when confronted with divergent sequences. To tackle this challenge, we introduce Jaeger, a novel deep-learning method designed specifically for identifying bacteriophage genome fragments. Extensive benchmarking on the IMG/VR database and real-world metagenomes reveals Jaeger’s consistent high sensitivity (0.87) and precision (0.92). Applying Jaeger to over 16,000 metagenomic assemblies from the MGnify database yielded over five million putative phage contigs. On average, Jaeger is around 20 times faster than the other state-of-the-art methods. Jaeger is available at https://github.com/MGXlab/Jaeger.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Viruses are integral to every biome on Earth, yet we still need a more comprehensive picture of their identity and global distribution. Global metagenomics sequencing efforts revealed the genomic content of tens of thousands of environmental samples, however identifying the viral sequences in these datasets remains challenging due to their vast genomic diversity. Here, we address identifying bacteriophage sequences in unlabeled sequencing data. In a recent benchmarking paper, we observed that existing deep-learning tools show a high true positive rate, but may also produce many false positives when confronted with divergent sequences. To tackle this challenge, we introduce Jaeger, a novel deep-learning method designed specifically for identifying bacteriophage genome fragments. Extensive benchmarking on the IMG/VR database and real-world metagenomes reveals Jaeger’s consistent high sensitivity (0.87) and precision (0.92). Applying Jaeger to over 16,000 metagenomic assemblies from the MGnify database yielded over five million putative phage contigs. On average, Jaeger is around 20 times faster than the other state-of-the-art methods. Jaeger is available at https://github.com/MGXlab/Jaeger.
Peng, Xue; Smith, Sophie Elizabeth; Huang, Wanqi; Ru, Jinlong; Mirzaei, Mohammadali Khan; Deng, Li
Metagenomic analyses of single phages and phage cocktails show instances of contamination with temperate phages and bacterial DNA Journal Article
In: bioRxiv, 2024.
@article{Peng2024,
title = {Metagenomic analyses of single phages and phage cocktails show instances of contamination with temperate phages and bacterial DNA},
author = {Xue Peng and Sophie Elizabeth Smith and Wanqi Huang and Jinlong Ru and Mohammadali Khan Mirzaei and Li Deng},
doi = {10.1101/2024.09.12.612727},
year = {2024},
date = {2024-09-12},
journal = {bioRxiv},
abstract = {Increasing antibiotic resistance has led to renewed attention being paid to bacteriophage therapy. Commercial phage cocktails are available but often their contents of the phages are not well defined. Some metagenomic studies have been done to retrospectively characterise these cocktails, but little is known about the replication cycle of the included phages, or about the possible bacterial DNA contamination. In this study, published metagenomic sequences were reanalysed using recent advances in viromics tools. Signs of temperate phage contigs were found in all cocktail metagenomes, as well as host DNA, which could poses a risk as it may lead to horizontal gene transfer of virulence factors to commensals and pathogens. This suggests the need to implement further quality measures before using phage cocktails therapeutically.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Increasing antibiotic resistance has led to renewed attention being paid to bacteriophage therapy. Commercial phage cocktails are available but often their contents of the phages are not well defined. Some metagenomic studies have been done to retrospectively characterise these cocktails, but little is known about the replication cycle of the included phages, or about the possible bacterial DNA contamination. In this study, published metagenomic sequences were reanalysed using recent advances in viromics tools. Signs of temperate phage contigs were found in all cocktail metagenomes, as well as host DNA, which could poses a risk as it may lead to horizontal gene transfer of virulence factors to commensals and pathogens. This suggests the need to implement further quality measures before using phage cocktails therapeutically.
Trgovec-Greif, Lovro; Hellinger, Hans-Jörg; Mainguy, Jean; Pfundner, Alexander; Frishman, Dmitrij; Kiening, Michael; Webster, Nicole Suzanne; Laffy, Patrick William; Feichtinger, Michael; Rattei, Thomas
VOGDB—Database of Virus Orthologous Groups Journal Article
In: Viruses, vol. 16, iss. 8, pp. 1191, 2024.
@article{Trgovec-Greif2024,
title = {VOGDB—Database of Virus Orthologous Groups},
author = {Lovro Trgovec-Greif and Hans-Jörg Hellinger and Jean Mainguy and Alexander Pfundner and Dmitrij Frishman and Michael Kiening and Nicole Suzanne Webster and Patrick William Laffy and Michael Feichtinger and Thomas Rattei},
doi = {10.3390/v16081191},
year = {2024},
date = {2024-07-25},
urldate = {2024-07-25},
journal = {Viruses},
volume = {16},
issue = {8},
pages = {1191},
abstract = {Computational models of homologous protein groups are essential in sequence bioinformatics. Due to the diversity and rapid evolution of viruses, the grouping of protein sequences from virus genomes is particularly challenging. The low sequence similarities of homologous genes in viruses require specific approaches for sequence- and structure-based clustering. Furthermore, the annotation of virus genomes in public databases is not as consistent and up to date as for many cellular genomes. To tackle these problems, we have developed VOGDB, which is a database of virus orthologous groups. VOGDB is a multi-layer database that progressively groups viral genes into groups connected by increasingly remote similarity. The first layer is based on pair-wise sequence similarities, the second layer is based on the sequence profile alignments, and the third layer uses predicted protein structures to find the most remote similarity. VOGDB groups allow for more sensitive homology searches of novel genes and increase the chance of predicting annotations or inferring phylogeny. VOGD B uses all virus genomes from RefSeq and partially reannotates them. VOGDB is updated with every RefSeq release. The unique feature of VOGDB is the inclusion of both prokaryotic and eukaryotic viruses in the same clustering process, which makes it possible to explore old evolutionary relationships of the two groups. VOGDB is freely available at vogdb.org under the CC BY 4.0 license.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Computational models of homologous protein groups are essential in sequence bioinformatics. Due to the diversity and rapid evolution of viruses, the grouping of protein sequences from virus genomes is particularly challenging. The low sequence similarities of homologous genes in viruses require specific approaches for sequence- and structure-based clustering. Furthermore, the annotation of virus genomes in public databases is not as consistent and up to date as for many cellular genomes. To tackle these problems, we have developed VOGDB, which is a database of virus orthologous groups. VOGDB is a multi-layer database that progressively groups viral genes into groups connected by increasingly remote similarity. The first layer is based on pair-wise sequence similarities, the second layer is based on the sequence profile alignments, and the third layer uses predicted protein structures to find the most remote similarity. VOGDB groups allow for more sensitive homology searches of novel genes and increase the chance of predicting annotations or inferring phylogeny. VOGD B uses all virus genomes from RefSeq and partially reannotates them. VOGDB is updated with every RefSeq release. The unique feature of VOGDB is the inclusion of both prokaryotic and eukaryotic viruses in the same clustering process, which makes it possible to explore old evolutionary relationships of the two groups. VOGDB is freely available at vogdb.org under the CC BY 4.0 license.
Deboutte, Ward; Smet, Lina De; Brunain, Marleen; Basler, Nikolas; Rycke, Riet De; Smets, Lena; de Graaf, Dirk C.; Matthijnssens, Jelle
Known and novel viruses in Belgian honey bees: yearly differences, spatial clustering, and associations with overwintering loss Journal Article
In: Microbiol Spectrum, vol. 12, iss. 7, pp. e0358123, 2024.
@article{Deboutte2024,
title = {Known and novel viruses in Belgian honey bees: yearly differences, spatial clustering, and associations with overwintering loss},
author = {Ward Deboutte and Lina De Smet and Marleen Brunain and Nikolas Basler and Riet De Rycke and Lena Smets and Dirk C. de Graaf and Jelle Matthijnssens},
doi = {10.1128/spectrum.03581-23},
year = {2024},
date = {2024-07-02},
journal = {Microbiol Spectrum},
volume = {12},
issue = {7},
pages = {e0358123},
abstract = {In recent years, managed honey bee colonies have been suffering from an increasing number of biotic and abiotic stressors, resulting in numerous losses of colonies worldwide. A pan-European study, EPILOBEE, estimated the colony loss in Belgium to be 32.4% in 2012 and 14.8% in 2013. In the current study, absolute viral loads of four known honey bee viruses (DWV-A, DWV-B, AmFV, and BMLV) and three novel putative honey bee viruses (Apis orthomyxovirus 1, apthili virus, and apparli virus) were determined in 300 Flemish honey bee samples, and associations with winter survival were determined. This revealed that, in addition to the known influence of DWV-A and DWV-B on colony health, one of the newly described viruses (apthili virus) shows a strong yearly difference and is also associated with winter survival. Furthermore, all scrutinized viruses revealed significant spatial clustering patterns, implying that despite the limited surface area of Flanders, local virus transmission is paramount. The vast majority of samples were positive for at least one of the seven investigated viruses, and up to 20% of samples were positive for at least one of the three novel viruses. One of those three, Apis orthomyxovirus 1, was shown to be a genuine honey bee-infecting virus, able to infect all developmental stages of the honey bee, as well as the Varroa destructor mite. These results shed light on the most prevalent viruses in Belgium and their roles in the winter survival of honey bee colonies.
Importance: The western honey bee (Apis mellifera) is a highly effective pollinator of flowering plants, including many crops, which gives honey bees an outstanding importance both ecologically and economically. Alarmingly high annual loss rates of managed honey bee colonies are a growing concern for beekeepers and scientists and have prompted a significant research effort toward bee health. Several detrimental factors have been identified, such as varroa mite infestation and disease from various bacterial and viral agents, but annual differences are often not elucidated. In this study, we utilize the viral metagenomic survey of the EPILOBEE project, a European research program for bee health, to elaborate on the most abundant bee viruses of Flanders. We complement the existing metagenomic data with absolute viral loads and their spatial and temporal distributions. Furthermore, we identify Apis orthomyxovirus 1 as a potentially emerging pathogen, as we find evidence for its active replication honey bees.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
In recent years, managed honey bee colonies have been suffering from an increasing number of biotic and abiotic stressors, resulting in numerous losses of colonies worldwide. A pan-European study, EPILOBEE, estimated the colony loss in Belgium to be 32.4% in 2012 and 14.8% in 2013. In the current study, absolute viral loads of four known honey bee viruses (DWV-A, DWV-B, AmFV, and BMLV) and three novel putative honey bee viruses (Apis orthomyxovirus 1, apthili virus, and apparli virus) were determined in 300 Flemish honey bee samples, and associations with winter survival were determined. This revealed that, in addition to the known influence of DWV-A and DWV-B on colony health, one of the newly described viruses (apthili virus) shows a strong yearly difference and is also associated with winter survival. Furthermore, all scrutinized viruses revealed significant spatial clustering patterns, implying that despite the limited surface area of Flanders, local virus transmission is paramount. The vast majority of samples were positive for at least one of the seven investigated viruses, and up to 20% of samples were positive for at least one of the three novel viruses. One of those three, Apis orthomyxovirus 1, was shown to be a genuine honey bee-infecting virus, able to infect all developmental stages of the honey bee, as well as the Varroa destructor mite. These results shed light on the most prevalent viruses in Belgium and their roles in the winter survival of honey bee colonies.
Importance: The western honey bee (Apis mellifera) is a highly effective pollinator of flowering plants, including many crops, which gives honey bees an outstanding importance both ecologically and economically. Alarmingly high annual loss rates of managed honey bee colonies are a growing concern for beekeepers and scientists and have prompted a significant research effort toward bee health. Several detrimental factors have been identified, such as varroa mite infestation and disease from various bacterial and viral agents, but annual differences are often not elucidated. In this study, we utilize the viral metagenomic survey of the EPILOBEE project, a European research program for bee health, to elaborate on the most abundant bee viruses of Flanders. We complement the existing metagenomic data with absolute viral loads and their spatial and temporal distributions. Furthermore, we identify Apis orthomyxovirus 1 as a potentially emerging pathogen, as we find evidence for its active replication honey bees.
Importance: The western honey bee (Apis mellifera) is a highly effective pollinator of flowering plants, including many crops, which gives honey bees an outstanding importance both ecologically and economically. Alarmingly high annual loss rates of managed honey bee colonies are a growing concern for beekeepers and scientists and have prompted a significant research effort toward bee health. Several detrimental factors have been identified, such as varroa mite infestation and disease from various bacterial and viral agents, but annual differences are often not elucidated. In this study, we utilize the viral metagenomic survey of the EPILOBEE project, a European research program for bee health, to elaborate on the most abundant bee viruses of Flanders. We complement the existing metagenomic data with absolute viral loads and their spatial and temporal distributions. Furthermore, we identify Apis orthomyxovirus 1 as a potentially emerging pathogen, as we find evidence for its active replication honey bees.
Rozwalak, Piotr; Barylski, Jakub; Wijesekara, Yasas; Dutilh, Bas E.; Zielezinski, Andrzej
Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces Journal Article
In: Nat Commun, vol. 15, iss. 1, pp. 495, 2024.
@article{nokey,
title = {Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces},
author = {Piotr Rozwalak and Jakub Barylski and Yasas Wijesekara and Bas E. Dutilh and Andrzej Zielezinski
},
doi = {10.1038/s41467-023-44370-0},
year = {2024},
date = {2024-01-23},
urldate = {2024-01-23},
journal = {Nat Commun},
volume = {15},
issue = {1},
pages = {495},
abstract = {Bacteriophages are widely recognised as rapidly evolving biological entities. However, knowledge about ancient bacteriophages is limited. Here, we analyse DNA sequence datasets previously generated from ancient palaeofaeces and human gut-content samples, and identify an ancient phage genome nearly identical to present-day Mushuvirus mushu, a virus that infects gut commensal bacteria. The DNA damage patterns of the genome are consistent with its ancient origin and, despite 1300 years of evolution, the ancient Mushuvirus genome shares 97.7% nucleotide identity with its modern counterpart, indicating a long-term relationship between the prophage and its host. In addition, we reconstruct and authenticate 297 other phage genomes from the last 5300 years, including those belonging to unknown families. Our findings demonstrate the feasibility of reconstructing ancient phage genome sequences, thus expanding the known virosphere and offering insights into phage-bacteria interactions spanning several millennia.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bacteriophages are widely recognised as rapidly evolving biological entities. However, knowledge about ancient bacteriophages is limited. Here, we analyse DNA sequence datasets previously generated from ancient palaeofaeces and human gut-content samples, and identify an ancient phage genome nearly identical to present-day Mushuvirus mushu, a virus that infects gut commensal bacteria. The DNA damage patterns of the genome are consistent with its ancient origin and, despite 1300 years of evolution, the ancient Mushuvirus genome shares 97.7% nucleotide identity with its modern counterpart, indicating a long-term relationship between the prophage and its host. In addition, we reconstruct and authenticate 297 other phage genomes from the last 5300 years, including those belonging to unknown families. Our findings demonstrate the feasibility of reconstructing ancient phage genome sequences, thus expanding the known virosphere and offering insights into phage-bacteria interactions spanning several millennia.
Luo, Shiqi; Ru, Jinlong; Mirzaei, Mohammadali Khan; Xue, Jinling; Peng, Xue; Ralser, Anna; Luque, Raquel Mejías; Gerhard, Markus; Deng, Li
Gut virome profiling identifies an association between temperate phages and colorectal cancer promoted by Helicobacter pylori infection Journal Article
In: Gut Microbes, vol. 15, iss. 2, pp. 2257291, 2023.
@article{nokey,
title = {Gut virome profiling identifies an association between temperate phages and colorectal cancer promoted by Helicobacter pylori infection},
author = {Shiqi Luo and Jinlong Ru and Mohammadali Khan Mirzaei and Jinling Xue and Xue Peng and Anna Ralser and Raquel Mejías Luque and Markus Gerhard and Li Deng},
doi = {10.1080/19490976.2023.2257291},
year = {2023},
date = {2023-09-25},
journal = {Gut Microbes},
volume = {15},
issue = {2},
pages = {2257291},
abstract = {Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide. While a close correlation between chronic Helicobacter pylori infection and CRC has been reported, the role of the virome has been overlooked. Here, we infected Apc-mutant mouse models and C57BL/6 mice with H. pylori and conducted a comprehensive metagenomics analysis of H. pylori-induced changes in lower gastrointestinal tract bacterial and viral communities. We observed an expansion of temperate phages in H. pylori infected Apc+/1638N mice at the early stage of carcinogenesis. Some of the temperate phages were predicted to infect bacteria associated with CRC, including Enterococcus faecalis. We also observed a high prevalence of virulent genes, such as flgJ, cwlJ, and sleB, encoded by temperate phages. In addition, we identified phages associated with pre-onset and onset of H. pylori-promoted carcinogenesis. Through co-occurrence network analysis, we found strong associations between the viral and bacterial communities in infected mice before the onset of carcinogenesis. These findings suggest that the expansion of temperate phages, possibly caused by prophage induction triggered by H. pylori infection, may have contributed to the development of CRC in mice by interacting with the bacterial community.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide. While a close correlation between chronic Helicobacter pylori infection and CRC has been reported, the role of the virome has been overlooked. Here, we infected Apc-mutant mouse models and C57BL/6 mice with H. pylori and conducted a comprehensive metagenomics analysis of H. pylori-induced changes in lower gastrointestinal tract bacterial and viral communities. We observed an expansion of temperate phages in H. pylori infected Apc+/1638N mice at the early stage of carcinogenesis. Some of the temperate phages were predicted to infect bacteria associated with CRC, including Enterococcus faecalis. We also observed a high prevalence of virulent genes, such as flgJ, cwlJ, and sleB, encoded by temperate phages. In addition, we identified phages associated with pre-onset and onset of H. pylori-promoted carcinogenesis. Through co-occurrence network analysis, we found strong associations between the viral and bacterial communities in infected mice before the onset of carcinogenesis. These findings suggest that the expansion of temperate phages, possibly caused by prophage induction triggered by H. pylori infection, may have contributed to the development of CRC in mice by interacting with the bacterial community.
Ritsch, Muriel; Cassman, Noriko A.; Saghaei, Shahram; Marz, Manja
Navigating the Landscape: A Comprehensive Review of Current Virus Databases Journal Article
In: Viruses, vol. 15, iss. 9, pp. 1834, 2023.
@article{Ritsch2023,
title = {Navigating the Landscape: A Comprehensive Review of Current Virus Databases},
author = {Muriel Ritsch and Noriko A. Cassman and Shahram Saghaei and Manja Marz},
doi = {10.3390/v15091834},
year = {2023},
date = {2023-08-29},
journal = {Viruses},
volume = {15},
issue = {9},
pages = {1834},
abstract = {Viruses are abundant and diverse entities that have important roles in public health, ecology, and agriculture. The identification and surveillance of viruses rely on an understanding of their genome organization, sequences, and replication strategy. Despite technological advancements in sequencing methods, our current understanding of virus diversity remains incomplete, highlighting the need to explore undiscovered viruses. Virus databases play a crucial role in providing access to sequences, annotations and other metadata, and analysis tools for studying viruses. However, there has not been a comprehensive review of virus databases in the last five years. This study aimed to fill this gap by identifying 24 active virus databases and included an extensive evaluation of their content, functionality and compliance with the FAIR principles. In this study, we thoroughly assessed the search capabilities of five database catalogs, which serve as comprehensive repositories housing a diverse array of databases and offering essential metadata. Moreover, we conducted a comprehensive review of different types of errors, encompassing taxonomy, names, missing information, sequences, sequence orientation, and chimeric sequences, with the intention of empowering users to effectively tackle these challenges. We expect this review to aid users in selecting suitable virus databases and other resources, and to help databases in error management and improve their adherence to the FAIR principles. The databases listed here represent the current knowledge of viruses and will help aid users find databases of interest based on content, functionality, and scope. The use of virus databases is integral to gaining new insights into the biology, evolution, and transmission of viruses, and developing new strategies to manage virus outbreaks and preserve global health.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Viruses are abundant and diverse entities that have important roles in public health, ecology, and agriculture. The identification and surveillance of viruses rely on an understanding of their genome organization, sequences, and replication strategy. Despite technological advancements in sequencing methods, our current understanding of virus diversity remains incomplete, highlighting the need to explore undiscovered viruses. Virus databases play a crucial role in providing access to sequences, annotations and other metadata, and analysis tools for studying viruses. However, there has not been a comprehensive review of virus databases in the last five years. This study aimed to fill this gap by identifying 24 active virus databases and included an extensive evaluation of their content, functionality and compliance with the FAIR principles. In this study, we thoroughly assessed the search capabilities of five database catalogs, which serve as comprehensive repositories housing a diverse array of databases and offering essential metadata. Moreover, we conducted a comprehensive review of different types of errors, encompassing taxonomy, names, missing information, sequences, sequence orientation, and chimeric sequences, with the intention of empowering users to effectively tackle these challenges. We expect this review to aid users in selecting suitable virus databases and other resources, and to help databases in error management and improve their adherence to the FAIR principles. The databases listed here represent the current knowledge of viruses and will help aid users find databases of interest based on content, functionality, and scope. The use of virus databases is integral to gaining new insights into the biology, evolution, and transmission of viruses, and developing new strategies to manage virus outbreaks and preserve global health.
Wu, Ling-Yi; Pappas, Nikolaos; Wijesekara, Yasas; Piedade, Gonçalo J.; Brussaard, Corina P. D.; Dutilh, Bas E.
Benchmarking Bioinformatic Virus Identification Tools Using Real-World Metagenomic Data across Biomes Journal Article
In: bioRxiv, 2023.
@article{nokey,
title = {Benchmarking Bioinformatic Virus Identification Tools Using Real-World Metagenomic Data across Biomes},
author = {Ling-Yi Wu and Nikolaos Pappas and Yasas Wijesekara and Gonçalo J. Piedade and Corina P.D. Brussaard and Bas E. Dutilh},
doi = {10.1101/2023.04.26.538077},
year = {2023},
date = {2023-04-28},
journal = {bioRxiv},
abstract = {As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinformatic virus identification tools have been developed for this task, making it challenging to choose the right tools, parameters, and cutoffs. As all these tools measure different biological signals, and use different algorithms and training/reference databases, it is imperative to conduct an independent benchmarking to give users objective guidance. We compared the performance of ten state-of-the-art virus identification tools in thirteen modes on eight paired viral and microbial datasets from three distinct biomes, including a new complex dataset from Antarctic coastal waters. The tools had highly variable true positive rates (0 – 68%) and false positive rates (0 – 15%). PPR-Meta best distinguished viral from microbial contigs, followed by DeepVirFinder, VirSorter2, and VIBRANT. Different tools identified different subsets of the benchmarking data and all tools, except for Sourmash, found unique viral contigs. Tools performance could be improved with adjusted parameter cutoffs, indicating that adjustment of parameter cutoffs before usage should be considered. Together, our independent benchmarking provides guidance on choices of bioinformatic virus identification tools and gives suggestions for parameter adjustments for viromics researchers.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinformatic virus identification tools have been developed for this task, making it challenging to choose the right tools, parameters, and cutoffs. As all these tools measure different biological signals, and use different algorithms and training/reference databases, it is imperative to conduct an independent benchmarking to give users objective guidance. We compared the performance of ten state-of-the-art virus identification tools in thirteen modes on eight paired viral and microbial datasets from three distinct biomes, including a new complex dataset from Antarctic coastal waters. The tools had highly variable true positive rates (0 – 68%) and false positive rates (0 – 15%). PPR-Meta best distinguished viral from microbial contigs, followed by DeepVirFinder, VirSorter2, and VIBRANT. Different tools identified different subsets of the benchmarking data and all tools, except for Sourmash, found unique viral contigs. Tools performance could be improved with adjusted parameter cutoffs, indicating that adjustment of parameter cutoffs before usage should be considered. Together, our independent benchmarking provides guidance on choices of bioinformatic virus identification tools and gives suggestions for parameter adjustments for viromics researchers.
Ru, Jinlong; Mirzaei, Mohammadali Khan; Xue, Jinling; Peng, Xue; Deng, Li
ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis Journal Article
In: Gut Microbes, vol. 15, iss. 1, pp. 2192522, 2023.
@article{nokey,
title = {ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis},
author = {Jinlong Ru and Mohammadali Khan Mirzaei and Jinling Xue and Xue Peng and Li Deng
},
doi = {10.1080/19490976.2023.2192522},
year = {2023},
date = {2023-03-30},
journal = {Gut Microbes},
volume = {15},
issue = {1},
pages = {2192522},
abstract = {Bacteriophages play central roles in the maintenance and function of most ecosystems by regulating bacterial communities. Yet, our understanding of their diversity remains limited due to the lack of robust bioinformatics standards. Here we present ViroProfiler, an in-silico workflow for analyzing shotgun viral metagenomic data. ViroProfiler can be executed on a local Linux computer or cloud computing environments. It uses the containerization technique to ensure computational reproducibility and facilitate collaborative research. ViroProfiler is freely available at https://github.com/deng-lab/viroprofiler.
},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bacteriophages play central roles in the maintenance and function of most ecosystems by regulating bacterial communities. Yet, our understanding of their diversity remains limited due to the lack of robust bioinformatics standards. Here we present ViroProfiler, an in-silico workflow for analyzing shotgun viral metagenomic data. ViroProfiler can be executed on a local Linux computer or cloud computing environments. It uses the containerization technique to ensure computational reproducibility and facilitate collaborative research. ViroProfiler is freely available at https://github.com/deng-lab/viroprofiler.
Goettsch, Winfried; Beerenwinkel, Niko; Deng, Li; Dölken, Lars; Dutilh, Bas E.; Erhard, Florian; Kaderali, Lars; von Kleist, Max; Marquet, Roland; Matthijnssens, Jelle; McCallin, Shawna; McMahon, Dino; Rattei, Thomas; van Rij, Ronald P.; Robertson, David L.; Schwemmle, Martin; Stern-Ginossar, Noam; Marz, Manja
ITN -- VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics Journal Article
In: Viruses, vol. 13, no. 5, pp. 766, 2021.
@article{nokey,
title = {ITN -- VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics},
author = {Winfried Goettsch and Niko Beerenwinkel and Li Deng and Lars Dölken and Bas E. Dutilh and Florian Erhard and Lars Kaderali and Max von Kleist and Roland Marquet and Jelle Matthijnssens and Shawna McCallin and Dino McMahon and Thomas Rattei and Ronald P. {van Rij} and David L. Robertson and Martin Schwemmle and Noam Stern-Ginossar and Manja Marz},
doi = {10.3390/v13050766},
year = {2021},
date = {2021-04-27},
urldate = {2021-04-27},
journal = {Viruses},
volume = {13},
number = {5},
pages = {766},
abstract = {Many recent studies highlight the fundamental importance of viruses. Besides their important role as human and animal pathogens, their beneficial, commensal or harmful functions are poorly understood. By developing and applying tailored bioinformatical tools in important virological models, the Marie Skłodowska-Curie Initiative International Training Network VIROINF will provide a better understanding of viruses and the interaction with their hosts. This will open the door to validate methods of improving viral growth, morphogenesis and development, as well as to control strategies against unwanted microorganisms. The key feature of VIROINF is its interdisciplinary nature, which brings together virologists and bioinformaticians to achieve common goals.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Many recent studies highlight the fundamental importance of viruses. Besides their important role as human and animal pathogens, their beneficial, commensal or harmful functions are poorly understood. By developing and applying tailored bioinformatical tools in important virological models, the Marie Skłodowska-Curie Initiative International Training Network VIROINF will provide a better understanding of viruses and the interaction with their hosts. This will open the door to validate methods of improving viral growth, morphogenesis and development, as well as to control strategies against unwanted microorganisms. The key feature of VIROINF is its interdisciplinary nature, which brings together virologists and bioinformaticians to achieve common goals.
Presentations
Basler, Nikolas; de Graaf, Dirk C.; Smet, Lina De; Matthijnssens, Jelle
The honey bee gut microbiome – a diversity profile of different gut parts and seasons across eight European countries Presentation
Oral presentation at 9th European Congress of Apidology (EurBee9), 20.09.2022, (Best Oral Presentation).
@misc{nokey,
title = {The honey bee gut microbiome – a diversity profile of different gut parts and seasons across eight European countries},
author = {Nikolas Basler and Dirk C. de Graaf and Lina De Smet and Jelle Matthijnssens},
year = {2022},
date = {2022-09-20},
urldate = {2022-09-20},
abstract = {As a highly productive pollinator of flowering plants, the honey bee (Apis mellifera) plays an important role in ecology and agriculture. However, managed honey bee colonies are suffering from a number of stressors, including pathogens, parasites, and the use of pesticides. Studying and improving the health of honey bees is therefore of great ecologic and economic interest. Previous studies have shown that the honey bee gut houses a stable bacterial microbiome of only approximately eight core species. On the other hand, recent studies described a higher diversity in bacteria on the sub-species level as well as in bacteriophages (or phages, i.e. viruses that infect bacteria). Additionally, it has been shown that the gut microbiome affects the bees’ development, immune signalling and behaviour.
This project is part of the EU-funded Innovative Training Network VIROINF (grant agreement No 955974) which revolves around virus-host interactions and aims to facilitate the connections between the fields of virology and bioinformatics. Honey bees from eight different European countries (Belgium, France, Germany, Netherlands, Portugal, Romania, Switzerland and United Kingdom) were collected during spring, summer and autumn 2020 as part of the EU-funded B-GOOD project (grant agreement No 817622). From each sample, midguts, ileums and rectums of 10 individual bees have been pooled and processed to generate Illumina libraries for shotgun sequencing. From the resulting data, the diversity of the microbiome was assessed based on species-level abundances as well as shared fractions of single-nucleotide variations (SNVs) in orthologous core genes within species. Preliminary analysis of the core species abundance profiles suggests that the rectum contains the entire bacterial community, of which ileum and midgut contain nested subsets. Unlike species abundances, SNV profiles within some core species appear to separate by geographic origin.
These findings will also inform future experiments to gain more insight into the complex interactions between the honey bee, its gut bacteria and their viruses. We thereby aim to contribute to a better understanding of honey bee health and disease.},
howpublished = {Oral presentation at 9th European Congress of Apidology (EurBee9)},
note = {Best Oral Presentation},
keywords = {},
pubstate = {published},
tppubtype = {presentation}
}
As a highly productive pollinator of flowering plants, the honey bee (Apis mellifera) plays an important role in ecology and agriculture. However, managed honey bee colonies are suffering from a number of stressors, including pathogens, parasites, and the use of pesticides. Studying and improving the health of honey bees is therefore of great ecologic and economic interest. Previous studies have shown that the honey bee gut houses a stable bacterial microbiome of only approximately eight core species. On the other hand, recent studies described a higher diversity in bacteria on the sub-species level as well as in bacteriophages (or phages, i.e. viruses that infect bacteria). Additionally, it has been shown that the gut microbiome affects the bees’ development, immune signalling and behaviour.
This project is part of the EU-funded Innovative Training Network VIROINF (grant agreement No 955974) which revolves around virus-host interactions and aims to facilitate the connections between the fields of virology and bioinformatics. Honey bees from eight different European countries (Belgium, France, Germany, Netherlands, Portugal, Romania, Switzerland and United Kingdom) were collected during spring, summer and autumn 2020 as part of the EU-funded B-GOOD project (grant agreement No 817622). From each sample, midguts, ileums and rectums of 10 individual bees have been pooled and processed to generate Illumina libraries for shotgun sequencing. From the resulting data, the diversity of the microbiome was assessed based on species-level abundances as well as shared fractions of single-nucleotide variations (SNVs) in orthologous core genes within species. Preliminary analysis of the core species abundance profiles suggests that the rectum contains the entire bacterial community, of which ileum and midgut contain nested subsets. Unlike species abundances, SNV profiles within some core species appear to separate by geographic origin.
These findings will also inform future experiments to gain more insight into the complex interactions between the honey bee, its gut bacteria and their viruses. We thereby aim to contribute to a better understanding of honey bee health and disease.
This project is part of the EU-funded Innovative Training Network VIROINF (grant agreement No 955974) which revolves around virus-host interactions and aims to facilitate the connections between the fields of virology and bioinformatics. Honey bees from eight different European countries (Belgium, France, Germany, Netherlands, Portugal, Romania, Switzerland and United Kingdom) were collected during spring, summer and autumn 2020 as part of the EU-funded B-GOOD project (grant agreement No 817622). From each sample, midguts, ileums and rectums of 10 individual bees have been pooled and processed to generate Illumina libraries for shotgun sequencing. From the resulting data, the diversity of the microbiome was assessed based on species-level abundances as well as shared fractions of single-nucleotide variations (SNVs) in orthologous core genes within species. Preliminary analysis of the core species abundance profiles suggests that the rectum contains the entire bacterial community, of which ileum and midgut contain nested subsets. Unlike species abundances, SNV profiles within some core species appear to separate by geographic origin.
These findings will also inform future experiments to gain more insight into the complex interactions between the honey bee, its gut bacteria and their viruses. We thereby aim to contribute to a better understanding of honey bee health and disease.