2024
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.
Abstract | Links | BibTeX | Tags: Project 05, WP 1.1 Virus identification, WP 1.2 Host prediction
@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 = {Project 05, WP 1.1 Virus identification, WP 1.2 Host prediction},
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.
2023
Luo, Shiqi; Ru, Jinlong; Mirzaei, Mohammadali Khan; Xue, Jinling; Peng, Xue; Ralser, Anna; Hadi, Joshua Lemuel; Mejías-Luque, Raquel; Gerhard, Markus; Deng, Li
Helicobacter pylori infection alters gut virome by expanding temperate phages linked to increased risk of colorectal cancer Journal Article
In: Gut, pp. gutjnl-2023-330362, 2023.
Abstract | Links | BibTeX | Tags: Project 05, WP 1.2 Host prediction
@article{nokey,
title = {Helicobacter pylori infection alters gut virome by expanding temperate phages linked to increased risk of colorectal cancer},
author = {Shiqi Luo and Jinlong Ru and Mohammadali Khan Mirzaei and Jinling Xue and Xue Peng and Anna Ralser and Joshua Lemuel Hadi and Raquel Mejías-Luque and Markus Gerhard and Li Deng},
doi = {10.1136/gutjnl-2023-330362},
year = {2023},
date = {2023-11-02},
journal = {Gut},
pages = {gutjnl-2023-330362},
abstract = {No abstract available.},
keywords = {Project 05, WP 1.2 Host prediction},
pubstate = {published},
tppubtype = {article}
}
No abstract available.
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.
Abstract | Links | BibTeX | Tags: Project 05, WP 1.1 Virus identification, WP 1.2 Host prediction
@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 = {Project 05, WP 1.1 Virus identification, WP 1.2 Host prediction},
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.
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.
Abstract | Links | BibTeX | Tags: Project 05, WP 1.1 Virus identification, WP 1.2 Host prediction
@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 = {Project 05, WP 1.1 Virus identification, WP 1.2 Host prediction},
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.
2022
Peng, Xue; Ru, Jinlong; Mirzaei, Mohammadali Khan; Deng, Li
Replidec - Use naive Bayes classifier to identify virus lifecycle from metagenomics data Journal Article
In: bioRxiv, 2022.
Abstract | Links | BibTeX | Tags: Project 05, WP 1.2 Host prediction
@article{nokey,
title = {Replidec - Use naive Bayes classifier to identify virus lifecycle from metagenomics data},
author = {Xue Peng and Jinlong Ru and Mohammadali Khan Mirzaei and Li Deng
},
doi = {10.1101/2022.07.18.500415},
year = {2022},
date = {2022-07-19},
journal = {bioRxiv},
abstract = {Motivation: Viruses are the most abundant biological entities on earth. The majority of these entities are bacterial viruses or phages which specifically infect bacteria. Phages can use different replication strategies to invade their hosts including lytic, lysogenic, chronic cycle and pseudolysogeny. While the determination of the replication strategy used by phages is important to explore the phage-bacteria relationships in different ecosystems there are not many tools that can predict this in metagenomic data. In addition, most of the tools available can only predict lytic and lysogenic cycles. To address this issue, we have developed a new software called Replidec to identify three most common phage replication cycles (virulent, temperate, chronic) in viral sequences.
Results: Replidec uses Naive Bayes classifier combined with alignment-based methods to improve the prediction accuracy in metagenomic data. We test Replidec on viral genomes with known replication cycle and simulated metagenomic sequences. Replidec perform relatively good both in isolated genomes (F1 score: 92.29% ± 0.81; mcc: 89.14% ± 1.22) and simulated metagenomic sequences(F1 score: 87.55% ± 2.12; mcc: 88.23% ± 2.55). Moreover, Replidec can also accurately predict the replication cycle in small viral fragments(∼3000bp). In conclusion, Replidec can achieve the best performance in simulated metagenomic data compared to most prediction softwares including BACPHLIP.},
keywords = {Project 05, WP 1.2 Host prediction},
pubstate = {published},
tppubtype = {article}
}
Motivation: Viruses are the most abundant biological entities on earth. The majority of these entities are bacterial viruses or phages which specifically infect bacteria. Phages can use different replication strategies to invade their hosts including lytic, lysogenic, chronic cycle and pseudolysogeny. While the determination of the replication strategy used by phages is important to explore the phage-bacteria relationships in different ecosystems there are not many tools that can predict this in metagenomic data. In addition, most of the tools available can only predict lytic and lysogenic cycles. To address this issue, we have developed a new software called Replidec to identify three most common phage replication cycles (virulent, temperate, chronic) in viral sequences.
Results: Replidec uses Naive Bayes classifier combined with alignment-based methods to improve the prediction accuracy in metagenomic data. We test Replidec on viral genomes with known replication cycle and simulated metagenomic sequences. Replidec perform relatively good both in isolated genomes (F1 score: 92.29% ± 0.81; mcc: 89.14% ± 1.22) and simulated metagenomic sequences(F1 score: 87.55% ± 2.12; mcc: 88.23% ± 2.55). Moreover, Replidec can also accurately predict the replication cycle in small viral fragments(∼3000bp). In conclusion, Replidec can achieve the best performance in simulated metagenomic data compared to most prediction softwares including BACPHLIP.
Results: Replidec uses Naive Bayes classifier combined with alignment-based methods to improve the prediction accuracy in metagenomic data. We test Replidec on viral genomes with known replication cycle and simulated metagenomic sequences. Replidec perform relatively good both in isolated genomes (F1 score: 92.29% ± 0.81; mcc: 89.14% ± 1.22) and simulated metagenomic sequences(F1 score: 87.55% ± 2.12; mcc: 88.23% ± 2.55). Moreover, Replidec can also accurately predict the replication cycle in small viral fragments(∼3000bp). In conclusion, Replidec can achieve the best performance in simulated metagenomic data compared to most prediction softwares including BACPHLIP.
2021
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.
Abstract | Links | BibTeX | Tags: Project 01, Project 02, Project 03, Project 04, Project 05, Project 06, Project 07, Project 08, Project 09, Project 10, Project 11, Project 12, Project 13, Project 14, Project 15, WP 1.1 Virus identification, WP 1.2 Host prediction, WP 1.3 Virus-host interactions, WP 1.4 Virus regulation, WP 1.5 Virus products, WP 2.1 Microevolution: Virus quasispecies, WP 2.2 Macroevolution: Natural selection of viruses
@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 = {Project 01, Project 02, Project 03, Project 04, Project 05, Project 06, Project 07, Project 08, Project 09, Project 10, Project 11, Project 12, Project 13, Project 14, Project 15, WP 1.1 Virus identification, WP 1.2 Host prediction, WP 1.3 Virus-host interactions, WP 1.4 Virus regulation, WP 1.5 Virus products, WP 2.1 Microevolution: Virus quasispecies, WP 2.2 Macroevolution: Natural selection of viruses},
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.