PhD Projects » ESR 5: Bacteriophage–host relationships 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 = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@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}

}

@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 = {},

pubstate = {published},

tppubtype = {article}

}