Article
Virology
Bas E. Dutilh, Arvind Varsani, Yigang Tong, Peter Simmonds, Sead Sabanadzovic, Luisa Rubino, Simon Roux, Alejandro Reyes Munoz, Cedric Lood, Elliot J. Lefkowitz, Jens H. Kuhn, Mart Krupovic, Robert A. Edwards, J. Rodney Brister, Evelien M. Adriaenssens, Matthew B. Sullivan
Summary: The development of virus taxonomy relies on advances in metagenomic analysis and other technologies, which have brought a wealth of previously unknown virus sequence data and provided unprecedented insights into the vastness of the virosphere. Properly classifying viruses is crucial to understanding the diversity of viruses, and the inclusion of uncultivated viruses has already improved this process.
CURRENT OPINION IN VIROLOGY
(2021)
Article
Biochemical Research Methods
Florian Mock, Adrian Viehweger, Emanuel Barth, Manja Marz
Summary: Zoonosis, the transmission of infections from animals to humans, is a global issue that requires accurate prediction of the viral host to prevent further spread. A new deep learning approach based on viral genome sequence shows high accuracy in predicting the host of viruses, even with limited sequences and unbalanced data.
Article
Medicine, General & Internal
Muhammad Nabeel Asim, Ahtisham Fazeel, Muhammad Ali Ibrahim, Andreas Dengel, Sheraz Ahmed
Summary: The research aims to develop a robust meta predictor for accurately predicting protein-protein interactions between viral pathogens and host organisms. The proposed predictor utilizes two encoding methods and a feature agglomeration method, achieving excellent performance on multiple benchmark datasets.
FRONTIERS IN MEDICINE
(2022)
Article
Virology
Clement Coclet, Simon Roux
Summary: Bacterial communities play critical roles in Earth's biomes, influenced by viruses like bacteriophages. Metagenomics approaches have enabled exploration of phage genomic diversity, but a major challenge is the lack of direct host information. Various methods and experimental assays are being used to validate and refine predictions for uncultivated phages.
CURRENT OPINION IN VIROLOGY
(2021)
Review
Microbiology
Chonghui Xu, Jizheng Chen, Xinwen Chen
Summary: Hepatitis viruses are the primary causative agents of hepatitis and pose a major public health issue globally. The host innate immune system acts as the first line of defense against these viruses. However, hepatitis viruses evade host immune surveillance through various strategies, compromising the innate immune response and creating a favorable environment for viral replication.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Haoran Ma, Tin Wee Tan, Kenneth Hon Kim Ban
Summary: This study developed a pipeline that combines a multi-task learning model and Bayesian ranking approach to accurately identify and rank human viruses with divergent sequences. By incorporating genomic region assignment and Bayesian methodology, this pipeline improves the accuracy and sensitivity of taxonomic assignment from sequence data.
BMC BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Kelsey M. Haas, Michael J. Mcgregor, Mehdi Bouhaddou, Benjamin J. Polacco, Eun-Young Kim, Thong T. Nguyen, Billy W. Newton, Matthew Urbanowski, Heejin Kim, Michael A. P. Williams, Veronica V. Rezelj, Alexandra Hardy, Andrea Fossati, Erica J. Stevenson, Ellie Sukerman, Tiffany Kim, Sudhir Penugonda, Elena Moreno, Hannes Braberg, Yuan Zhou, Giorgi Metreveli, Bhavya Harjai, Tia A. Tummino, James E. Melnyk, Margaret Soucheray, Jyoti Batra, Lars Pache, Laura Martin-Sancho, Jared Carlson-Stevermer, Alexander S. Jureka, Christopher F. Basler, Kevan M. Shokat, Brian K. Shoichet, Leah P. Shriver, Jeffrey R. Johnson, Megan L. Shaw, Sumit K. Chanda, Dan M. Roden, Tonia C. Carter, Leah C. Kottyan, Rex L. Chisholm, Jennifer A. Pacheco, Maureen E. Smith, Steven J. Schrodi, Randy A. Albrecht, Marco Vignuzzi, Lorena Zuliani-Alvarez, Danielle L. Swaney, Manon Eckhardt, Steven M. Wolinsky, Kris M. White, Judd F. Hultquist, Robyn M. Kaake, Adolfo Garcia-Sastre, Nevan J. Krogan
Summary: This study provides a comprehensive network model of IAV infection in human cells, identifying functional host targets for pan-viral HDT. Key host proteins essential for IAV infection are revealed, and gene variants associated with severe influenza are discovered. Moreover, compounds targeting identified host factors suppress IAV replication and exhibit broad antiviral activity across influenza and coronavirus families.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Ian N. Boys, Alex G. Johnson, Meghan R. Quinlan, Philip J. Kranzusch, Nels C. Elde
Summary: Viruses can acquire host genes through horizontal transfer and use them to manipulate host biology during infections. In this study, structural homology modeling was used to compare vaccinia virus proteins with metazoan proteomes. The researchers identified a homolog of gasdermins, proteins involved in cell death, as well as a fusion protein combining a Bcl-2-related fold with a pyrin domain. These findings highlight the power of structural homology screens in uncovering unique protein combinations captured by viruses from host genes.
Article
Biology
Congyu Lu, Zheng Zhang, Zena Cai, Zhaozhong Zhu, Ye Qiu, Aiping Wu, Taijiao Jiang, Heping Zheng, Yousong Peng
Summary: This study focuses on predicting hosts for prokaryotic viruses, introducing a Gaussian model software tool that outperforms previous computational methods, facilitating the rapid identification of hosts for newly identified prokaryotic viruses.
Article
Automation & Control Systems
Talha Burak Alakus, Ibrahim Turkoglu
Summary: This study predicted viral-host interactions between SARS-CoV-2 virus and human proteins using computational-based approaches. Protein sequences were converted into numerical expressions and a deep learning model was designed for classification. The entropy-based method showed the best performance, followed by the Z-scale method.
CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS
(2022)
Article
Computer Science, Interdisciplinary Applications
Pravin Narayan Kathavate
Summary: This research introduces a unique viral host prediction method using genomic datasets, including preprocessing, feature extraction, and prediction phase. The raw genomic datasets are preprocessed and various statistical features are extracted. The SVM, NN, RF, and CNN classifiers are then used for prediction, with an optimized CNN fine-tuned using the AFPA algorithm to increase accuracy.
ADVANCES IN ENGINEERING SOFTWARE
(2023)
Article
Multidisciplinary Sciences
Lulu Li, Hehong Zhang, Changhai Chen, Haijian Huang, Xiaoxiang Tan, Zhongyan Wei, Junmin Li, Fei Yan, Chuanxi Zhang, Jianping Chen, Zongtao Sun
Summary: Plant viruses use transcriptional repressors to interfere with the jasmonic acid signaling pathway in plants, promoting infection and increasing feeding by insect vectors. These strategies have independently evolved in different plant RNA viruses, revealing a common feature of plant viruses in favoring viral pathogenicity and transmission.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Virology
Shanshan Zhao, Yuansheng Wu, Jianguo Wu
Summary: Research has shown that virus-derived small-interfering RNAs, host microRNAs, and phytohormones play important roles in regulating antiviral responses in rice plants. The interactions between viral virulence proteins and host susceptibility factors shape the ongoing arms race between viruses and rice.
CURRENT OPINION IN VIROLOGY
(2021)
Article
Microbiology
Khyati Girdhar, Amaya Powis, Amol Raisingani, Martina Chrudinova, Ruixu Huang, Tu Tran, Kaan Sevgi, Yusuf Dogus Dogru, Emrah Altindis
Summary: Viral infections manipulate host metabolic pathways to increase replication and mimic host hormones to affect the endocrine system. These mechanisms create a multidimensional network of interactions between host and viral proteins.
ANNUAL REVIEW OF VIROLOGY, VOL 8
(2021)
Article
Biology
Ujjwal Neogi, Nazif Elaldi, Sofia Appelberg, Anoop Ambikan, Emma Kennedy, Stuart Dowall, Binnur K. Bagci, Soham Gupta, Jimmy E. Rodriguez, Sara Svensson-Akusjarvi, Vanessa Monteil, Akos Vegvari, Rui Benfeitas, Akhil Banerjea, Friedemann Weber, Roger Hewson, Ali Mirazimi
Summary: Through system biology analysis of CCHF patients and cell infection models, this study found that CCHFV infection causes host metabolic reprogramming and negative coordination with biological signaling systems. Blocking key metabolic pathways can inhibit viral replication. Interferon-mediated antiviral mechanisms play an important role at the system level and during viral replication.
Article
Ecology
Robert M. Bowers, Stephen Nayfach, Frederik Schulz, Sean P. Jungbluth, Ilona A. Ruhl, Andriy Sheremet, Janey Lee, Danielle Goudeau, Emiley A. Eloe-Fadrosh, Ramunas Stepanauskas, Rex R. Malmstrom, Nikos C. Kyrpides, Peter F. Dunfield, Tanja Woyke
Summary: Advancements in single-cell genomics have enabled rapid and affordable sequencing of microbial communities, providing a comprehensive snapshot of community composition and function. This approach also allows for the direct linkage of mobile elements to hosts and analysis of population heterogeneity among dominant community members.
Article
Biochemistry & Molecular Biology
William B. Andreopoulos, Alexander M. Geller, Miriam Lucke, Jan Balewski, Alicia Clum, Natalia N. Ivanova, Asaf Levy
Summary: Plasmids are mobile genetic elements that play a key role in microbial ecology and evolution by mediating horizontal transfer of important genes. Deeplasmid is a deep learning tool that accurately identifies plasmids from bacterial chromosomes. It can predict the presence of novel plasmids with high reliability, demonstrating its ability to detect new genetic elements.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Agronomy
Pilar Martinez-Hidalgo, Ethan A. Humm, David W. Still, Baochen Shi, Matteo Pellegrini, Gabriela de la Roca, Esteban Veliz, Maskit Maymon, Pierrick Bru, Marcel Huntemann, Alicia Clum, Krishnaveni Palaniappan, Neha Varghese, Supratim Mukherjee, T. B. K. Reddy, Chris Daum, Natalia N. Ivanova, Nikos C. Kyrpides, Nicole Shapiro, Emiley A. Eloe-Fadrosh, Ann M. Hirsch
Summary: By studying the legume nodule microbiome, researchers were able to identify potential Plant Growth-Promoting Bacteria from Medicago nodules. They isolated and characterized 51 bacterial strains, including Bacillus and Micromonospora, which showed growth-promoting activities in planta. The comparison of biodiversity between undomesticated and cultivated Medicago roots and nodules highlighted the potential of these microbes for sustainable agriculture.
Article
Biochemistry & Molecular Biology
Brayon J. Fremin, Nikos C. Kyrpides
Summary: In this study, a large-scale comparative genomics approach was used to predict 156 novel candidate structured RNAs from 36,111 CRISPR-Cas systems, some of which overlapped with coding genes. This highlights the importance of expanding the search windows in coding regions for the identification of novel structured RNAs.
Article
Microbiology
Bertrand Eardly, Wan Adnawani Meor Osman, Julie Ardley, Jaco Zandberg, Margaret Gollagher, Peter van Berkum, Patrick Elia, Dora Marinova, Rekha Seshadri, T. B. K. Reddy, Natalia Ivanova, Amrita Pati, Tanja Woyke, Nikos Kyrpides, Matthys Loedolff, Damian W. Laird, Wayne Reeve
Summary: The study identified the genome features of R. favelukesii OR191 important for symbiotic interactions with Medicago and Phaseolus vulgaris, including acid adaptation loci, Nod factor synthesis genes, and nitrogen fixation genes. These findings provide insights into the genetic basis of nodulation requirements and symbiotic effectiveness with different hosts.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Ecology
Naihao Ye, Wentao Han, Andrew Toseland, Yitao Wang, Xiao Fan, Dong Xu, Cock van Oosterhout, Igor Grigoriev, Alessandro Tagliabue, Jian Zhang, Yan Zhang, Jian Ma, Huan Qiu, Youxun Li, Xiaowen Zhang, Thomas Mock
Summary: This study reveals that polar microalgae have a higher demand for zinc due to elevated cellular levels of zinc-binding proteins. Zinc plays an important role in supporting photosynthetic growth in eukaryotic polar phytoplankton, which is critical for algal colonization of low-temperature polar oceans.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Supratim Mukherjee, Dimitri Stamatis, Cindy Tianqing Li, Galina Ovchinnikova, Jon Bertsch, Jagadish Chandrabose Sundaramurthi, Mahathi Kandimalla, Paul A. Nicolopoulos, Alessandro Favognano, I-Min A. Chen, Nikos C. Kyrpides, T. B. K. Reddy
Summary: The Genomes OnLine Database (GOLD) continues to serve as a flagship genomic metadata repository, providing freely available projects and metadata for large-scale comparative genomics analysis. New features and components have been added in the latest GOLD v.9 version.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Benjamin D. Lee, Uri Neri, Simon Roux, Yuri I. Wolf, Antonio Pedro Camargo, Mart Krupovic, Peter Simmonds, Nikos Kyrpides, Uri Gophna, Valerian V. Dolja, Eugene V. Koonin
Summary: We developed a computational pipeline to identify viroid-like cccRNAs and found a 5-fold increase in the number of identified elements compared to previous studies. The presence of viroid-like cccRNAs in diverse transcriptomes and ecosystems suggests that their host range is broader than currently known.
Article
Ecology
Antonio P. Camargo, Rafael S. C. de Souza, Juliana Jose, Isabel R. Gerhardt, Ricardo A. Dante, Supratim Mukherjee, Marcel Huntemann, Nikos C. Kyrpides, Marcelo F. Carazzolle, Paulo Arruda
Summary: The grassland ecosystem of Brazilian campos rupestres has low concentrations of phosphorus and nitrogen, yet supports a high plant diversity. This study explores the taxonomic profile and functional potential of microbial communities associated with two plant species of the campos rupestres. The results show that the soil and rock communities associated with these plants share a core group of efficient colonizers enriched in certain bacterial families. The microbial populations associated with plant roots have a genetic repertoire for organic compound intake, phosphorus and nitrogen turnover, highlighting their role in nutrient availability.
Article
Biochemistry & Molecular Biology
Antonio Pedro Camargo, Stephen Nayfach, I-Min A. Chen, Krishnaveni Palaniappan, Anna Ratner, Ken Chu, Stephan J. Ritter, T. B. K. Reddy, Supratim Mukherjee, Frederik Schulz, Lee Call, Russell Y. Neches, Tanja Woyke, Natalia N. Ivanova, Emiley A. Eloe-Fadrosh, Nikos C. Kyrpides, Simon Roux
Summary: Viruses play critical roles in all microbiomes and their genomic diversity and impacts on biological processes are extensively explored through metagenomics. IMG/VR is a platform providing access to a large collection of viral sequences along with functional annotation and metadata. The latest version, IMG/VR v4, contains over 15 million virus genomes and genome fragments.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
I-Min A. Chen, Ken Chu, Krishnaveni Palaniappan, Anna Ratner, Jinghua Huang, Marcel Huntemann, Patrick Hajek, Stephan J. Ritter, Cody Webb, Dongying Wu, Neha J. Varghese, T. B. K. Reddy, Supratim Mukherjee, Galina Ovchinnikova, Matt Nolan, Rekha Seshadri, Simon Roux, Axel Visel, Tanja Woyke, Emiley A. Eloe-Fadrosh, Nikos C. Kyrpides, Natalia N. Ivanova
Summary: The Integrated Microbial Genomes & Microbiomes system (IMG/M) at the Department of Energy Joint Genome Institute (JGI) provides support for comparative analysis of various genomes, metagenomes, and metatranscriptomes. It includes datasets from JGI, as well as imported datasets from public sources and user-submitted datasets. In recent years, efforts have been made to improve annotation pipeline, upgrade reference database versions, and add new analysis functionalities.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Irene Garcia, Bessem Chouaia, Merce Llabres, Marta Simeoni
Summary: Metabolism is a complex network structure composed of interconnected chemical reactions. An abstract metabolic network, represented by metabolic pathways as nodes and shared compounds as edges, is a suitable model for large-scale comparison of organisms' metabolism. By using graph kernel methods, pairwise comparisons of abstract metabolic networks show that they can discriminate macro evolutionary events and capture key steps in metabolism evolution.
Article
Mathematical & Computational Biology
Supratim Mukherjee, Galina Ovchinnikova, Dimitri Stamatis, Cindy Tianqing Li, I-Min A. Chen, Nikos C. Kyrpides, T. B. K. Reddy
Summary: The power of next-generation sequencing has led to a massive increase in projects aiming to understand the diversity of complex microbial environments. However, the lack of standardized reporting standards for microbiome data and samples poses a challenge for follow-up studies. The Genomes OnLine Database (GOLD) has developed a standardized naming system for microbiome samples to address this issue and has continued to enrich the research community with well-curated and understandable names for metagenomes and metatranscriptomes. This naming system should be adopted as a best practice to improve the interoperability and reusability of microbiome data.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)
Article
Cell Biology
Rekha Seshadri, Simon Roux, Katharina J. Huber, Dongying Wu, Sora Yu, Dan Udwary, Lee Call, Stephen Nayfach, Richard L. Hahnke, Rudiger Pukall, James R. White, Neha J. Varghese, Cody Webb, Krishnaveni Palaniappan, Lorenz C. Reimer, Joaquim Sarda, Jonathon Bertsch, Supratim Mukherjee, T. B. K. Reddy, Patrick P. Hajek, Marcel Huntemann, I-Min A. Chen, Alex Spunde, Alicia Clum, Nicole Shapiro, Zong-Yen Wu, Zhiying Zhao, Yuguang Zhou, Lyudmila Evtushenko, Sofie Thijs, Vincent Stevens, Emiley A. Eloe-Fadrosh, Nigel J. Mouncey, Yasuo Yoshikuni, William B. Whitman, Hans-Peter Klenk, Tanja Woyke, Markus Goeker, Nikos C. Kyrpides, Natalia N. Ivanova
Summary: The study presents a comprehensive analysis of actinobacterial diversity, showing that only a small portion of this diversity is represented by sequenced genomes. The comparison of gene functions reveals novel determinants of host-microbe interaction and environment-specific adaptations. The analysis of biosynthetic gene clusters highlights the role of horizontal gene transfer and gene loss in shaping secondary metabolite repertoire.