Article
Virology
Zhenqi Wu, Ting Chu, Yijian Sheng, Yongxin Yu, Yongjie Wang
Summary: Virophages, small double-stranded DNA viruses that rely on the viral factory of large host viruses, are found abundantly in global marine environments. Analysis of the Global Ocean Viromes 2.0 dataset revealed 94 virophage sequences, including 8 complete genomes. Additionally, 45 large virus sequences were identified, possibly involved in cell-virus-virophage trisome relationships.
Article
Fisheries
Sivasankar Panchavarnam, Riji John Kollanoor, Rosalind George Mulloorpeedikayil, Mohamed Mansoor Mohaideenpitchai, Magesh Kumar Palraj, Selvamagheswaran Muthumariyapan
Summary: An experimental recombinant major capsid protein vaccine was developed and tested for its efficacy in marine ornamental fish. The results showed that the vaccine provided only marginal protection against the targeted virus.
FISH & SHELLFISH IMMUNOLOGY
(2023)
Article
Microbiology
Hannah-Marie Martiny, Patrick Munk, Christian Brinch, Judit Szarvas, Frank M. Aarestrup, Thomas Nordahl Petersen
Summary: This study presents a large-scale metagenomic analysis of sequencing reads from over 200,000 samples to investigate the dissemination and emergence of mobilized colistin resistance genes. The results show that the distribution of gene variants depends on sampling source and location, and new subvariants can emerge in specific environments. The study highlights the importance of sharing genomic data for monitoring antimicrobial resistance.
Article
Microbiology
Frederik Teudt, Saria Otani, Frank M. Aarestrup
Summary: This study investigates the dynamics of sewage plasmidomes globally and finds that plasmid-backbone gene combinations are more prevalent in European sewage, with Acinetobacter being the dominant host due to selective pressure for macrolide resistance genes. The presence of macrolide resistance genes in Firmicutes and Acinetobacter hosts highlights a potential reservoir for antibiotic resistance among pathogens worldwide.
Article
Microbiology
Liang Shen, Yongqin Liu, Michelle A. Allen, Baiqing Xu, Ninglian Wang, Timothy J. Williams, Feng Wang, Yuguang Zhou, Qing Liu, Ricardo Cavicchioli
Summary: The study revealed a new bacterial clade, Group C, with superior ability to grow at -1 degrees C and distinct genomic traits in comparison to non-polar or alpine Group A. Metagenomic analysis showed an over-representation of Group C in Canadian permafrost communities and an under-representation of Group A in polar and alpine samples, indicating niche adaptation and environmental temperature responses. The findings suggest the potential value of defining genomic markers for specific taxa in monitoring cold environments and understanding environmental changes.
Article
Geology
J. L. Dickson, M. P. Lamb, R. M. E. Williams, A. T. Hayden, W. W. Fischer
Summary: This study conducted the first systematic global survey of fluvial ridges on Mars using data from the NASA Context Camera, revealing their widespread distribution across the southern highlands and intercrater plains, representing ancient fluvial deposits that may offer a rich archive of Mars history, including fluvial activity on early Mars.
Article
Microbiology
Mingji Lu, Dominik Schneider, Rolf Daniel
Summary: This study explores novel and/or extremophilic lipolytic enzymes by analyzing microbial consortia in composts through function-driven and sequence-based metagenomic approaches. The results reveal the diversity and distribution of lipolytic genes in metagenomes of various habitats, driven by ecological factors.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Yisong Li, Yeshun Fan, Xiaofang Ma, Ying Wang, Jie Liu
Summary: Sialic acids are important nine-carbon amino sugars found in humans and other higher metazoans, playing significant roles in cell interactions and other cell functions. Our study revealed that microbial sialic acid catabolism (SAC) exists in non-host associated environments globally, although less frequently than in mammal hosts. We also found that the ecological significance and taxonomic diversity of microbial SAC have been largely underestimated.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Karen L. Bell, Katherine J. Turo, Abigail Lowe, Kevin Nota, Alexander Keller, Francisco Encinas-Viso, Laura Parducci, Rodney T. Richardson, Richard M. Leggett, Berry J. Brosi, Kevin S. Burgess, Yoshihisa Suyama, Natasha de Vere
Summary: Anthropogenic activities are causing global changes in the environment, leading to restructuring and decline of plant-pollinator communities. To understand and manage these impacts, it is necessary to characterize plant-pollinator communities across different habitats using rapid and high-throughput methods like pollen DNA metabarcoding. This technique is advantageous for understanding complex ecological networks and can be used to assess plant-pollinator interactions, monitor ecosystem change, and model the distribution of allergenic pollen.
Article
Public, Environmental & Occupational Health
Jurgen P. Moonen, Michelle Schinkel, Tom van der Most, Pascal Miesen, Ronald P. van Rij
Summary: Mosquitoes are important vectors for infectious viral diseases, and understanding the mosquito virome is crucial for studying disease emergence and outbreak dynamics. A searchable database of insect-specific viruses associated with mosquitoes has been constructed, providing valuable information on their global distribution and the challenges of integrating virome data.
Article
Virology
Xiaojing Hong, Liang Xue, Junshan Gao, Yueting Jiang, Xiaoxia Kou
Summary: The study reveals the coevolution of the minor capsid protein VP2 with the major capsid protein VP1 of GII.4 noroviruses over the past 50 years, highlighting their interactions and the non-random nature of VP2 variation.
Article
Ecology
Se Hyeon Jang
Summary: This study used DNA metabarcoding to reveal the hidden biodiversity and global distribution of suessiacean dinoflagellates, and discovered at least five new phylogenetic groups and three new individual species within the family. These findings highlight the significance of suessiacean dinoflagellates in global aquatic ecosystems.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Microbiology
Perrine Florent, Henry-Michel Cauchie, Malte Herold, Stephan Jacquet, Leslie Ogorzaly
Summary: This study examines the influence of abiotic and biotic factors on the distribution of DNA bacteriophages in soil. The results suggest that pH and calcium cations play a significant role in shaping the diversity of bacteriophage populations, and there are important relationships between bacteriophages and bacterial communities.
Article
Biology
Lucie Mahaut, Samuel Pironon, Jean-Yves Barnagaud, Francois Bretagnolle, Colin K. K. Khoury, Zia Mehrabi, Ruben Milla, Charlotte Phillips, Loren H. H. Rieseberg, Cyrille Violle, Delphine Renard
Summary: Humans have moved crops from their regions of origin to new locations, causing differences between crop distributions and their climate suitability. These differences are important for developing agricultural strategies to adapt to climate change. Study findings show that high-income regions have a better match between crop distribution and climate suitability.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Computer Science, Information Systems
Zhenfei Wang, Hongju Wang
Summary: This paper introduces a novel oversampling method, GDDSYN, which tackles imbalanced learning by optimizing sample selection criteria and utilizing clustering information to generate synthetic samples. Extensively evaluated on artificial and real-world datasets, it is found that using artificial data generated by GDDSYN can achieve better or comparable assessment metrics compared to other existing methods.
Article
Biochemical Research Methods
Chunyu Zhao, Boris Dimitrov, Miriam Goldman, Stephen Nayfach, Katherine S. Pollard
Summary: The Metagenomic Intra-Species Diversity Analysis System (MIDAS) is a scalable metagenomic pipeline that identifies single nucleotide variants (SNVs) and gene copy number variants in microbial populations. MIDAS2 addresses computational challenges of large reference genome databases and allows custom database building and improved SNV accuracy with paired-end reads. This fast and scalable improvement of the MIDAS pipeline enables efficient genotyping of thousands of metagenomic samples.
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
Geriatrics & Gerontology
Maria G. Grammatikopoulou, Efstathios Skoufas, Spyridon Kanellakis, Despina Sanoudou, Georgios A. Pavlopoulos, Aristides G. Eliopoulos, Kalliopi K. Gkouskou
Summary: Undeniably, there is a significant variation in biological age among individuals with similar chronological age. Through deep multi-omic profiling, researchers have identified distinct aging phenotypes known as 'ageotypes'. This research has provided valuable insights into the molecular mechanisms underlying aging and has led to potential opportunities for nutritional interventions to slow down the aging process.
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
Biochemistry & Molecular Biology
Simon Roux, Matthias G. Fischer, Thomas Hackl, Laura A. Katz, Frederik Schulz, Natalya Yutin
Summary: Virophages are small dsDNA viruses that hijack the machinery of giant viruses during co-infection and play a unique role in the viral world. However, the lack of clarity in nomenclature and taxonomy has hindered further studies on virophages and related viruses. In this study, we propose delineation criteria and classification methods for virophages based on comparative genomics and phylogenetic analysis, establishing a taxonomic framework for this group of viruses. This classification provides a necessary first step for future research in this field.
Article
Biochemistry & Molecular Biology
Simon E. Roux, Antonio Pedro Camargo, Felipe H. Coutinho, Shareef M. Dabdoub, Bas E. Dutilh, Stephen Nayfach, Andrew Tritt
Summary: The extraordinary diversity of viruses infecting bacteria and archaea can be studied through metagenomics. However, metagenome-derived viral sequences lack key information about host association. We introduce iPHoP, a framework that integrates multiple methods to predict host taxonomy for a range of uncultivated viruses, while maintaining a low false discovery rate. Using a large dataset from the IMG/VR database, iPHoP shows promise in providing extensive host prediction for uncultivated viruses.
Article
Biochemical Research Methods
Zhou Jason Shi, Stephen Nayfach, Katherine S. Pollard
Summary: This protocol describes a computational pipeline for fast and accurate SNP genotyping using metagenomic data, which includes generating a SNP catalog, extracting unique SNP-covering k-mer sequences, and performing metagenotyping to achieve strain-level quantification.
Editorial Material
Ecology
Simon Roux, Jennifer R. Brum
Article
Biochemistry & Molecular Biology
Fotis A. Baltoumas, Evangelos Karatzas, Sirui Liu, Sergey Ovchinnikov, Yorgos Sofianatos, I-Min Chen, Nikos C. Kyrpides, Georgios A. Pavlopoulos
Summary: NMPFamsDB is a database of metagenome- and metatranscriptome-derived protein families that do not have hits to proteins of reference genomes or Pfam domains. It provides useful information such as sequence alignments, taxonomic information, structure predictions, and 3D structure models, and significantly expands the understanding of known protein sequence clusters.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Antonio Pedro Camargo, Lee Call, Simon Roux, Stephen Nayfach, Marcel Huntemann, Krishnaveni Palaniappan, Anna Ratner, Ken Chu, Supratim Mukherjeep, T. B. K. Reddy, I-Min A. Chen, Natalia N. Ivanova, Emiley A. Eloe-Fadrosh, Tanja Woyke, David A. Baltrus, Salvador Castaneda-Barba, Fernando de la Cruz, Barbara E. Funnell, James P. J. Hall, Aindrila Mukhopadhyay, Eduardo P. C. Rocha, Thibault Stalder, Eva Top, Nikos C. Kyrpides
Summary: This study introduces the IMG/PR database, which collects a large number of plasmid sequences from various microbiome samples and provides rich metadata and multiple browsing methods.
NUCLEIC ACIDS RESEARCH
(2023)
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)