Article
Microbiology
Hans W. Singh, Kaitlin E. Creamer, Alexander B. Chase, Leesa J. Klau, Sheila Podell, Paul R. Jensen
Summary: Microbial polyketide synthase (PKS) genes encode biosynthesis of important natural products. Metagenomic analyses suggest that only a fraction of polyketide biosynthetic potential has been discovered. Type I PKSs (T1PKSs) contribute to this potential and can be classified based on their domain organization. Access to metagenomic data allows assessment of T1PKS biosynthetic diversity. This study detected and classified over 35,000 T1PKS domains from 137 metagenomes, revealing biome-specific distribution patterns and potential for novel polyketide structures.
Article
Biology
Ying-Li Zhou, Paraskevi Mara, Dean Vik, Virginia P. Edgcomb, Matthew B. Sullivan, Yong Wang
Summary: This study investigates the diversity and ecological impact of previously undescribed viruses in the Challenger Deep of the Mariana trench. By collecting sediment samples from different sites in the deep, the researchers identify 1,628 viral operational taxonomic units at the species level. The study reveals a significant variation in viral diversity across the trench, with higher diversity at the bottom-axis sites. These viruses are predicted to infect key prokaryotes involved in carbon and nitrogen cycling in the hadal zone, and they may modulate the metabolic capabilities and stabilize cell membranes of their potential hosts. The findings contribute to our understanding of deep-sea ecology and the functional adaptations of viruses in extreme environments.
COMMUNICATIONS BIOLOGY
(2022)
Article
Genetics & Heredity
Larisa Fedorova, Andrey Khrunin, Gennady Khvorykh, Jan Lim, Nicholas Thornton, Oleh A. Mulyar, Svetlana Limborska, Alexei Fedorov
Summary: Common alleles are more ancient and reflect human evolution. Region-specific alleles were identified, with Africa having the highest number. Genes associated with these alleles were analyzed, particularly those related to the nervous system.
Article
Green & Sustainable Science & Technology
Xiang Li, Zhanwen Cheng, Chenyuan Dang, Miao Zhang, Yan Zheng, Yu Xia
Summary: Activated sludge treatment process effectively removes a large spectrum of microorganisms, but its impact on the entire viral community remains unclear. Research showed that viral removal efficacy in wastewater treatment plants is suboptimal, highlighting potential viral threats in biologically treated domestic wastewater.
ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Jiamin Pan, Likai Ji, Haisheng Wu, Xiaochun Wang, Yan Wang, Yan Wu, Shixing Yang, Quan Shen, Yuwei Liu, Wen Zhang, Keshan Zhang, Tongling Shan
Summary: This study investigated the viral communities of herbivorous mammals in the Northwest Plateau, revealing the diversity and stability of these communities. It provides valuable insights into potentially pathogenic viruses in herbivorous mammals.
Article
Microbiology
Xun Qian, Santosh Gunturu, Jiarong Guo, Benli Chai, James R. Cole, Jie Gu, James M. Tiedje
Summary: The study revealed high diversity and abundance of antibiotic resistance genes in soil across different ecosystems, with multidrug resistance and efflux pump being dominant. Regulatory genes accounted for a portion of resistome abundances in soil, with some non-regulatory ARGs shared by all studied soils. Bacterial community structure was significantly correlated with resistome profile, indicating that variance in resistome profile was mainly driven by the bacterial community composition.
Article
Food Science & Technology
Yang Liu, Leilei Yu, Fengwei Tian, Wei Chen, Qixiao Zhai
Summary: Through a high-resolution meta-analysis of 57 fermented vegetable samples from China, Ireland, the UK, and Germany, we found significant differences in the microbiota composition and functional pathway diversity of fermented vegetables that are correlated with their geographical origins. Our metagenomic analysis also revealed the characteristics of carbohydrate-active enzymes and antibiotic resistance genes in fermented vegetable metagenomes. This study provides new ecological insights and emphasizes the importance of high-resolution metagenomic analysis in studying the fermented food microbiome.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Biochemical Research Methods
Guowei Chen, Xubo Tang, Mang Shi, Yanni Sun
Summary: In this study, we developed VirBot, a simple yet effective RNA virus identification tool based on protein families and adaptive score cutoffs. Compared to seven popular tools for virus identification, VirBot demonstrated high specificity in metagenomic datasets and superior sensitivity in detecting novel RNA viruses on both simulated and real sequencing data.
Article
Biology
Guilhem Sempere, Adrien Petel, Magsen Abbe, Pierre Lefeuvre, Philippe Roumagnac, Frederic Mahe, Gael Baurens, Denis Filloux
Summary: metaXplor is a scalable, distributable, fully web-interfaced application for managing, sharing, and exploring metagenomic data. It offers a flexible data model, supports incremental data feeding, allows for exhaustive content browsing, rapid narrowing to find specific records, and features various interactive data visualization tools.
Article
Gastroenterology & Hepatology
Jinlong Ru, Mohammadali Khan Mirzaei, Jinling Xue, Xue Peng, Li Deng
Summary: ViroProfiler is a computer analysis tool for analyzing shotgun viral metagenomic data. It can be run on a local or cloud computing environment. It uses containerization technology to ensure computational reproducibility and facilitate collaborative research.
Article
Biology
Isobel Grindrod, Stephen J. Martin
Summary: The deadly association between the ecto-parasitic mite and Deformed wing virus has led to the deaths of millions of bee colonies, particularly in the Northern Hemisphere, requiring regular acaricide application for survival. However, an increasing number of bee populations globally have been surviving without mite control methods, showing long-term survival associated with specific traits.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Microbiology
E. Anders Kiledal, Mark Shaw, Shawn W. Polson, Julia A. Maresca
Summary: This article introduces an improved DNA extraction method for concrete, which can efficiently extract DNA and reduce laboratory contamination. DNA extracted by this method was sequenced using the Illumina MiSeq system, revealing a microbial community dominated by halophilic bacteria and archaea in concrete, with enriched functional pathways related to osmotic stress responses. The study demonstrates that metagenomic sequencing can be used to characterize microbial communities in concrete, and older concrete structures may host different microbes compared to recently poured concrete.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Stefanie Widder, Irene Goerzer, Benjamin Friedel, Nina Rahimi, Stefan Schwarz, Peter Jaksch, Sylvia Knapp, Elisabeth Puchhammer-Stoeckl
Summary: This study provides a detailed analysis of virome dynamics after lung transplantation, revealing host, body compartment, and time-specific dependency patterns among viruses. The results also suggest genetic adaptation to the host microenvironment at the level of the virome and support the hypothesis of functional complementarity between Anellovirus groups and other persistent viruses.
Article
Virology
Neelam M. Nathani, Priyanka P. Vatsa, Mayur S. Mahajan, Solly Solomon, Chandrashekar Mootapally
Summary: The study provides insights into the viral communities in deep sediments of the Gulfs of Gujarat, revealing a high diversity of viruses dominated by phages infecting Cyanobacterium, Bacillus, and Vibrio. Most viral sequences belong to double-stranded DNA phages.
Article
Biology
Johan Rollin, Wei Rong, Sebastien Massart
Summary: This article introduces a bioinformatics tool called Cont-ID, which can detect cross-contamination by analyzing the relative abundance and duplication of virus sequencing reads in sequence metagenomic datasets. By using 273 real datasets, including 68 virus species from different hosts and several library preparation protocols, the study demonstrates that Cont-ID can accurately classify viral species detection into true infection or contamination, with an accuracy rate of 91%. This classification increases confidence in the detection results and facilitates the downstream interpretation and confirmation by prioritizing the virus detections that should be confirmed.
Article
Ecology
Elsa Gadoin, Christelle Desnues, Emmanuelle Roque D'Orbcastel, Thierry Bouvier, Jean-Christophe Auguet, Laurent Dagorn, Jean-Luc Moroh, Antoinette Adingra, Yvan Bettarel
Summary: Although tunas represent a significant part of the global fish economy and a major nutritional resource worldwide, their microbiome remains poorly documented. This study analyzed the taxonomic composition of bacterial communities in the gut, skin, and liver of two widely consumed tuna species. The results showed that the composition of the tuna microbiome was independent of fish sex, but varied according to tuna species and sampling site. The study also discovered a unique and diverse bacterial assemblage in the tuna liver, including potential histamine-producing bacteria.
Article
Biochemistry & Molecular Biology
Corinne Biderre-Petit, Jean-Christophe Charvy, Gisele Bronner, Marina Chauvet, Didier Debroas, Helene Gardon, Claire Hennequin, Isabelle Jouan-Dufournel, Anne Mone, Arthur Monjot, Viviane Ravet, Agnes Vellet, Cecile Lepere
Summary: Freshwater is vital for human survival but facing threats from human activities and climate change. To understand the roles of microbial communities in freshwater ecosystems, researchers have developed a comprehensive database containing information on various microbial taxa from freshwater ecosystems worldwide.
MOLECULAR ECOLOGY RESOURCES
(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
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
Virology
Eric Olo Ndela, Simon Roux, Christian Henke, Alexander Sczyrba, Telesphore Sime Ngando, Arvind Varsani, Francois Enault
Summary: Through the analysis of metagenomic data sets from various aquatic ecosystems, we discovered sixteen complete microvirus genomes that are significantly smaller than previously known ones. These microviruses belong to two new subfamilies, named Reekeekeevirinae and Roodoodoovirinae. These small genome microviruses have a lower number of genes and shorter gene length, with fewer overprinted genes compared to phiX174. They exhibit differences in gene content and conserved protein sequences, indicating different strategies used by these related groups of small genome microviruses to complete their lifecycle with limited genes.
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
Microbiology
Naomi E. Gilbert, Gary R. LeCleir, Helena L. Pound, Robert F. Strzepek, Michael J. Ellwood, Benjamin S. Twining, Simon Roux, Philip W. Boyd, Steven W. Wilhelm
Summary: Viruses can impact the abundance, evolution, and metabolism of microorganisms in the ocean, playing a critical role in biogeochemistry and carbon cycles. This study investigates the diversity and activity of giant viruses in the subpolar Southern Ocean and finds that these viruses exhibit depth-dependent structuring and metabolic reprogramming of their hosts under different physicochemical conditions. Additionally, the study shows that iron availability affects the activity of giant viruses. These findings enhance our understanding of how the water column and environmental factors shape the viral community in the Southern Ocean.
Article
Multidisciplinary Sciences
Anthony Duncan, Kerrie Barry, Chris Daum, Emiley Eloe-Fadrosh, Simon Roux, Katrin Schmidt, Susannah G. Tringe, Klaus U. Valentin, Neha Varghese, Asaf Salamov, Igor Grigoriev, Richard M. Leggett, Vincent Moulton, Thomas Mock
Summary: This article presents metagenome-assembled genomes (MAGs) for both eukaryotic and prokaryotic organisms from the Arctic and Atlantic oceans, along with gene prediction and functional annotation for MAGs from both domains. These data provide draft genomes for uncultured marine microbes, including some of the first MAGs for polar eukaryotes, and can be used for genomic comparisons between environments.
Editorial Material
Ecology
Simon Roux, Jennifer R. Brum
Article
Environmental Sciences
Jeanne Naudet, Emmanuelle Roque d'Orbcastel, Thierry Bouvier, Sylvain Godreuil, Sabrina Dyall, Simon Bouvy, Fabien Rieuvilleneuve, Claudia Ximena Restrepo-Ortiz, Yvan Bettarel, Jean-Christophe Auguet
Summary: This study reveals that macroplastics commonly found in aquaculture can serve as a habitat for bacterial biofilm, including potential human pathogens and antibiotic-resistant bacteria. The presence of pathogenic and resistant bacteria was significantly higher in plastic samples compared to environmental samples, posing a potential threat to the health of farmed fish and human consumers.
MARINE POLLUTION BULLETIN
(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)
Review
Microbiology
David T. Jones, Frederik Schulz, Simon Roux, Steven D. Brown
Summary: The review provides an overview of the current status and history of solvent-producing clostridia, as well as the recent interest in biobutanol production. It discusses the availability of genomic data for these species and the analysis facilitated by this expanded database. The common features, molecular taxonomy, and phylogeny of solvent-producing clostridia are evaluated, as well as the presence of prophages and R-type tailocins in these organisms.
Article
Environmental Sciences
Azibar Rodriguez-Iruretagoiena, Ainara Gredilla, Silvia Fdez-Ortiz de Vallejuelo, Gorka Arana, Maite Meaurio, Juan Manuel Madariaga, Jean Christophe Auguet, Aridane Gonzalez Gonzalez, Oleg S. Pokrovsky, Luis Camarero, Alberto de Diego
Summary: This study aimed to assess the impact of human activity on 18 high-altitude Pyrenean lakes located on both sides of the France-Spain frontier. Sediment cores were collected in summer 2013 and analyzed for the concentration of 24 elements. The results showed that geographical position and lithogenic features influenced the trapping of pollutants in each lake basin. The majority of the lakes exhibited enrichment factor values above 2 for at least one element, indicating historical anthropogenic inputs. The data also highlighted the natural origin of some elements and the significant contribution of mining activities as the main historical source of pollution.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)