Review
Biotechnology & Applied Microbiology
Sarah D'Adamo, Richard Kormelink, Dirk Martens, Maria J. Barbosa, Rene H. Wijffels
Summary: Viruses, besides being pathogens, play a crucial role in evolution and can influence host fitness, population dynamics, and community structures. Microalgae biotechnology is a rapidly advancing field that investigates the use of photosynthetic microorganisms for various industries. The study of viruses infecting microalgae has become an important subject of ecological research, and so far, 63 viruses that infect eukaryotic microalgae have been identified and cultured.
BIOTECHNOLOGY ADVANCES
(2022)
Article
Virology
Jean-Marie Alempic, Audrey Lartigue, Artemiy E. E. Goncharov, Guido Grosse, Jens Strauss, Alexey N. N. Tikhonov, Alexander N. N. Fedorov, Olivier Poirot, Matthieu Legendre, Sebastien Santini, Chantal Abergel, Jean-Michel Claverie
Summary: A quarter of the Northern hemisphere is covered by permafrost, releasing organic matter and reviving ancient viruses and microbial cells as it thaws due to climate warming, contributing to greenhouse gas emissions. While previous studies mainly focused on bacteria in permafrost, this study reports the preliminary characterization of 13 new viruses isolated from ancient Siberian permafrost samples, suggesting that zombie viruses are not as rare as previously believed. This highlights the potential public health threat of these revived viruses.
Article
Immunology
Kristine A. Lacek, Benjamin L. Rambo-Martin, Dhwani Batra, Xiao-Yu Zheng, Norman Hassell, Hitoshi Sakaguchi, Thomas Peacock, Natalie Groves, Matthew Keller, Malania M. Wilson, Mili Sheth, Morgan L. Davis, Mark Borroughs, Jonathan Gerhart, Samuel S. Shepard, Peter W. Cook, Justin Lee, David E. Wentworth, John R. Barnes, Rebecca Kondor, Clinton R. Paden
Summary: In order to detect new and changing SARS-CoV-2 variants, this study investigated candidate Delta-Omicron recombinant genomes from the national genomic surveillance conducted by the Centers for Disease Control and Prevention. Laboratory and bioinformatic investigations identified and validated 9 genetically related SARS-CoV-2 viruses with a hybrid Delta-Omicron spike protein.
EMERGING INFECTIOUS DISEASES
(2022)
Article
Environmental Sciences
Warish Ahmed, Aaron Bivins, Paul M. Bertsch, Kyle Bibby, Pradip Gyawali, Samendra P. Sherchan, Stuart L. Simpson, Kevin V. Thomas, Rory Verhagen, Masaaki Kitajima, Jochen F. Mueller, Asja Korajkic
Summary: The study found that 24-hour composite samples offer increased analytical sensitivity and decreased variability compared to 1-hour composite samples when monitoring wastewater, especially for pathogenic viruses with low infection rates within a community. This suggests that 24-hour composite samples are less likely to produce false negative results and erroneous public health information in wastewater-based epidemiology applications.
ENVIRONMENTAL RESEARCH
(2021)
Article
Microbiology
Ruonan Wu, Eric M. Bottos, Vincent G. Danna, James C. Stegen, Janet K. Jansson, Michelle R. Davison
Summary: Arctic permafrost thawing leads to the emergence of RNA viruses that target eukaryotic hosts and pose potential threats to humans, animals, and plants. This study identifies a diverse RNA viral community in thawed permafrost samples, showing distinct compositions compared to other habitats. The detection of potential pathogens highlights the importance of environmental reservoirs for RNA viral pathogens, particularly in the context of the ongoing COVID-19 pandemic. Understanding viral-host interactions and the ecological roles of RNA viruses in thawed permafrost is crucial.
Article
Multidisciplinary Sciences
Christopher Bellas, Thomas Hackl, Marie-Sophie Plakolb, Anna Koslova, Matthias G. Fischer, Ruben Sommaruga
Summary: Eukaryotic genomes contain endogenous viral elements (EVEs) derived from RNA and ssDNA viruses, which are considered genomic fossils. However, the study of EVEs has focused mostly on animals and plants, neglecting protists. This study reveals that protist genomes contain diverse dsDNA viruses, including virophages and Polinton-like viruses, which were hidden due to their repetitive nature. The study suggests that many protist EVEs are intact, actively colonizing hosts across the eukaryotic tree, and may be functional viruses.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Microbiology
Hamid Reza Sodagari, Csaba Varga
Summary: This study evaluated the AMR patterns and temporal trends in commensal E. coli isolated from swine at slaughter in the United States. The results showed a high prevalence of resistance to tetracycline, streptomycin, and ampicillin. Significant increasing temporal trends were observed for several antimicrobials, including amoxicillin-clavulanic acid and ceftriaxone. The increase in antimicrobial resistance over the years is concerning and further studies are needed.
Review
Engineering, Environmental
Yazan Ibrahim, Mariam Ouda, Dana Kadadou, Fawzi Banat, Vincenzo Naddeo, Habiba Alsafar, Ahmed F. Yousef, Damia Barcelo, Shadi W. Hasan
Summary: This review paper discusses the types, concentration, detection, and removal technologies of waterborne enteric viruses found in wastewater. Efforts have been made in using membrane-based and hybrid technologies to effectively eliminate these viruses, but challenges remain in membrane performance and sustainable operation. The advantages, limitations, and future research opportunities of these technologies will also be explored in this review.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2021)
Article
Microbiology
Eniko Feher, Eszter Mihalov-Kovacs, Eszter Kaszab, Yashpal S. Malik, Szilvia Marton, Krisztian Banyai
Summary: This study identified a diversity of CRESS DNA viruses in fecal samples collected from apparently healthy swine herd, with multiple novel CRESS DNA viruses found to infect the swine herd simultaneously. Investigation of the association between presence of CRESS DNA viruses and swine health conditions seems to be justified.
Article
Engineering, Environmental
Ling-Dong Shi, Xiyang Dong, Zongbao Liu, Yuchun Yang, Jih-Gaw Lin, Meng Li, Ji-Dong Gu, Li-Zhong Zhu, He-Ping Zhao
Summary: The diversity of both microorganisms and viruses in activated sludge of wastewater treatment plants plays a crucial role in controlling microbial dynamics and metabolisms. This study reveals the presence of unknown viral genera in activated sludge, indicating an unexplored reservoir for new viruses and viral diversity. The study also shows that viruses can enhance the performance of activated sludge by encoding auxiliary metabolic genes (AMGs) involved in biodegradation, but can also facilitate the spread of antibiotic resistance genes (ARGs) among microorganisms. Overall, this study highlights the mixed blessing of viruses in wastewater treatment plants and their impact on biochemical processes.
Article
Chemistry, Analytical
Bilge Guvenc Tuna, Dilara Buse Durdabak, Meltem Kazak Ercan, Soner Dogan, Murat Kavruk, Ali Dogan Dursun, Serap Demir Tekol, Caner Celik, Veli Cengiz Ozalp
Summary: This study presents a direct and fast detection method for the CoV-2 genome in nose-throat swab samples, without the need for further processing. The method utilizes fluorescein-loaded mesoporous silica nanoparticles with specific gene sequence probes on their surface, which are released upon hybridization with the target viral genome.
Article
Medicine, General & Internal
Orly Termeie, Lawrence Fiedler, Lisa Martinez, Jennifer Foster, Parvathi Perumareddi, Robert S. Levine, Charles H. Hennekens
Summary: This study compared the trends in mortality from alcoholic cirrhosis in the United States between 1999 and 2019 using data from the CDC. The results showed a significant increase in the mortality rate of alcoholic cirrhosis, which may be attributed to heavy alcohol consumption and the obesity epidemic. Further research and intervention are needed to address these alarming trends.
AMERICAN JOURNAL OF MEDICINE
(2022)
Article
Microbiology
Harry T. Child, George Airey, Daniel M. Maloney, Abby Parker, Jonathan Wild, Suzie Mcginley, Nicholas Evens, Jonathan Porter, Kate Templeton, Steve Paterson, Ronny van Aerle, Matthew J. Wade, Aaron R. Jeffries, Irene Bassano
Summary: Wastewater-based epidemiology is a powerful tool for monitoring the emergence and spread of viral pathogens at the population scale. Metagenomic sequencing methods, which are target-agnostic, can detect a wide range of target viruses. Deep shotgun metagenomic sequencing is unable to provide sufficient genome coverage, while hybrid-capture enrichment sequencing and tiled-PCR sequencing have stronger capabilities for detecting and genotyping viruses in wastewater samples.
Article
Virology
Endrya do Socorro Foro Ramos, Geovani de Oliveira Ribeiro, Fabiola Villanova, Flavio Augusto de Padua Milagres, Rafael Brustulin, Emerson Luiz Lima Araujo, Ramendra Pati Pandey, V. Samuel Raj, Xutao Deng, Eric Delwart, Adriana Luchs, Antonio Charlys da Costa, Elcio Leal
Summary: Metagenomics based on NGS was used to characterize the enteric virome of 250 individuals with gastroenteritis in northeastern and northern Brazil. The study revealed common viral sequences associated with GI, as well as emerging human viruses and viral contigs from various sources. This approach proved to be a powerful tool for detecting and characterizing a wide range of viruses in clinical GI samples.
Letter
Medicine, General & Internal
Jemma Alarcon, Moon Kim, Dawn Terashita, Kusha Davar, Jacob M. Garrigues, Jack P. Guccione, Mark G. Evans, Peera Hemarajata, Noah Wald-Dickler, Paul Holtom, Rodrigo Garcia Tome, Lovelyn Anyanwu, Naman K. Shah, Matthew Miller, Todd Smith, Audrey Matheny, Whitni Davidson, Christina L. Hutson, Jonathan Lucas, Odey C. Ukpo, Nicole M. Green, Sharon E. Balter
Summary: A case of mpox-related death in the United States is reported, where the patient had a compromised immune system, and evaluation indicated widespread viral infection.
NEW ENGLAND JOURNAL OF MEDICINE
(2023)
Article
Oceanography
L. E. Timm, H. D. Bracken-Grissom, A. Sosnowski, M. Breitbart, M. Vecchione, H. Judkins
DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS
(2020)
Article
Limnology
Adrienne P. Hollister, Makenzie Kerr, Kema Malki, Eric Muhlbach, Maya Robert, Charles L. Tilney, Mya Breitbart, Katherine A. Hubbard, Kristen N. Buck
LIMNOLOGY AND OCEANOGRAPHY
(2020)
Article
Fisheries
Makenzie Kerr, Jeremy Browning, Eva-Maria Bonnelycke, Yingjun Zhang, Chuanmin Hu, Maickel Armenteros, Steven Murawski, Ernst Peebles, Mya Breitbart
FISHERIES OCEANOGRAPHY
(2020)
Letter
Virology
Mart Krupovic, Arvind Varsani, Darius Kazlauskas, Mya Breitbart, Eric Delwart, Karyna Rosario, Natalya Yutin, Yuri I. Wolf, Balazs Harrach, F. Murilo Zerbini, Valerian V. Dolja, Jens H. Kuhn, Eugene V. Koonin
JOURNAL OF VIROLOGY
(2020)
Article
Microbiology
Kema Malki, Karyna Rosario, Natalie A. Sawaya, Anna J. Szekely, Michael J. Tisza, Mya Breitbart
Article
Engineering, Environmental
Adriana Gonzalez-Fernandez, Erin M. Symonds, Javier F. Gallard-Gongora, Bonnie Mull, Jerzy O. Lukasik, Pablo Rivera Navarro, Andrei Badilla Aguilar, Jayme Peraud, Megan L. Brown, Darner Mora Alvarado, Mya Breitbart, Maryann R. Cairns, Valerie J. Harwood
Summary: The study revealed that microbial concentrations in tropical coastal waters vary by season and tidal stage, with a close relationship between rainfall and pathogen prevalence, which may impact the health risks of beach users.
Article
Biotechnology & Applied Microbiology
Kema Malki, Natalie A. Sawaya, Michael J. Tisza, Felipe H. Coutinho, Karyna Rosario, Anna J. Szekely, Mya Breitbart
Summary: High-magnitude springs fed by the Floridan aquifer system contribute significant amounts of water to rivers, creating unique lotic systems. Little is known about the composition and spatiotemporal variability of prokaryotic and viral communities in these spring systems, but the study found that the springs play a minor role in seeding downstream communities.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Microbiology
Sarah Schmid, Dale Chaput, Mya Breitbart, Rebecca Hines, Samantha Williams, Hunter K. Gossett, Sheila D. Parsi, Rebecca Peterson, Robert A. Whittaker, Angela Tarver, Kathleen M. Scott
Summary: Different complexes have been found to increase intracellular DIC concentrations in various bacteria and archaea, indicating this trait is shared across diverse taxa and physiological backgrounds. Successful expression in E. coli suggests potential for their use in engineered organisms for industrial applications involving CO2 utilization.
JOURNAL OF BACTERIOLOGY
(2021)
Letter
Geosciences, Multidisciplinary
Michele Cooke, Mya Breitbart, Emily Cooperdock, Naomi Levin, Nathan Niemi, Christopher Bell, Liane Stevens, Karen Viskupic
Article
Microbiology
Natalie A. Sawaya, Nava Baran, Shelby Mahank, Arvind Varsani, Debbie Lindell, Mya Breitbart
Summary: Advances in metagenomics have revealed the prevalence of single-stranded DNA phages of the Gokushovirinae subfamily in oceans, but little was known about their abundance and ecological roles. This study used the polony method to quantify these phages in the Gulf of Aqaba, Red Sea, and found that they were most abundant in the upper 40 meters of the water column. The study also suggested that different gokushoviruses infect bacterial hosts that are distributed differently in the water column.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Karyna Rosario, Noemi Van Bogaert, Natalia B. Lopez-Figueroa, Haris Paliogiannis, Mason Kerr, Mya Breitbart
Summary: Research on aquatic plant viruses lags behind their terrestrial counterparts. In this study, viruses associated with freshwater macrophytes were identified using next generation sequencing. Putative plant viruses were detected in asymptomatic vascular plants, indicating that persistent viruses are widespread in macrophytes. The presence of terrestrial plant viruses in submerged macrophytes suggests a potential terrestrial-freshwater plant virus continuum.
Article
Biotechnology & Applied Microbiology
Adriana Gonzalez-Fernandez, Erin M. Symonds, Javier F. Gallard-Gongora, Bonnie Mull, Jerzy O. Lukasik, Pablo Rivera Navarro, Andrei Badilla Aguilar, Jayme Peraud, Darner Mora Alvarado, Allison Cantor, Mya Breitbart, Maryann R. Cairns, Valerie J. Harwood
Summary: Population growth and changing climate are expected to increase human exposure to pathogens in tropical coastal waters. A study conducted in Costa Rican beach found that rivers impacting the beach consistently exceeded the U.S. EPA risk threshold for gastroenteritis, while the ocean samples met the criteria only 13% of the time. Norovirus genogroup I (NoVGI) was the main contributor to the risk, and the risk was greater in the dry season. Quantitative microbial risk assessment (QMRA) that considers seasonal and local variability of water quality contributes to improved beach management.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Mya Breitbart, Makenzie Kerr, Michael J. Schram, Ian Williams, Grace Koziol, Ernst Peebles, Christopher D. Stallings
Summary: A study on the West Florida Shelf used DNA metabarcoding to identify fish eggs from 49 stations. They found 37 different taxa from 4,719 fish eggs, and the distribution of eggs corresponded with known habitat types. Metabarcoding was faster and cheaper than barcoding individual eggs; however, it had limitations in determining absolute taxon proportions and detecting contaminating DNA. The study also reviewed the advantages and disadvantages of using metabarcoding vs individual fish egg barcoding for long-term monitoring programs.
Article
Education, Scientific Disciplines
Makenzie Kerr, Mya Breitbart
JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION
(2021)
Article
Microbiology
Noah Yonas, Paige Boleman, Y. Nguyen, Makenzie Kerr, Kema Malki, Anthony M. Greco, Mya Breitbart
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2020)