Article
Microbiology
German V. Roev, Nadezhda I. Borisova, Nadezhda V. Chistyakova, Matvey R. Agletdinov, Vasily G. Akimkin, Kamil Khafizov
Summary: Next-generation sequencing technologies have transformed virology by enabling complete viral genome sequencing, metagenomic studies, and identification of new viral pathogens. However, metagenomic sequencing faces challenges in data analysis and identifying novel viruses using traditional homology-based strategies. This study used advanced computational methods and experimental strategies to analyze bat feces from different Russian cities and identified a diverse range of viral pathogens.
Review
Biochemistry & Molecular Biology
Yu Shi, Guoping Wang, Harry Cheuk-Hay Lau, Jun Yu
Summary: Whole genome metagenomic sequencing is a powerful technology that allows the identification of all genes from different organisms in a complex sample. However, the presence of excessive host DNA poses a challenge in metagenomic studies, and various methods have been developed to remove host DNA and improve microbial detection sensitivity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Virology
Rachel L. Tulloch, Karan Kim, Chisha Sikazwe, Alice Michie, Rebecca Burrell, Edward C. Holmes, Dominic E. Dwyer, Philip N. Britton, Jen Kok, John-Sebastian Eden
Summary: The RAPIDprep assay is a simple and fast protocol for diagnosing infections within 24 hours of sample collection by sequencing ribosomal RNA-depleted total RNA. It effectively depletes human and microbial rRNA and amplifies genomic yield without the need for nucleic acid quantification or quality assessment. This assay can detect known and undiagnosed pathogens, providing valuable information for molecular epidemiological investigations and vaccine design.
Article
Mathematics, Applied
Ashaq Hussain Bhat, Tu N. Nguyen, Korhan Cengiz, Puniethaa Prabhu
Summary: The HBEA clustering algorithm uses exact pairwise global alignment algorithm to improve cluster quality and extract cluster representatives. Experimental investigation showed that HBEA produces better operational taxonomic unit (OTU) clusters and computational complexity than other algorithms.
MATHEMATICAL METHODS IN THE APPLIED SCIENCES
(2021)
Article
Microbiology
Coralie Bouchiat, Christophe Ginevra, Yvonne Benito, Tiphaine Gaillard, Helene Salord, Olivier Dauwalder, Frederic Laurent, Francois Vandenesch
Summary: The study evaluates the performance of Nanopore-based 16S rRNA metagenomic approach as a diagnostic tool for bacterial infections in clinical laboratories. The method demonstrates high sensitivity and accurate bacterial identification. Cost optimization is achieved by using Flongle flow cells.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Immunology
Yawei Fu, Hu Gao, Xiaohong Hou, Yue Chen, Kang Xu
Summary: The study showed that IPA has preventive effects on DSS-induced colitis in mice, alleviating growth performance decrease and intestinal damage while enhancing immunity. This effect is achieved by regulating inflammatory cytokines, balancing colonic microbiota, and modulating gene expression related to inflammation.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Biochemical Research Methods
Matteo Comin, Barbara Di Camillo, Cinzia Pizzi, Fabio Vandin
Summary: The study of microbial communities relies on comparing metagenomic next-generation sequencing data sets, facing challenges such as species identification and quantification, computation of distances between samples, and identification of features associated with a phenotype. Solutions involve reference-based methods using a database of reference genomes and reference-free methods working directly on sequencing reads.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Chemistry, Multidisciplinary
Na Zhao, Jiabao Cao, Jiayue Xu, Beibei Liu, Bin Liu, Dingqiang Chen, Binbin Xia, Liang Chen, Wenhui Zhang, Yuqing Zhang, Xuan Zhang, Zhimei Duan, Kaifei Wang, Fei Xie, Kun Xiao, Wei Yan, Lixin Xie, Hongwei Zhou, Jun Wang
Summary: Utilizing RNA sequencing and third-generation sequencing technology for pathogen identification can improve the ratio of microbial reads and accelerate clinical diagnosis, showing significant potential.
Article
Microbiology
Laure Flurin, Joseph J. Hemenway, Cody R. Fisher, James J. Vaillant, Marisa Azad, Matthew J. Wolf, Kerryl E. Greenwood-Quaintance, Matthew P. Abdel, Robin Patel
Summary: Preoperative pathogen identification in patients with periprosthetic joint infection (PJI) is typically limited to synovial fluid culture. In this study, the accuracy of a 16S rRNA gene-based PCR followed by Sanger sequencing and/or targeted metagenomic sequencing approach (tMGS) performed on synovial fluid for PM diagnosis was analyzed. The results showed that the sequencing-based approach did not have a significant advantage over conventional culture for diagnosing PJI, but yielded positive results in some culture-negative samples.
Article
Cardiac & Cardiovascular Systems
Isabel S. Naarmann-de Vries, Jessica Eschenbach, Christoph Dieterich
Summary: RNA sequencing is a powerful tool for analyzing gene expression, but it is still low-throughput and cost-intensive. Concentrating sequencing capacity on specific parts of the transcriptome is an important design choice. Various methods exist to reduce ribosomal RNA read numbers, but there is currently no solution for highly abundant tissue-specific transcripts.
JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY
(2022)
Article
Microbiology
Ellen C. Carbo, Anne Russcher, Margriet E. M. Kraakman, Caroline S. de Brouwer, Igor A. Sidorov, Mariet C. W. Feltkamp, Aloys C. M. Kroes, Eric C. J. Claas, Jutte J. C. de Vries
Summary: In this study, the mNGS approach was used for the identification and load monitoring of transplantation-related DNA viruses in immunocompromised patients. The results showed that the mNGS method performed comparably to qPCR in detection and viral load determination.
Article
Virology
Zhangfu Chen, Haiyu Zhao, Zhongkuan Li, Mengkun Huang, Nan Si, Hui Zhao, Xiaolu Wei, Bo Sun, George F. Gao, Ziqian Xu, William J. Liu
Summary: A study found that the Asiatic toad harbors novel RNA viruses, including those belonging to the Bunyavirales order and 7 families of Astroviridae, Dicistroviridae, Leviviridae, Partitiviridae, Picornaviridae, Rhabdoviridae, and Virgaviridae. These viruses are distinct from previously described viruses and form new clusters. Additionally, phenuiviruses were discovered for the first time in amphibians, along with several invertebrate RNA viruses. These findings enhance our understanding of RNA viral diversity in the Asiatic toad and the evolution of RNA viruses in amphibians.
Article
Biotechnology & Applied Microbiology
Mingyu Gan, Bingbing Wu, Gangfeng Yan, Gang Li, Li Sun, Guoping Lu, Wenhao Zhou
Summary: Enzyme-based host depletion and nanopore adaptive sequencing both significantly improved the microbial enrichment efficiency, resulting in increased diversity of microorganisms. The combined method showed the highest microbial enrichment efficiency compared to standard methods.
Review
Microbiology
Sven Kleine Bardenhorst, Tom Berger, Frank Klawonn, Marius Vital, Andre Karch, Nicole Ruebsamen
Summary: Reproducibility in microbiome studies is hindered by a lack of consensus on data analysis strategies. The complex nature of microbiome data, combined with increasingly sophisticated research questions, requires more advanced analytical methods. Current analysis strategies in microbiome studies show significant heterogeneity, particularly in differential abundance testing, indicating a need for better guidance in analyzing increasingly complex research questions.
Article
Genetics & Heredity
Moritz Kohls, Magdalena Kircher, Jessica Krepel, Pamela Liebig, Klaus Jung
Summary: Estimating the taxonomic composition of viral sequences using artificial neural networks and machine learning models proved to be more accurate than traditional mapping approaches. Training data sampled from the NCBI database with a focus on the biological order of viruses allowed for a higher prediction accuracy in classifying test reads to their viral order. The use of auxiliary test sets helped to estimate conditional class probabilities and correct the prior estimation of taxonomic distribution in the test set.
Article
Biochemical Research Methods
Atif Khurshid Wani, Chirag Chopra, Daljeet Singh Dhanjal, Nahid Akhtar, Himanshu Singh, Poorvi Bhau, Anjuvan Singh, Varun Sharma, Rafael Silvio Bonilha Pinheiro, Juliana Heloisa Pine Americo-Pinheiro, Reena Singh
Summary: Zoonotic viral infections pose significant threats to global public health. Understanding the origins and dynamics of these infections is crucial for prevention and management of future outbreaks. Metagenomics is a powerful tool for studying the diversity of viral populations and potential zoonotic events.
JOURNAL OF VIROLOGICAL METHODS
(2024)
Article
Biochemical Research Methods
Michel V. F. Sucupira, Ana P. C. Argondizzo, Mariana Miguez, Anna E. de Araujo, Leila B. R. Silva, Marcelle B. Mello, Christiane F. S. Marques, Danielle Brito Cunha, Renata C. Bastos, Vanessa S. de Paula, Luciane A. Amado Leon
Summary: This study focuses on improving the purification, solubility, and protein expression levels of recombinant VP1-2A, a hepatitis A virus (HAV) structural protein with immunogenic activity. The results show that the modified approach successfully produces biologically active HAV VP1-2A, which can be used as a diagnostic tool for HAV infection.
JOURNAL OF VIROLOGICAL METHODS
(2024)
Article
Biochemical Research Methods
Arun K. Dhar, Roberto Cruz-Flores, Hung N. Mai, Janet Warg
Summary: A sensitive and robust TaqMan PCR method for detecting IHHNV in three commercially important shrimp species was developed and compared with other published methods. Multiple primer/probe sets, including qIH-Fw/qIH-Rv and 3144F/3232R, are recommended for the detection of IHHNV. These findings are valuable for large-scale screening of shrimp using a TaqMan real-time PCR assay.
JOURNAL OF VIROLOGICAL METHODS
(2024)
Article
Biochemical Research Methods
Kemal Mehinagic, Matthias Liniger, Maksym Samoilenko, Nick Soltermann, Markus Gerber, Nicolas Ruggli
Summary: A plasmid-based reporter assay has been developed for sensitive detection and titration of infectious African swine fever virus (ASFV). This novel method allows accurate measurement of ASFV titers and is applicable to ASFV of different genotypes, virulence, and sources.
JOURNAL OF VIROLOGICAL METHODS
(2024)
Article
Biochemical Research Methods
Jan Van Slambrouck, Charlotte Schoenaers, Lies Laenen, Xin Jin, Kurt Beuselinck, Ann Verdonck, Joost Wauters, Geert Molenberghs, Bart M. Vanaudenaerde, Robin Vos, Peter Mombaerts, Katrien Lagrou, Laurens J. Ceulemans
Summary: The ability to detect SARS-CoV-2 RNA or antigen in BAL fluid samples using point-of-care tests (POCTs) can reduce the risk of developing severe COVID-19 after lung transplantation.
JOURNAL OF VIROLOGICAL METHODS
(2024)