Article
Agricultural Engineering
Nathan Innard, James P. J. Chong
Summary: Mixed anaerobic microbial communities play a key role in valorizing waste biomass through anaerobic digestion, and are important in soil and animal microbiomes. Understanding interactions between individual species within these communities is crucial for improving the performance and potential applications of green technology. The challenges associated with assessing the status of anaerobic microbial communities, incorporating measurements into control philosophies, and enhancing their potential to produce higher value products from waste materials are discussed.
BIORESOURCE TECHNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Laura Ciuffreda, Hector Rodriguez-Perez, Carlos Flores
Summary: The introduction of nanopore sequencing technology has significantly improved our ability to study complex microbial samples, allowing real-time sequencing of long reads with low cost and portability. This technology plays a crucial role in resolving complex genomic structures, accessing metagenome assembled genomes, and shows great potential in environmental microbial analysis.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Multidisciplinary Sciences
Yunxi Liu, R. A. Leo Elworth, Michael D. Jochum, Kjersti M. Aagaard, Todd J. Treangen
Summary: Contaminant sequences in metagenomic samples can impact interpretation of microbiome studies, especially in low biomass environments. The authors propose a computational approach called Squeegee, which can detect microbial contamination and identify contaminants in publicly available datasets lacking negative controls.
NATURE COMMUNICATIONS
(2022)
Review
Microbiology
Maliha Batool, Jessica Galloway-Pena
Summary: Infections without precise diagnosis can be caused by rare or uncharacterized pathogens, combination of pathogens, or known pathogens carrying undocumented or newly acquired genes. Despite medical advances, many patients still suffer from mortality or long-term consequences due to undiagnosed or misdiagnosed infections. Therefore, there is a need for an exhaustive and universal diagnostic strategy to reduce the fraction of undocumented infections.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Food Science & Technology
Meghana Srinivas, Orla O'Sullivan, Paul D. Cotter, Douwe van Sinderen, John G. Kenny
Summary: Microbial communities in fermented foods play crucial roles in the fermentation processes. High throughput sequencing methods, particularly metagenomics, have been widely used in the study of fermented foods and have shown great potential in conjunction with synthetic biology techniques for addressing waste issues.
Article
Biotechnology & Applied Microbiology
Ko Abe, Masaaki Hirayama, Kinji Ohno, Teppei Shimamura
Summary: The BALSAMICO hierarchical Bayesian framework accurately estimates parameters needed to analyze the connections between microbial community systems and their environments, and effectively detects these communities in real-world circumstances.
Article
Multidisciplinary Sciences
Hyunmin Koo, Casey D. Morrow
Summary: This study developed an analytic method to detect indicators of microbial strain dysbiosis and found shared gut commensal microbes in both healthy individuals and COVID-19 patients, suggesting a potential dysbiosis in the microbial strain community.
SCIENTIFIC REPORTS
(2022)
Review
Microbiology
Alla L. Lapidus, Anton I. Korobeynikov
Summary: Metagenomics is a branch of microbial genomics that focuses on sequencing and analyzing the combined genomic DNA of entire environmental samples. The key step in metagenomic data analysis is the reconstruction of individual genes and genomes of microorganisms in communities using computational programs known as metagenomic assemblers.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Carl-Eric Wegner, Raphaela Stahl, Irina Velsko, Alex Huebner, Zandra Fagernaes, Christina Warinner, Robert Lehmann, Thomas Ritschel, Kai U. Totsche, Kirsten Kuesel
Summary: By adapting methods from microbial archaeology and paleogenomics, we recovered sufficient DNA from seven rock specimens for metagenomic analysis. Limestones serve as archives for genetic records of past microbial communities, including those sensitive to environmental stress, due to specific conditions facilitating long-term DNA preservation.
Article
Biochemistry & Molecular Biology
Nanyan Zhu, Qiaoqiao Yu, Lingqi Song, Haijun Sheng
Summary: This study investigates the effects and mechanisms of high-dose biochar applications on rice production and soil biological characteristics. The results show that high-dose biochar applications slightly increase grain yield but have significant negative effects on soil bacterial and archaeal communities.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Oncology
Noemi Laprovitera, Mattia Riefolo, Elisa Ambrosini, Christiane Klec, Martin Pichler, Manuela Ferracin
Summary: Patients with cancer of unknown primary site face reduced therapeutic opportunities and poor prognosis. Advancements in molecular characterization help infer tumor site-of-origin and develop novel therapies independent of tumor type, greatly benefiting these patients.
Article
Soil Science
Qiong Wang, Qingyi Zhang, Yingchun Han, Delu Zhang, Cheng-Cai Zhang, Chunxiang Hu
Summary: This study used metagenomic sequencing to investigate the carbon cycle in biocrusts. It found that there are assimilation and dissimilation modules in the carbon cycle, and the relationships between these modules change during succession.
SOIL BIOLOGY & BIOCHEMISTRY
(2022)
Review
Engineering, Marine
Cora Hoerstmann, Sylke Wohlrab, Uwe John
Summary: High-throughput sequencing technologies have advanced our understanding of microbial diversity in the oceans, but research on microbial eukaryotes (protists) lags behind. This review discusses the challenges and opportunities of high-throughput sequencing methods for studying the evolutionary, ecological, and functional aspects of oceanic protists. These approaches allow for a deeper understanding of the functional role of protists and the changes in marine ecosystems.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2022)
Article
Biochemical Research Methods
Byunghan Lee, Hyeyoung Min, Sungroh Yoon, Inanc Birol
Summary: This study proposes an efficient method for error correction in metagenomic sequencing, reducing denoising time demands and overestimation of OTUs. By utilizing data-level parallelism and multiple processing units, the approach significantly improves the efficiency of denoising efforts and provides web-based visualization of results.
Article
Microbiology
Erica M. Lopes, Maicon R. Z. Passini, Luciano T. Kishi, Tsute Chen, Bruce J. Paster, Brenda P. F. A. Gomes
Summary: Periodontal and Endodontic diseases are biofilm-related diseases with distinct microbial compositions, indicating potential interactions and communication between the microbiomes of the two sites. The microbial diversity and antibiotic resistance markers differ between infected root canals and periodontal pockets, with the latter showing a higher abundance of species and broader spectrum resistance. The study also identified markers related to systemic diseases in the microbial communities, highlighting the need for further research on the potential implications of cross-infection between endodontic and periodontal diseases.
Meeting Abstract
Virology
K. Ranellou, C. Crump, R. Misra, D. Wooldridge, G. Rose, S. Gharbia, S. Parmar, M. Curran, N. Verlander, H. Zhang, H. Jalal
JOURNAL OF CLINICAL VIROLOGY
(2015)
Article
Evolutionary Biology
Graham Rose, Elzbieta Krzywinska, Jan Kim, Loic Revuelta, Luca Ferretti, Jaroslaw Krzywinski
GENOME BIOLOGY AND EVOLUTION
(2016)
Article
Immunology
Edward T. Mee, Mark D. Preston, CSS Study Participant, Philip D. Minor, Silke Schepelmann
Article
Multidisciplinary Sciences
Graham Rose, Alexander G. Shaw, Kathleen Sim, David J. Wooldridge, Ming-Shi Li, Saheer Gharbia, Raju Misra, John Simon Kroll
Article
Evolutionary Biology
Graham Rose, Teresa Cortes, Inaki Comas, Mireia Coscolla, Sebastien Gagneux, Douglas B. Young
GENOME BIOLOGY AND EVOLUTION
(2013)
Article
Multidisciplinary Sciences
Midori Kato-Maeda, Christine Ho, Ben Passarelli, Niaz Banaei, Jennifer Grinsdale, Laura Flores, Jillian Anderson, Megan Murray, Graham Rose, L. Masae Kawamura, Nader Pourmand, Muhammad A. Tariq, Sebastien Gagneux, Philip C. Hopewell
Article
Multidisciplinary Sciences
Joanna Houghton, Teresa Cortes, Olga Schubert, Graham Rose, Angela Rodgers, Megan De Ste Croix, Rudolf Aebersold, Douglas B. Young, Kristine B. Arnvig
Review
Genetics & Heredity
Borna Mueller, Sonia Borrell, Graham Rose, Sebastien Gagneux
TRENDS IN GENETICS
(2013)
Article
Cell Biology
Teresa Cortes, Olga T. Schubert, Graham Rose, Kristine B. Arnvig, Inaki Comas, Ruedi Aebersold, Douglas B. Young
Correction
Cell Biology
Teresa Cortes, Olga T. Schubert, Graham Rose, Kristine B. Arnvig, Inaki Comas, Ruedi Aebersold, Douglas B. Young
Article
Microbiology
Alexander G. Shaw, Kathleen Sim, Graham Rose, David J. Wooldridge, Ming-Shi Li, Raju Misra, Saheer Gharbia, J. Simon Kroll
Summary: The study identified two distinct microbial community patterns in infants with necrotising enterocolitis (NEC): one with low levels of CpG DNA and another with high abundances of LPS-expressing organisms. These patterns may represent extremes of TLR4 pathway stimulation.
Article
Microbiology
Joanna Houghton, Angela Rodgers, Graham Rose, Alexandre D'Halluin, Terry Kipkorir, Declan Barker, Simon J. Waddell, Kristine B. Arnvig
Summary: Studies have found that the sRNA F6 of Mycobacterium tuberculosis is up-regulated under starvation conditions, which may play a role in the long-term survival of the bacterium in human granulomas.
MICROBIOLOGY SPECTRUM
(2021)
Article
Microbiology
Graham Rose, Kyriaki Ranellou, Raju Misra, Colin Crump, David Wooldridge, Surendra Parmar, Christopher Maddren, Saheer Gharbia, Hamid Jalal
GENOME ANNOUNCEMENTS
(2017)
Article
Microbiology
Tom Gaulton, Raju Misra, Graham Rose, Primo Baybayan, Richard Hall, Jane Freeman, Jane Turton, Steve Picton, Jonas Korlach, Saheer Gharbia, Haroun Shah
GENOME ANNOUNCEMENTS
(2015)