Article
Microbiology
Hwee Sze Tee, Susanna A. Wood, Keith Bouma-Gregson, Gavin Lear, Kim M. Handley
Summary: Comparative analysis revealed significant genetic differences between toxic and nontoxic Microcoleus strains, with toxic strains potentially having reduced metabolic flexibility and dependence on coexisting nontoxic strains. The study sheds light on metabolic and evolutionary discrepancies between toxic and nontoxic Microcoleus, aiding in the prediction and management of aquatic blooms.
Article
Microbiology
Justin C. Podowski, Sara F. Paver, Ryan J. Newton, Maureen L. Coleman
Summary: Microorganisms play critical roles in Earth's nitrogen cycle. However, little is known about freshwater nitrifiers. In this study, genomes of freshwater nitrifiers in the Laurentian Great Lakes were reconstructed, revealing their unique biodiversity and filling important knowledge gaps.
Article
Multidisciplinary Sciences
Taras Y. Nechitaylo, Mario Sandoval-Calderon, Tobias Engl, Natalie Wielsch, Diane M. Dunn, Alexander Goesmann, Erhard Strohm, Ales Svatos, Colin Dale, Robert B. Weiss, Martin Kaltenpoth
Summary: The study characterized the genomic architecture and functional gene content of a culturable symbiont in solitary beewolf wasps, revealing incipient genome erosion with frameshift mutations affecting more than a third of protein-coding genes. The symbiont also exhibited mutations in central metabolic pathways, resulting in auxotrophies, and differential expression analyses indicated overexpression of genes for antibiotic biosynthesis in the host environment.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Microbiology
Roshan Nepal, Ghais Houtak, Sumeena Karki, Gunaraj Dhungana, Sarah Vreugde, Rajani Malla
Summary: This study reports the isolation of three newly discovered phages from river water in Kathmandu, Nepal. These phages have the potential to lyse pathogenic bacteria and may be used in bacterial biocontrol. Genome analysis showed that these phages are safe options for treatment as they do not contain virulence factors, toxins, or known antimicrobial resistance genes.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Chemistry, Analytical
Guangpei Qi, Haixia Zou, Xiaohong Peng, Shiliang He, Qiqi Zhang, Wei Ye, Yizhou Jiang, Wentao Wang, Guangli Ren, Xiangmeng Qu
Summary: Metabolic footprinting is a convenient and non-invasive cell metabolomics strategy used to monitor the entire extracellular metabolic process. However, its universality is limited due to the need for pre-treatment of cell medium and specialized equipment. In this study, we developed a fluorescently labeled single-stranded DNA-AuNP encoder that can detect extracellular metabolites, allowing for metabolic response profiling and the identification of cell heterogeneity in tumor cells.
ANALYTICAL CHEMISTRY
(2023)
Review
Multidisciplinary Sciences
Anastasiia V. Sadybekov, Vsevolod Katritch
Summary: Computer-aided drug discovery has experienced a significant shift towards computational technologies for efficient ligand screening. This shift is driven by the availability of vast ligand data, abundant computing capacities, and virtual libraries of drug-like small molecules. Recent advances in deep learning predictions of ligand properties and target activities, as well as structure-based virtual screening, have the potential to reshape the drug discovery and development process. The rapid identification of diverse, potent, target-selective, and drug-like ligands to protein targets can democratize the drug discovery process, enabling cost-effective development of safer and more effective treatments.
Article
Microbiology
George W. Liechti
Summary: Regulation of cell size in bacteria involves the expansion and constriction of the cell envelope, with peptidoglycan playing a crucial role. The study on Chlamydia species revealed different structural forms of PG, with varying synthesis to degradation ratios, indicating differential regulation of PG synthases during cell growth and division.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Oncology
Enrico Moiso, Paolo Provero
Summary: This study systematically investigates the associations between metabolic alterations and other tumor features using a comprehensive collection of data. The results provide a guide for formulating specific mechanistic hypotheses and contribute to our understanding of the role of metabolic alterations in cancer and the development of precision therapeutic strategies.
Article
Physics, Multidisciplinary
Timothy Cohen, Xiaochuan Lu, Zhengkang Zhang
Summary: This paper presents STrEAM, a Mathematica package that calculates all functional supertraces when matching a generic UV model onto a relativistic Effective Field Theory. The package implements the covariant derivative expansion to automate the most tedious step of the streamlined functional matching prescription.
Article
Microbiology
Elizabeth A. McDaniel, Francisco Moya-Flores, Natalie Keene Beach, Pamela Y. Camejo, Ben O. Oyserman, Matthew Kizaric, Eng Hoe Khor, Daniel R. Noguera, Katherine D. McMahon
Summary: The study explored the gene expression patterns of coexisting Accumulibacter strains in a bioreactor system, identifying putative pathways and functions that may confer distinct functions to the strains. The research provides key functional insights into this biotechnologically significant microbial lineage and offers an approach for elucidating ecologically relevant functions based on gene expression patterns between closely related microbial populations.
Article
Medicine, General & Internal
Jesus Sojo-Dorado, Inmaculada Lopez-Hernandez, Clara Rosso-Fernandez, Isabel M. Morales, Zaira R. Palacios-Baena, Alicia Hernandez-Torres, Esperanza Merino de Lucas, Laura Escola-Verge, Elena Bereciartua, Elisa Garcia-Vazquez, Vicente Pintado, Lucia Boix-Palop, Clara Natera-Kindelan, Luisa Sorli, Nuria Borrell, Livia Giner-Oncina, Concha Amador-Prous, Evelyn Shaw, Alfredo Jover-Saenz, Jose Molina, Rosa M. Martinez-Alvarez, Carlos J. Duenas, Jorge Calvo-Montes, Jose T. Silva, Miguel A. Cardenes, Maria Lecuona, Virginia Pomar, Lucia Valiente de Santis, Genoveva Yague-Guirao, Maria Angeles Lobo-Acosta, Vicente Merino-Bohorquez, Alvaro Pascual, Jesus Rodriguez-Bano
Summary: This study aimed to compare the noninferiority of fosfomycin to ceftriaxone or meropenem in the treatment of bacteremic urinary tract infections caused by multidrug-resistant Escherichia coli. The results showed that there was no significant difference in clinical and microbiological cure rates between the fosfomycin group and the comparator group, but the rate of adverse event-related discontinuations was higher in the fosfomycin group.
Article
Geriatrics & Gerontology
Kamar Ghaibour, Melanie Schuh, Sirine Souali-Crespo, Celine Chambon, Anouk Charlot, Joe Rizk, Daniela Rovito, Anna-Isavella Rerra, Qingshuang Cai, Nadia Messaddeq, Joffrey Zoll, Delphine Duteil, Daniel Metzger
Summary: Disrupting the androgen/androgen receptor axis impairs glycolytic activity and promotes the development of type 2 diabetes in male mice, but not in females. It also leads to oxidative stress and necrosis in muscle fibers.
JOURNAL OF CACHEXIA SARCOPENIA AND MUSCLE
(2023)
Review
Plant Sciences
Mutsumi Watanabe, Takayuki Tohge
Summary: Functional genomics approaches have successfully detected key metabolic polymorphisms in plant specialized metabolism through comparative omics analyses of wild-accessions and cultivars/wild species, as well as comparative genomic analyses in plant species focusing on gene clusters. In recent decades, intra-species specific metabolic polymorphisms, new functionalization of tandem duplicated genes, and metabolic gene clusters have been found as the main factors creating metabolic diversity of specialized metabolites in plants. However, strategic approaches depending on the target metabolic pathways are required for gene identification in plant specialized metabolism. The increasing availability of plant genome sequences and transcriptome data has facilitated inter-specific comparative analyses, including genomic analysis and gene co-expression network analysis. Here, we introduce functional genomics approaches with the integration of inter-/intra-species comparative metabolomics, their key roles in providing genomic signatures of metabolic evolution, and discuss future prospects of functional genomics on plant specialized metabolism.
CURRENT OPINION IN PLANT BIOLOGY
(2023)
Editorial Material
Medicine, General & Internal
Shawheen J. Rezaei, Oren Ganor
Summary: This Viewpoint explains the obstacles individuals face when seeking gender-affirming care and suggests necessary changes to improve quality and access to such care.
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
(2023)
Article
Agricultural Engineering
Zhenqiang Zhao, Mengmeng Cai, Yunran Liu, Mengkai Hu, Fengyu Yang, Rongshuai Zhu, Meijuan Xu, Zhiming Rao
Summary: L-arginine is an important amino acid used in food and pharmaceutical industries. This study investigated the metabolic mechanisms and fermentation conditions affecting L-arginine production. By generating mutant strains and conducting multi-omic analysis, vital mutations in the L-arginine operon and glutamate synthase were identified. The study also applied systematic metabolic engineering to enhance L-arginine production by modifying key enzymes and increasing cofactor availability. Through fermentation optimization, the engineered strain produced a high yield of L-arginine. This study provides new insights into boosting L-arginine production.
BIORESOURCE TECHNOLOGY
(2022)
Article
Veterinary Sciences
Sara Frosth, Ellen Ruth A. Morris, Hayley Wilson, Lars Frykberg, Karin Jacobsson, Julian Parkhill, Jan-Ingmar Flock, Tim Wood, Bengt Guss, David M. Aanensen, Ashley G. Boyle, Miia Riihimaki, Noah D. Cohen, Andrew S. Waller
Summary: This study analysed the antigen sequences of 759 isolates of Streptococcus equi from around the world and found that the antigen sequences in the Strangvac vaccine are highly conserved.
EQUINE VETERINARY JOURNAL
(2023)
Article
Immunology
Refath Farzana, Lim S. Jones, Md Anisur Rahman, Kirsty Sands, Andries J. van Tonder, Edward Portal, Jose Munoz Criollo, Julian Parkhill, Martyn F. Guest, W. John Watkins, Monira Pervin, Ian Boostrom, Brekhna Hassan, Jordan Mathias, Md Abul Kalam, Timothy R. Walsh
Summary: This study is the largest study from a South Asian public hospital combining clinical outcomes, microbiology, and genomics. The findings demonstrate the urgent need for targeted diagnostics, appropriate antibiotic use, and infection-control interventions in South Asian public institutions.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Multidisciplinary Sciences
Jody Phelan, Paula Josefina Gomez-Gonzalez, Nuria Andreu, Yosuke Omae, Licht Toyo-Oka, Hideki Yanai, Reiko Miyahara, Supalert Nedsuwan, Paola Florez de Sessions, Susana Campino, Neneh Sallah, Julian Parkhill, Nat Smittipat, Prasit Palittapongarnpim, Taisei Mushiroda, Michiaki Kubo, Katsushi Tokunaga, Surakameth Mahasirimongkol, Martin L. Hibberd, Taane G. Clark
Summary: This study identified eight genetic interaction points associated with susceptibility to tuberculosis, including human loci DAP and RIMS3, as well as FSTL5. The analysis supports the co-evolution and adaptation between host and pathogen in tuberculosis.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Laura Carrilero, Steven J. J. Dunn, Robert A. A. Moran, Alan McNally, Michael A. A. Brockhurst
Article
Genetics & Heredity
Felipe Pinheiro Vilela, Dalia dos Prazeres Rodrigues, Marc William Allard, Juliana Pfrimer Falcao
Summary: This study characterized 11 Salmonella Heidelberg strains isolated from various sources in Brazil using whole-genome sequencing and antimicrobial resistance testing. The results showed that all strains were multidrug-resistant and had a global genomic relationship with strains from other countries. This highlights the need for stronger surveillance measures to prevent the spread of these strains through food.
Article
Microbiology
Romney M. Humphries, Eugene Bragin, Julian Parkhill, Grace Morales, Jonathan E. Schmitz, Paul A. Rhodes
Summary: The declining cost of bacterial whole-genome sequencing and the availability of sequence data have allowed the development of machine-learning models for predicting drug susceptibility in Escherichia coli. In this study, a ML-based model was tested for predicting the susceptibility of cefepime, a commonly used drug, in E. coli isolates. The results showed that the ML model had a high level of agreement with the reference method, indicating its potential use in clinical practice.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Ram P. Maharjan, Geraldine J. Sullivan, Felise G. Adams, Bhumika S. Shah, Jane Hawkey, Natasha Delgado, Lucie Semenec, Hue Dinh, Liping Li, Francesca L. Short, Julian Parkhill, Ian T. Paulsen, Lars Barquist, Bart A. Eijkelkamp, Amy K. Cain
Summary: Using functional genomics, we have identified the transcriptional regulator DksA as a master regulator for broad stress protection and virulence in Acinetobacter baumannii. DksA controls various aspects such as ribosomal protein expression, metabolism, mutation rates, desiccation, antibiotic resistance, and host colonization. This study lays the groundwork for understanding the role of DksA as a major regulator in stress response and virulence in this important pathogen.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Infectious Diseases
Luis Roger Esquivel Gomez, Cyril Savin, Voahangy Andrianaivoarimanana, Soloandry Rahajandraibe, Lovasoa Nomena Randriantseheno, Zhemin Zhou, Arthur Kocher, Xavier Didelot, Minoarisoa Rajerison, Denise Kuehnert
Summary: Plague reappeared in the city of Mahajanga, Madagascar in 1991 after a plague-free period of over 60 years. This study used a phylogeographic model to analyze the genome sequences of Yersinia pestis and identified two migrations from the Central Highlands that caused the outbreaks in the 1990s. The pathogen likely survived in wild reservoirs before spillover to humans.
PLOS NEGLECTED TROPICAL DISEASES
(2023)
Article
Infectious Diseases
Carolina Nogueira Gomes, Fabio Campioni, Dillon Oliver Reese Barker, Emily Victoria Che, Sheila da Silva Duque, Eduardo Napoleon Taboada, Juliana Pfrimer Falcao
Summary: This study used whole genome sequencing tools to identify antimicrobial resistance genotypes in 63 Campylobacter coli strains in Brazil. The strains were isolated from humans, animals, the environment, and food. The study found that there is a concern of resistance to certain important antimicrobials in C. coli strains, and there is a partial agreement between the results obtained by antimicrobial susceptibility testing and whole genome sequencing.
JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE
(2023)
Article
Genetics & Heredity
Jo Dicks, Mohammed-Abbas Fazal, Karen Oliver, Nicholas E. Grayson, Jake D. Turnbull, Evangeline Bane, Edward Burnett, Ana Deheer-Graham, Nancy Holroyd, Dorota Kaushal, Jacqueline Keane, Gemma Langridge, Jane Lomax, Hannah McGregor, Steve Picton, Michael Quail, Deepak Singh, Alan Tracey, Jonas Korlach, Julie E. Russell, Sarah Alexander, Julian Parkhill
Summary: The National Collection of Type Cultures (NCTC) was established in 1920 in the UK to centralize bacterial and fungal strains. It is one of the oldest collections of this kind worldwide, holding about 6000 strains with medical and scientific importance, available for global academic and veterinary institutions. The NCTC3000 project, a collaboration between NCTC, Pacific Biosciences and the Wellcome Sanger Institute, aims to sequence and assemble the genomes of up to 3000 NCTC strains.
MICROBIAL GENOMICS
(2023)
Article
Microbiology
Robert A. Moran, Baomo Liu, Emma L. Doughty, Yingyi Guo, Xiaoliang Ba, Willem van Schaik, Chao Zhuo, Alan McNally
Summary: ESBL resistance has a significant impact on the clinical management of E. coli infections in hospitals worldwide. This study aimed to understand the structures and dynamics of ESBL-EC populations in a Guangzhou ICU. The results revealed distinct populations of ESBL-EC strains in patients, staff, and clinical environments, with bla(CTX-M) genes playing a major role in conferring ESBL resistance.
MICROBIOLOGY SPECTRUM
(2023)
Article
Infectious Diseases
My H. Pham, Le Thi Hoi, Mathew A. Beale, Fahad A. Khokhar, Nguyen Thi Hoa, Patrick Musicha, Grace A. Blackwell, Hoang Bao Long, Dang Thi Huong, Nguyen Gia Binh, Dao Xuan Co, Tran Giang, Cuong Bui, Hai Ninh Tran, James Bryan, Archie Herrick, Theresa Feltwell, Behzad Nadjm, Julian Parkhill, Hindrik Rogier van Doorn, Nguyen Vu Trung, Nguyen Van Kinh, Mili Estee Torok, Nicholas R. Thomson
Summary: A study in Hanoi, Vietnam, highlights the high prevalence of ESBL-positive carbapenem-resistant K pneumoniae in intensive care units. The study also reveals that the important resistance genes are carried broadly by patients entering the two hospitals directly or through referral.
Article
Microbiology
Juan M. Belardinelli, Divya Arora, Charlotte Avanzi, William H. Wheat, Josephine M. Bryant, John S. Spencer, Tom L. Blundell, Julian Parkhill, R. Andres Floto, Mary Jackson
Summary: Functional genomics analysis of Mycobacterium abscessus clinical isolates revealed phoR as one of the genes under strong evolutionary pressure during lung adaptation. This study demonstrated that acidic pH upregulates phoP in M. abscessus and that clinically relevant non-synonymous mutations in PhoR exacerbate this response. PhoR modulates the autoregulation of its cognate response regulator, PhoP, by controlling its dephosphorylation.
MICROBIOLOGY SPECTRUM
(2023)
Article
Infectious Diseases
Ellisiv Nyhamar, Paige Webber, Olivia Liong, Ozgenur Yilmaz, Maria Pajunen, Mikael Skurnik, Xing Wan
Summary: In the battle against antimicrobial resistance, the need to find new antibiotic strategies is urgent. Bacteriophages, a largely unexplored resource, show potential as antimicrobial agents. This study focused on Hypothetical Proteins of Unknown Function (HPUFs) from a Staphylococcus phage Stab21, and found that some of these HPUFs exhibited cross-species toxicity towards E. coli, indicating shared molecular targets. By identifying a toxic antibacterial HPUF (toxHPUF) with homology to a homing endonuclease, this study contributes to the exploration of phage biology and offers promise in the search for potent antimicrobial agents.
Article
Microbiology
Susannah J. Salter, Robyn L. Marsh, Julian Parkhill
Summary: This study reports the complete genome sequence of the Ornithobacterium hominis type strain MSHR-COH1 (ATCC TSD-185/NCTC 14317), a bacterial species isolated from the human nasopharynx. Long-read sequencing reveals that the genome is 2,036,909 bp in length, with a GC content of 35.72%.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
