Article
Multidisciplinary Sciences
Brianna Chrisman, Chloe He, Jae-Yoon Jung, Nate Stockham, Kelley Paskov, Peter Washington, Dennis P. Wall
Summary: The unmapped readspace of whole genome sequencing data is often overlooked but contains valuable signals of human infection and contamination. By analyzing unmapped and poorly aligned reads from over 1000 families and nearly 5000 individuals, this study reveals insights into common viral, bacterial, and computational contamination in whole genome sequencing studies. It also highlights the need for standard protocols to identify and remove contamination in order to ensure the accuracy of sequencing-based research results.
SCIENTIFIC REPORTS
(2022)
Article
Microbiology
Christian Salgard Jensen, Katrine Hojholt Iversen, Rimtas Dargis, Patricia Shewmaker, Simon Rasmussen, Jens Jorgen Christensen, Xiaohui Chen Nielsen
Summary: Different methods were used to identify Streptococcus pseudopneumoniae, with core genome analysis and CSI phylogeny proving effective in clustering strains accurately. However, single gene or MLSA methods could lead to misidentification. KmerFinder showed high accuracy in identifying S. pseudopneumoniae.
JOURNAL OF CLINICAL MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Kathy E. Raven, Sophia T. Girgis, Asha Akram, Beth Blane, Danielle Leek, Nicholas Brown, Sharon J. Peacock
Summary: The study introduces a universal protocol for simultaneous DNA extraction and sequencing of multiple bacterial species, demonstrating high reproducibility and effectiveness. The addition of lysozyme and lysostaphin together proved to be essential for generating sufficient DNA across all 20 tested species, supporting low-volume and rapid turnaround time for local clinical microbiology laboratories.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Chunyu Liu, Jessica L. Fetterman, Xianbang Sun, Kaiyu Yan, Poching Liu, Yan Luo, Jun Ding, Jun Zhu, Daniel Levy
Summary: This study compared mtDNA sequence variants between LCL and whole blood samples. The results showed that most homoplasmic variants were present in both LCL and blood samples, while most heteroplasmic variants were unique to either LCL or blood samples. LCL samples had a higher number of heteroplasmic variants compared to whole blood samples, but a similar number of homoplasmic variants. Additionally, LCL samples tended to have lower levels of heteroplasmy.
SCIENTIFIC REPORTS
(2022)
Article
Microbiology
Hiroshi Hamamoto, Akihiko Ano Ogasawara, Masahiro Iwasa, Kazuhisa Sekimizu
Summary: Controlling and managing bacterial species is crucial in the development and manufacture of fermented foods. A research study successfully identified specific fermentation strains by comparing their genome sequences. A PCR method was designed to amplify DNA fragments of these specific strains under different conditions. This method is simple, accurate, and helpful in controlling the quality of fermented foods.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biodiversity Conservation
Rebecca S. Taylor, Micheline Manseau, Bridget Redquest, Sonesinh Keobouasone, Patrick Gagne, Christine Martineau, Paul J. Wilson
Summary: Conservation genomics is a crucial tool for managing threatened species in the face of biodiversity loss. Recent advances in sequencing technology have enabled the extraction and re-sequencing of high-quality whole genomes from fecal DNA, as demonstrated in the case of caribou in Canada. This represents a significant advancement in non-invasive conservation genomics.
CONSERVATION GENETICS RESOURCES
(2022)
Article
Chemistry, Multidisciplinary
Ana Paula Mulet, Magdalena Ripoll, Lorena Betancor
Summary: Biocatalysis has emerged as a promising alternative to conventional chemical processes, and CRISPR-based technologies have the potential to enhance whole-cell bacterial biotransformations for more sustainable production of industrially important products.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Chuanxue Liu, Pei Peng, Weiguo Li, Changrong Ye, Shuhua Zhang, Ruiying Wang, Dong Li, Shiwu Guan, Lanmin Zhang, Xiaoqun Huang, Zhenhua Guo, Junxiang Guo, Yu Long, Le Li, Guojun Pan, Bingchuan Tian, Jinhua Xiao
Summary: This study resequenced 239 japonica rice elites to reveal the genetic diversity and relationships among them, constructed a japonica rice pan-genome, predicted numerous novel genes, and detected strong selection signals in genomic regions. The results provide a foundation for future whole genome sequences-enabled breeding in rice and serve as a paradigm for other species.
Article
Multidisciplinary Sciences
Rotem Raz, Zvi Roth, Moran Gershoni
Summary: This study obtained and analyzed raw data from 262 whole-exome sequencing samples of Bos Taurus, and established a comprehensively annotated database of over 20 million short variants, some of which contribute to diseases and traits.
Article
Plant Sciences
Yuhua Fu, Sirong Jiang, Meiling Zou, Jianjia Xiao, Long Yang, Chunfang Luo, Ping Rao, Wenquan Wang, Zhengui Ou, Fanzhi Liu, Zhiqiang Xia
Summary: This study assembled and compared the genomes of two species in the Cannaceae family, revealing recent genome-wide duplication events and molecular mechanisms underlying the differences in plant characteristics between C. edulis and C. indica.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Tom Verbeelen, Rob Van Houdt, Natalie Leys, Ramon Ganigue, Felice Mastroleo
Summary: A procedure for extracting high-quality RNA from low-biomass producing bacteria was developed, using ammonium-oxidizing and nitrite-oxidizing bacteria as model organisms for optimization. Enzymatic lysis generated high-quality RNA samples, suitable for experiments with limited sample volume or biomass. The procedure also resulted in higher RNA yields for whole transcriptome experiments.
Article
Multidisciplinary Sciences
Seong-Wan Kim, Min Jee Kim, Seong-Ryul Kim, Jeong Sun Park, Kee-Young Kim, Ki Hwan Kim, Woori Kwak, Iksoo Kim
Summary: This study reports the whole-genome sequences of 37 breeding line Bombyx mori strains established over the past 60 years, along with the description of their phenotypic characteristics. These data are valuable resources for studying B. mori and other insects.
Article
Biochemistry & Molecular Biology
Alastair J. Ludington, Kate L. Sanders
Summary: The question of whether spatial aspects of evolution differ in marine versus terrestrial realms has endured since Ernst Mayr's 1954 essay on marine speciation. Marine systems are often suggested to support larger and more highly connected populations, but quantitative comparisons with terrestrial systems have been lacking. The study compared the population histories of marine and terrestrial elapid snakes, revealing highly variable demographic patterns among species that do not clearly correspond to major ecological divisions.
Article
Agriculture, Dairy & Animal Science
Sihu Wang, Sayed Haidar Abbas Raza, Ke Zhang, Chugang Mei, Muna O. Alamoudi, Bandar H. Aloufi, Ahmed Mohajja Alshammari, Linsen Zan
Summary: Qinchuan cattle have undergone gradual improvements in body shape and growth rate through long-term breeding. Whole genome sequencing data revealed candidate genes related to the growth and development traits of Qinchuan cattle, including brain size, body characteristics, and limb development. Other genes were also found to be associated with meat quality, reproductive function, and coat color. These findings provide insights into breed formation and molecular genetic breeding, and can contribute to improving animal production and health.
ANIMAL BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Henry L. North, Angela McGaughran, Chris D. Jiggins
Summary: The use of genomic data in invasion biology can provide valuable insights into processes such as invasion routes reconstruction and the importance of balancing selection and hybridization. While currently only a few invasive systems have utilized whole-genome resequencing, these studies have confirmed the significance of leveraging new technologies and approaches for a more comprehensive understanding of invasive species.
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)
Review
Gastroenterology & Hepatology
L. R. Caley, H. White, M. C. de Goffau, R. A. Floto, J. Parkhill, B. Marsland, D. G. Peckham
Summary: Gut dysbiosis is evident in individuals with cystic fibrosis (CF), characterized by reduced diversity and taxonomic changes. The relationship between gut dysbiosis and systemic and lung inflammation is limited. The causes of gut dysbiosis are multifactorial and the impact of CFTR modulators on the gut microbiota is still unclear.
DIGESTIVE DISEASES AND SCIENCES
(2023)
Article
Respiratory System
Andries J. van Tonder, Huw C. Ellis, Colin P. Churchward, Kartik Kumar, Newara Ramadan, Susan Benson, Julian Parkhill, Miriam F. Moffatt, Michael R. Loebinger, William O. C. Cookson
Summary: This study investigates the transmission potential of Mycobacterium avium complex (MAC) among CF and non-CF patients. The results show possible transmission clusters for MAC species, but few epidemiological links were found. Global transmission clusters of Mycobacterium chimaera were associated with heater-cooler units, but the initial ancestor was already circulating among patients.
EUROPEAN RESPIRATORY JOURNAL
(2023)
Article
Immunology
Kelsey A. Gregg, Yihui Wang, Jason Warfel, Elizabeth Schoenfeld, Ewa Jankowska, John F. Cipollo, Matthew Mayho, Christine Boinett, Deepika Prasad, Timothy J. Brickman, Sandra K. Armstrong, Julian Parkhill, Ricardo Da Silva Antunes, Alessandro Sette, James F. Papin, Roman Wolf, Tod J. Merkel
Summary: Despite high vaccination rates, the United States has experienced a resurgence in reported cases of pertussis after switching to the acellular pertussis vaccine. This study identified B. pertussis antigens recognized by convalescent baboon serum and nasopharyngeal wash and identified genes essential for persistence in the baboon airway. The identified antigens are potential candidates for improving acellular pertussis vaccines.
JOURNAL OF 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
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
Microbiology
Dorota Jamrozy, Guduru Gopal Rao, Theresa Feltwell, Theresa Lamagni, Priya Khanna, Androulla Efstratiou, Julian Parkhill, Stephen D. D. Bentley
Summary: This study characterized the population structure of GBS isolates from pregnant women in London and found that the majority of isolates belonged to five main lineages. The study also identified nine serotypes, with III, V, II, and Ia being the most common. Moreover, it revealed associations between maternal ethnicity and GBS population structure.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Christopher Ruis, Thomas P. Peacock, Luis M. Polo, Diego Masone, Maria Soledad Alvarez, Angie S. Hinrichs, Yatish Turakhia, Ye Cheng, Jakob McBroome, Russell Corbett-Detig, Julian Parkhill, R. Andres Floto
Summary: Through mutational spectrum analysis, we found distinct mutational patterns in SARS-CoV-2 variants, with the Omicron variant showing reduced G>T mutations compared to other lineages. The mutational analysis also revealed a strong association of high G>T mutations with replication in the lower respiratory tract. Monitoring mutation rates over time showed early divergence of Omicron from Beta, Gamma, and Delta, while the mutational patterns in Alpha varied with changes in transmission source.
MICROBIAL GENOMICS
(2023)
Review
Genetics & Heredity
Gerry Tonkin-Hill, Jukka Corander, Julian Parkhill
Summary: Horizontal gene transfer (HGT) and patterns of gene gain and loss are essential in bacterial evolution. Understanding these patterns can shed light on selection's role in the evolution of bacterial pangenomes and bacterial adaptation to new niches. However, predicting gene presence or absence can be prone to errors, which can complicate the study of HGT dynamics. This review discusses the challenges of constructing accurate pangenomes and the potential consequences of errors on downstream analyses, with the goal of improving bacterial pangenome analyses.
MICROBIAL GENOMICS
(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
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
Multidisciplinary Sciences
Christopher Ruis, Aaron Weimann, Gerry Tonkin-Hill, Arun Prasad Pandurangan, Marta Matuszewska, Gemma G. R. Murray, Roger C. Levesque, Tom L. Blundell, R. Andres Floto, Julian Parkhill
Summary: The study reveals that mutagens and defects in DNA repair can generate context-specific mutational signatures in bacteria, similar to the findings in cancer cells. By reconstructing mutational spectra and analyzing bacterial lineages, the researchers identified mutational patterns associated with DNA repair defects and niche-specific mutagens. These mutational signatures were found to be influenced by both bacterial phylogeny and replication niche. The results suggest that mutational spectra can be used to infer transmission routes for bacterial pathogens.
NATURE COMMUNICATIONS
(2023)
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
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)