Article
Microbiology
Noel Djitro, Rebecca Roach, Rachel Mann, Paul R. Campbell, Brendan Rodoni, Cherie Gambley
Summary: A zucchini disease outbreak caused by Pseudomonas syringae was investigated in Bundaberg, Australia. The genetic diversity of the isolates obtained from the outbreak was compared to other strains in phylogroup 2. The study identified key factors contributing to virulence and provided new insights into the genomic features of these strains.
Article
Plant Sciences
Benedetta Orfei, Joel F. Pothier, Linda Fenske, Jochen Blom, Chiaraluce Moretti, Roberto Buonaurio, Theo H. M. Smits
Summary: This study sequenced the complete genome of Pseudomonas syringae pv. tomato strain DAPP-PG 215, which was described as a race 0 strain. The analysis revealed that although the strain is phylogenetically related to race 1 strains, it has a race 1 genetic background but harbors a complete ortholog of the avrPto1 gene.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Microbiology
Prem P. Kandel, Marina Naumova, Chad Fautt, Ravikumar R. Patel, Lindsay R. Triplett, Kevin L. Hockett
Summary: Bacterial toxin-antitoxin (TA) systems consisting of toxin and antitoxin genes play important roles in evolution and physiology, however, little is known about their abundance and diversity in plant pathogens. In this study, the genomes of 339 strains representing the Pseudomonas syringae species complex were screened for TA systems, and 26 different families were identified. Further functional characterization of these TA systems could reveal their potential impacts on the ecology, virulence, and disease management practices of P. syringae.
FRONTIERS IN MICROBIOLOGY
(2022)
Editorial Material
Cardiac & Cardiovascular Systems
Gudny A. Arnadottir, David O. Arnar
Summary: This editorial discusses the connection between infanticide and inherited cardiac arrhythmias, emphasizing the fine line between guilt and innocence.
Article
Biochemistry & Molecular Biology
Markus Pfenninger, Philipp Schoennenbeck, Tilman Schell
Summary: Accurate estimation of genome sizes is essential in biodiversity genomics, and this study introduces a method that can estimate genome size from the number of sequenced bases and mean sequencing depth. Simulations demonstrate that even from low-coverage genome drafts, reasonable estimates can be obtained using this method. Comparison with flow cytometry estimates suggests that both methods provide similar and interchangeable results.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Plant Sciences
Noel Djitro, Rebecca Roach, Rachel Mann, Brendan Rodoni, Cherie Gambley
Summary: This study reports the first identification of Pseudomonas syringae strains infecting zucchini in Australia, causing significant yield losses. The isolates exhibited variations in pathogenicity across different plant species and some produced fluorescent pigment. Additionally, it was discovered that different zucchini varieties showed varying levels of susceptibility to the isolates.
Article
Microbiology
Michela Ruinelli, Jochen Blom, Theo H. M. Smits, Joeel F. Pothier
Summary: A comparative genomics approach identified genes significantly associated with strains isolated from Prunus spp., with the HopAY gene predicted to encode a C58 cysteine protease being highly related to these strains, supporting co-evolution and host adaptation patterns.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Tamara Rankovic, Ivan Nikolic, Tanja Beric, Tatjana Popovic, Jelena Lozo, Olja Medic, Slavisa Stankovic
Summary: This study analyzed the draft genome sequences of two pathogenic strains of Pseudomonas syringae pv. aptata to evaluate their survival strategies and pathogenic potential. The results showed differences in genome size, GC content, and protein-coding sequences between the two strains. Furthermore, differences in effector sequences were found to be related to the type III secretion system. This study provides important information on the genomic features, epidemiology, and pathogenic strategies of P. syringae pv. aptata.
MICROBIOLOGY SPECTRUM
(2023)
Review
Agronomy
Balakrishnan Marudamuthu, Tamanna Sharma, Supriya Purru, S. K. Soam, Ch. Srinivasa Rao
Summary: Next-generation sequencing (NGS) is a game-changing technology in genomic research, enabling massively parallel sequencing. In agriculture, NGS has transformed enhancement strategies and simplified genetic modification approaches. This review highlights the available NGS platforms and their applications in agricultural genomics.
GENETIC RESOURCES AND CROP EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Ewa Sieliwonczyk, Bert Vandendriessche, Charlotte Claes, Evy Mayeur, Maaike Alaerts, Philip Holmgren, Tycho Canter Cremers, Dirk Snyders, Bart Loeys, Dorien Schepers
Summary: Despite challenges, researchers have developed a novel method to improve knock-in efficiency using CRISPR-Cas9 technique in zebrafish. By combining the early selection procedure with genotyping and next-generation sequencing, they achieved a significant increase in somatic editing efficiency and demonstrated potential for improving germline transmission in pre-selected embryos.
SCIENTIFIC REPORTS
(2023)
Article
Agronomy
Silvia Turco, Andrea Ferrucci, Mounira Inas Drais, Angelo Mazzaglia
Summary: In this study, the comparative genome analysis of 153 Psa genome sequences revealed new details about the pathogenicity features of different biovars, supporting previous phylogenetic characterisations.
EUROPEAN JOURNAL OF PLANT PATHOLOGY
(2023)
Article
Multidisciplinary Sciences
Amit Rawat, Madhubala Sharma, Pandiarajan Vignesh, Ankur Kumar Jindal, Deepti Suri, Jhumki Das, Vibhu Joshi, Rahul Tyagi, Jyoti Sharma, Gurjit Kaur, Yu-Lung Lau, Kohsuke Imai, Shigeaki Nonoyama, Michael Lenardo, Surjit Singh
Summary: Inborn errors of immunity (IEI) are a group of monogenic disorders that affect different aspects of the immune system. Next-generation sequencing (NGS) is a valuable tool for diagnosing IEI and providing genetic diagnoses for patients. This helps with genetic counseling, prenatal diagnosis, and appropriate therapeutic options for IEI patients.
SCIENTIFIC REPORTS
(2022)
Editorial Material
Plant Sciences
Jian Chen, Rouhallah Shari, Choong-Min Ryu
Summary: Sieber et al. discovered a new volatile signaling molecule, leudiazen, and showed that inactivating it can reduce the pathogenicity of Pseudomonas synngae pv. synngae, providing a new plant protection strategy compatible with organic farming.
TRENDS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Dario Kringel, Sebastian Malkusch, Eija Kalso, Jorn Lotsch
Summary: The genetic background of pain is being increasingly well understood, leading to the development of a cost-effective next generation sequencing-based pain-genotyping assay that identifies the most representative genes associated with pain.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Physical
R. Schwidetzky, P. Sudera, A. T. Backes, U. Poeschl, M. Bonn, J. Froehlich-Nowoisky, K. Meister
Summary: Research shows that ice-nucleating proteins alone are not enough to achieve maximum freezing efficiency. Intact cell membranes play a critical role, and components like phospholipids and lipopolysaccharides enable the assembly of INPs. Additionally, the size and level of order/disorder in these assemblies are crucial in determining bacterial INPs' ability to facilitate ice nucleation.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Surgery
Saranya Sivaraj, Julia K. Copeland, Anshu Malik, Elisa Pasini, Marc Angeli, Amirhossein Azhie, Shahid Husain, Deepali Kumar, Johane Allard, David S. Guttman, Atul Humar, Mamatha Bhat
Summary: By studying the intestinal microbiome of liver transplant recipients, an increase in specific bacterial communities and genes post-surgery was found to be associated with metabolic and infectious diseases.
CLINICAL TRANSPLANTATION
(2022)
Article
Medicine, Research & Experimental
Elissa G. Currie, Bryan Coburn, Elisa A. Porfilio, Ping Lam, Olga L. Rojas, Jan Novak, Stuart Yang, Raad B. Chowdhury, Lesley A. Ward, Pauline W. Wang, Khashayar Khaleghi, James An, Sarah Q. Crome, Michelle A. Hladunewich, Sean J. Barbour, Daniel C. Cattran, Rulan S. Parekh, Christoph Licht, Rohan John, Rupert Kaul, Kenneth Croitoru, Scott D. Gray-Owen, David S. Guttman, Jennifer L. Gommerman, Heather N. Reich
Summary: IgA nephropathy is a leading cause of kidney failure, and aberrant immune responses to mucosal microbiota, particularly Neisseria, may play a role in its pathogenesis. This study found increased carriage of Neisseria and elevated Neisseria-specific IgA levels in the tonsils of IgA nephropathy patients. Experimentally, mice with overexpression of BAFF and susceptible to Neisseria infection showed augmented levels of systemic Neisseria-specific IgA, as well as the presence of anti-Neisseria-specific IgA-secreting cells in the kidneys.
Review
Plant Sciences
Cedoljub Bundalovic-Torma, Fabien Lonjon, Darrell Desveaux, David S. Guttman
Summary: This review surveys the phylogenetic diversity of the P. syringae effectorome and highlights how avoidance of host immune detection has shaped effectorome diversity through functional redundancy, diversification, and horizontal transfer. Emerging avenues for research and novel insights can be gained via large-scale interaction screens and phylogenomic approaches.
ANNUAL REVIEW OF PHYTOPATHOLOGY
(2022)
Article
Gastroenterology & Hepatology
Williams Turpin, Mei Dong, Gila Sasson, Juan Antonio Raygoza Garay, Osvaldo Espin-Garcia, Sun-Ho Lee, Anna Neustaeter, Michelle Smith, Haim Leibovitzh, David S. Guttman, Ashleigh Goethel, Anne M. Griffiths, Hien Q. Huynh, Levinus A. Dieleman, Remo Panaccione, A. Hillary Steinhart, Mark S. Silverberg, Guy Aumais, Kevan Jacobson, David Mack, Sanjay K. Murthy, John K. Marshall, Charles N. Bernstein, Maria T. Abreu, Paul Moayyedi, Andrew D. Paterson, Wei Xu, Kenneth Croitoru
Summary: Mediterranean-like dietary patterns are associated with specific gut microbial compositions and lower levels of intestinal inflammation.
Article
Multidisciplinary Sciences
Clare Breit-McNally, Darrell Desveaux, David S. Guttman
Summary: The study found that the immune response of Arabidopsis thaliana is qualitatively conserved in oilseed crops, but quantitatively distinct. The level of immune conservation decreases with evolutionary distance from Arabidopsis thaliana.
SCIENTIFIC REPORTS
(2022)
Article
Gastroenterology & Hepatology
Haim Leibovitzh, Sun-Ho Lee, Mingyue Xue, Juan Antonio Raygoza Garay, Cristian Hernandez-Rocha, Karen L. Madsen, Jonathan B. Meddings, David S. Guttman, Osvaldo Espin-Garcia, Michelle Smith, Ashleigh Goethel, Anne M. Griffiths, Paul Moayyedi, A. Hillary Steinhart, Remo Panaccione, Hien Q. Huynh, Kevan Jacobson, Guy Aumais, David R. Mack, Maria T. Abreu, Charles N. Bernstein, John K. Marshall, Dan Turner, Wei Xu, Williams Turpin, Kenneth Croitoru
Summary: This study found that alterations in gut microbial composition and functional pathways are associated with changes in gut barrier function. These findings may identify potential microbial targets to modulate gut barrier.
Article
Microbiology
Renan N. D. Almeida, Michael Greenberg, Cedoljub Bundalovic-Torma, Alexandre Martel, Pauline W. Wang, Maggie A. Middleton, Syama Chatterton, Darrell Desveaux, David S. Guttman
Summary: The study investigates the virulence and host specificity of Pseudomonas syringae strains on common bean and demonstrates the power of machine learning in predicting host specific adaptation. The results show that PG3 strains have higher host specificity than PG2 strains, and a machine learning model based on whole genome data can accurately predict virulence. The study strengthens the hypothesis of different lifestyles between PG2 and other P. syringae strains.
Article
Microbiology
Angela Zou, Kerry Nadeau, Xuejian Xiong, Pauline W. Wang, Julia K. Copeland, Jee Yeon Lee, James St Pierre, Maxine Ty, Billy Taj, John H. Brumell, David S. Guttman, Shayan Sharif, Doug Korver, John Parkinson
Summary: This study systematically investigated the composition and function of the chicken gut microbiome in response to AGPs. Results revealed nuanced impacts of AGPs, dependent on age of bird, diet, and intestinal site sampled.
Article
Gastroenterology & Hepatology
Qiaochu Lin, Meggie Kuypers, Zhewei Liu, Julia K. Copeland, Donny Chan, Susan J. Robertson, Jean Kontogiannis, David S. Guttman, E. Kate Banks, Dana J. Philpott, Thierry Mallevaey
Summary: This study demonstrates that iNKT cells have minimal influence on regulating commensal bacteria in the gut at steady state.
Review
Plant Sciences
Clare Breit-McNally, Bradley Laflamme, Racquel A. Singh, Darrell Desveaux, David S. Guttman
Summary: A key aspect of innate immunity in plants involves the recognition of pathogen effector virulence proteins by host Nucleotide-Binding Leucine-Rich Repeat Receptors (NLRs). The ZAR1 NLR has the remarkable ability to recognize at least six different families of effectors from two bacterial genera. This broad recognition is achieved through interactions with two families of Receptor-Like Cytoplasmic Kinases (RLCKs): ZED1-Related Kinases (ZRKs) and PBS1-Like Kinases (PBLs).
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Connor R. Fitzpatrick, Julia Copeland, Pauline W. Wang, David S. Guttman, Peter M. Kotanen, Marc T. J. Johnson
Summary: The root microbiome consists of distinct epiphytic and endophytic habitats, with differences in abiotic and biotic factors driving diversity and composition differences between these habitats. Our study found significant differences in bacterial community between the rhizosphere and endosphere, with higher connectivity observed among core bacterial members in the endosphere. Taxonomic assortativity was higher in the endosphere, with positive co-occurrence more likely among bacteria within the same phylum and negative co-occurrence more likely between bacterial taxa from different phyla. Drought had limited effects on network properties but increased the proportion of shared co-occurrences between rhizosphere and endosphere networks.
MOLECULAR PLANT-MICROBE INTERACTIONS
(2023)
Article
Multidisciplinary Sciences
Amanda J. Morris, Yvonne C. W. Yau, Subin Park, Shafinaz Eisha, Nancy McDonald, Matthew R. Parsek, P. Lynne Howell, Lucas R. Hoffman, Dao Nguyen, Antonio DiGiandomenico, Ashley M. Rooney, Bryan Coburn, Lucia Grana-Miraglia, Pauline Wang, David S. Guttman, Daniel J. Wozniak, Valerie J. Waters
Summary: This study visualized P. aeruginosa in the sputum of children with cystic fibrosis to validate previous findings. The results showed that after inhaled tobramycin eradication treatment, patients with persistent infection had higher P. aeruginosa biovolume, more expressed Psl, and formed more numerous and larger aggregates in their sputum compared to those who successfully cleared the infection.
SCIENTIFIC REPORTS
(2022)
Article
Microbiology
Tatiana Ruiz-Bedoya, Pauline W. Wang, Darrell Desveaux, David S. Guttman
Summary: This study investigates whether non-virulent strains can contribute to the emergence of collective virulence through the secretion of effectors as public goods. The researchers found that, although individually unfit, a metaclone consisting of 36 coisogenic strains of Pseudomonas syringae could collectively exhibit the same level of virulence as the wild-type strain on Arabidopsis thaliana, suggesting the role of effectors in driving cooperation-based virulence. Furthermore, independently evolved effector suits and transferred effector alleles were found to drive this cooperative behavior.
NATURE MICROBIOLOGY
(2023)
Meeting Abstract
Gastroenterology & Hepatology
H. Leibovitzh, S. H. Lee, M. Xue, J. A. Raygoza Garay, C. Hernandez-Rocha, K. L. Madsen, J. B. Meddings, D. S. Guttman, O. Espin-Garcia, M. I. Smith, A. Goethel, P. Moayyedi, A. H. Steinhart, R. Panancionne, H. Huynh, K. Jacobson, G. Aumais, D. R. Mack, M. Abreu, C. N. Bernstein, J. K. Marshall, D. Turner, W. Xu, W. Turpin, K. Croitoru
JOURNAL OF CROHNS & COLITIS
(2022)
Meeting Abstract
Gastroenterology & Hepatology
Mingyue Xue, Haim Leibovitzh, Sun-Ho Lee, Anna Neustaeter, Wei Xu, Osvaldo Espin-Garcia, Karen Madsen, David S. Guttman, Anne M. Griffiths, Hien Q. Huynh, Dan Turner, Remo Panaccione, A. Hillary Steinhart, Guy L. Aumais, Alain Bitton, Kevan Jacobson, David R. Mack, Williams Turpin, Kenneth Croitoru
