Article
Biology
Hajime Nakatani, Katsutoshi Hori
Summary: By using zebrafish and Yersinia ruckeri, a pathogen causing redmouth disease in salmon and trout, we investigated the impact of cold stress, injury, and pathogen challenge on fish skin bacterial flora. Our results show that cold stress significantly alters the skin bacterial flora, and disrupting the intrinsic skin bacterial flora of fish allows pathogens to colonize and dominate their skin.
Article
Engineering, Environmental
Wenhui Qiu, Tang Liu, Xinjie Liu, Honghong Chen, Shusheng Luo, Qiqing Chen, Jason T. Magnuson, Chunmiao Zheng, Elvis Genbo Xu, Daniel Schlenk
Summary: The immunosuppressive effects of antibiotics and their association with the intestinal microbiota have been studied in zebrafish. The results showed that treatment with enrofloxacin resulted in a decrease in the diversity, richness, and evenness of the intestinal flora in zebrafish. The abundance of certain gut bacteria was significantly correlated with immunosuppressive biomarkers. The study also found that the immunosuppressive effects of enrofloxacin were mediated through alterations of the intestinal microbiome in zebrafish.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Ashwath Nayak, Mave Harshitha, Saurabh Dubey, Hetron Mweemba Munang'andu, Anirban Chakraborty, Indrani Karunasagar, Biswajit Maiti
Summary: The indiscriminate use of antibiotics in aquaculture has led to the emergence of resistance. This study isolated and evaluated bacteria as potential probiotics, finding Bacillus subtilis from Labeo rohita with broad-spectrum inhibitory activity against Aeromonas hydrophila and Edwardsiella tarda. In vitro and in vivo experiments confirmed its probiotic attributes and ability to inhibit the two fish pathogens, making it a promising alternative to antibiotics in aquaculture.
PROBIOTICS AND ANTIMICROBIAL PROTEINS
(2023)
Article
Microbiology
David Perez-Pascual, Sol Vendrell-Fernandez, Bianca Audrain, Joaquin Bernal-Bayard, Rafael Patino-Navarrete, Vincent Petit, Dimitri Rigaudeau, Jean-Marc Ghigo
Summary: The study focused on host-microbiota-pathogen interactions in rainbow trout, demonstrating the importance of specific probiotic bacterial strains in conferring resistance against Flavobacterium columnare infections.
Article
Environmental Sciences
Larissa Cristine de Carvalho Penha, Regina Coimbra Rola, Flavio Manoel da Silva Junior, Camila de Martinez Gaspar Martins
Summary: This study evaluated the effects of MeP on zebrafish larvae and adults, showing that adults were more sensitive to MeP than larvae. Exposure to MeP resulted in impaired biotransformation and suppressed biological responses in adult fish, while sublethal exposure did not cause toxicity to larvae. Results also indicated that MeP induced lipid peroxidation and genotoxicity in adult fish, highlighting the importance of regulating the presence of this compound in the environment and improving cleaning processes.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2021)
Article
Environmental Sciences
Hui Wang, Suzhen Qi, Xiyan Mu, Lilai Yuan, Yingren Li, Jing Qiu
Summary: This study found that long-term exposure to BPF can lead to liver-gut alteration and metabolic changes in zebrafish. The effects of BPF on liver metabolism were dose-dependent, affecting amino acid, purine, and one carbon metabolism in the 0.5, 5, and 50 mu g/L treatments, respectively. In addition, BPF also caused a shift in intestinal microbiome composition.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Environmental Studies
Cesar Saenz
Summary: The research results show that mining companies employ different strategies in community relations based on the level of economic partnership and community ownership, which can be categorized into competing, compliant, paternalistic, and sustainable strategies.
Article
Fisheries
Lei Zhu, Yiming Kong, Xulu Chang, Junchang Feng, Xinru Wang, Libo Hou, Xianliang Zhao, Chao Pei, Xianghui Kong
Summary: The study demonstrated that fish-derived probiotics can improve the growth performance, immune response, intestinal microbiota diversity, and pathogen resistance of crayfish, suggesting their potential as feed additives in aquaculture.
Article
Engineering, Environmental
Jun-Nan Huang, Yuan Zhang, Lei Xu, Kai-Xuan He, Bin Wen, Pei-Wen Yang, Jie-Yu Ding, Jing-Ze Li, Huan-Chao Ma, Jian-Zhong Gao, Zai-Zhong Chen
Summary: The exposure of Discus fish to polystyrene microplastics significantly inhibited growth performance and led to changes in microbial community in different tissues. The study also demonstrated tissue-specific effects of microplastics on oxidative stress and enzyme activity, highlighting the potential impacts of microplastics on aquatic organisms.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Biotechnology & Applied Microbiology
Chune Zhou, Wei Zhao, Shuqiang Zhang, Junguo Ma, Yousef Sultan, Xiaoyu Li
Summary: This study identified three key stages of cardiovascular development in zebrafish through transcriptome sequencing. It identified a large number of differentially expressed genes involved in cardiovascular development and demonstrated significant differences in gene expression between different developmental stages. These findings provide important insights for further research on cardiovascular development.
Article
Plant Sciences
Li-Ping Ban, Jin-Dong Li, Min Yan, Yu-Hao Gao, Jin-Jin Zhang, Timothy W. Moural, Fang Zhu, Xue-Min Wang
Summary: The study demonstrates that NGS is an effective and reliable method for monitoring microbial communities within turfgrass seeds. Various fungal and bacterial pathogens were detected through DNA sequencing, with traditional culturing and NGS methods complementing each other to ensure maximum sensitivity and specificity in seed pathogen testing. The combination of different techniques validates the reliability of culturing and NGS methods in seed pathogen identification.
Article
Immunology
Li Ding, Yanmin Liu, Xiaorong Wu, Minhao Wu, Xiaoqing Luo, Hui Ouyang, Jinyu Xia, Xi Liu, Tao Ding
Summary: This study characterized the distinct lung microbial features between bacteriologically confirmed and negative tuberculosis patients, revealing the influence of microbiota on tuberculosis patients. The correlation between unique features of lung microbial dynamics and clinical characteristics of tuberculosis patients was comprehensively demonstrated, underscoring the importance of studying the pulmonary microbiome in tuberculosis disease for precision diagnosis and treatment.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Environmental Sciences
Zhijuan Nie, Xiaotong Xu, Nailing Shao, Jian He, Pengfa Li, Pao Xu, Jiawen Hu, Wei Qin, Baozhan Wang, Gangchun Xu
Summary: This study investigated the gut microbiome and metabolome of fast-growing and slow-growing carp in a rice-fish coculture system. The results showed significant differences in the gut microbiota and metabolic pathways between the two groups. These differences led to increased steroid hormone biosynthesis and decreased pathways related to beta-alanine metabolism, biosynthesis of unsaturated fatty acids, and bile secretion in the slow-growing group. These findings have important implications for the development of microbiome technologies in aquaculture.
ENVIRONMENTAL RESEARCH
(2023)
Article
Microbiology
Jonas Schluter, Ana Djukovic, Bradford P. Taylor, Jinyuan Yan, Caichen Duan, Grant A. Hussey, Chen Liao, Sneh Sharma, Emily Fontana, Luigi A. Amoretti, Roberta J. Wright, Anqi Dai, Jonathan U. Peled, Ying Taur, Miguel-Angel Perales, Benjamin A. Siranosian, Ami S. Bhatt, Marcel R. M. van den Brink, Eric G. Pamer, Joao B. Xavier
Summary: TaxUMAP is a visualization tool that allows for the display of microbiome states in large clinical datasets. It was used to create a microbiome atlas of 1,870 cancer patients undergoing therapy-induced perturbations. The tool revealed associations between bacterial density, diversity, and antimicrobial resistance genes. It also identified certain species associated with lower risk for bacteremia, validating a competitive interaction. TaxUMAP provides valuable insights into the effects of the microbiome on human health.
CELL HOST & MICROBE
(2023)
Article
Microbiology
Raja Aadil Hussain Bhat, Victoria C. Khangembam, Dimpal Thakuria, Vinita Pant, Ritesh Shantilal Tandel, Gayatri Tripathi, Debajit Sarma
Summary: In this study, a peptide called KK16 was designed with potent antibacterial and antifungal activity and low toxicity to host cells. The peptide showed strong efficacy against various pathogenic bacteria and remained stable under different environmental conditions.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Biology
Francesc Coll, Theodore Gouliouris, Sebastian Bruchmann, Jody Phelan, Kathy E. Raven, Taane G. Clark, Julian Parkhill, Sharon J. Peacock
Summary: PowerBacGWAS is a computational pipeline that performs power calculations for bacterial genome-wide association studies using existing genomic data. This tool implements two alternative approaches for power calculations and can determine sample sizes required to detect causal variants of different minor allele frequencies, effect sizes, and phenotype heritability. It can also be applied to other bacterial populations to determine statistically significant associations or detectable associations with a given sample size.
COMMUNICATIONS BIOLOGY
(2022)
Article
Immunology
Nicole C. Thunes, Haitham H. Mohammed, Jason P. Evenhuis, Ryan S. Lipscomb, David Perez-Pascual, Rebecca J. Stevick, Clayton Birkett, Rachel A. Conrad, Jean-Marc Ghigo, Mark J. McBride
Summary: Flavobacterium columnare is a pathogen that causes columnaris disease in freshwater fish, both in natural water bodies and aquaculture settings. This disease is often fatal, especially in high fish population density, and current control options, such as vaccines, are limited. The type IX secretion system (T9SS) is crucial for the virulence of F. columnare, but the specific virulence factors that are secreted through this system are not fully known. This study found that peptidases, which are commonly known virulence factors in other pathogens, may also play a role in F. columnare virulence.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Lisa Neffe, Taya L. Forde, Katarina Oravcova, Ute Koehler, Wilfried Bautsch, Juergen Tomasch, Susanne Haeussler
Summary: This study used whole-genome sequencing to describe the population structure of ESBL-producing Escherichia coli and Klebsiella pneumoniae isolates from a German community hospital. The study found a high proportion of globally disseminated ST131 strains among E. coli isolates, while K. pneumoniae isolates showed wider diversity of STs. Genetic analysis revealed multiple introductions of ST131 strains and a regional clustering of clinical isolates. Patient-to-patient transmission was rare, suggesting a primarily community and regional acquisition of ESBL-producing strains.
MICROBIAL GENOMICS
(2022)
Article
Microbiology
Michal Koska, Adrian Kordes, Jelena Erdmann, Sven D. Willger, Janne G. Thoeming, Heike Baehre, Susanne Haeussler
Summary: This study reveals that the regulation of c-di-GMP levels and colony morphology in Pseudomonas aeruginosa can follow different evolutionary paths. The delayed switching of c-di-GMP levels in response to fluctuating environmental conditions may provide a unique opportunity to close the gap between short-term phenotypic and long-term genetic adaptation.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Francesca D'Angelo, Eduardo P. C. Rocha, Olaya Rendueles
Summary: The extracellular capsule, a virulence factor found in many pathogens, has a controversial role in antimicrobial resistance. Our study found that noncapsulated strains of Klebsiella pneumoniae exhibited increased resistance to polymyxins, but not to other antibiotics. These findings caution against the use of therapeutic agents targeting the capsule, as it may lead to its inactivation.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2023)
Article
Biochemistry & Molecular Biology
Julia Aguilera-Herce, Concepcion Panadero-Medianero, Maria Antonia Sanchez-Romero, Roberto Balbontin, Joaquin Bernal-Bayard, Francisco Ramos-Morales
Summary: Type III secretion systems are commonly found in many Gram-negative pathogens and symbionts. Salmonella enterica possess two type III secretion systems associated with virulence, one for host cell invasion and another for intracellular niche maintenance. This study investigates the biochemical function of the SrfJ effector and its impact on mammalian host cells. The results indicate that SrfJ acts as a glucosylceramidase, altering the lipidome and transcriptome of host cells, both in epithelial cells and macrophages during Salmonella infection. Furthermore, analysis of gene expression changes suggests that SrfJ may play a role in protecting Salmonella from host immune defenses.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Leticia Larotonda, Damien Mornico, Varun Khanna, Joaquin Bernal-Bayard, Jean-Marc Ghigo, Marie-Eve Val, Diego Comerci, Didier Mazel, Alfonso Soler-Bistue
Summary: The location of ribosomal protein genes on the bacterial chromosome conditions the evolutionary trajectory of Vibrio cholerae. Moving these genes away from the replication origin reduces growth rate, fitness, and infectivity. No mutation can compensate for the growth defect caused by gene relocation.
Article
Biology
Olaya Rendueles, Jorge A. M. de Sousa, Eduardo P. C. Rocha
Summary: Many bacterial genomes carry prophages that can eliminate competitors, and bacteria can develop resistance through various mechanisms, such as surface receptor modification or lysogenization. The adaptation process of phage resistance involves both genetic and non-genetic changes. Our study showed that the frequency of capsulated cells in phage-sensitive populations increased over time, indicating the fine-tuning of capsule production as an adaptation to reduce phage absorption.
Article
Microbiology
Kathrin Alpers, Elisabeth Vatareck, Lothar Groebe, Mathias Muesken, Maren Scharfe, Susanne Haeussler, Jurgen Tomasch
Summary: Pseudomonas aeruginosa undergoes a transition from fast growth with overlapping cell cycles to sustained slow growth with non-overlapping cell cycles when cultivated under standard laboratory conditions. This transition is characterized by sequential changes in transcriptional activity along the chromosome and a shift in quorum sensing activity. RNA sequencing of subpopulations identified distinct gene expression patterns for replicating and nonreplicating cells.
Article
Oncology
Leah S. Stockman, Daniel A. Gundersen, Ajami Gikandi, Ruth N. Akindele, Ludmila Svoboda, Sarah Pohl, Mark R. Drews, Christopher S. Lathan
Summary: Cancer disparities among historically marginalized populations are addressed through a clinical outreach program that integrates cancer diagnostic services and patient navigation within a community-based primary healthcare setting. The program aims to expedite cancer diagnoses and establish collaborative care between oncology specialists and primary care providers. The majority of patients self-identified as Black and Hispanic, with a high prevalence of comorbid health conditions and financial distress.
JCO ONCOLOGY PRACTICE
(2023)
Article
Biochemical Research Methods
Debbie Pankratz, Nicolas Oswaldo Gomez, Agnes Nielsen, Ayten Mustafayeva, Melisa Guer, Fabian Arce-Rodriguez, Pablo Ivan Nikel, Susanne Haeussler, Alejandro Arce-Rodriguez
Summary: Much of our current understanding of microbiology is based on the application of genetic engineering procedures. In this article, a method for precise and efficient engineering of Pseudomonas aeruginosa is presented. This method utilizes targeted double-strand DNA breaks and efficient recombinase to introduce a range of genetic modifications, reducing the time required for these manipulations.
Article
Biotechnology & Applied Microbiology
Amandine Nucci, Eduardo P. C. Rocha, Olaya Rendueles
Summary: Adaptation to one environment can impact an organism's ability to thrive in other environmental conditions. Biofilm formation can increase survival rates against host immune system or antibiotic therapy. However, how adaptation affects biofilm formation and changes over time is poorly studied. Using Klebsiella pneumoniae, we found that biofilm formation ability changed rapidly initially but reverted to ancestral levels. Nutrient availability, genetic background, and other phenotypic and genotypic changes influenced the evolution of biofilm formation. These findings suggest that small environmental differences can affect an organism's fate in complex niches like the host.
NPJ BIOFILMS AND MICROBIOMES
(2023)
