Review
Agronomy
Muhammad Fazle Rabbee, Buyng-Su Hwang, Kwang-Hyun Baek
Summary: Microbial biocontrol agents, particularly Bacillus velezensis, have gained popularity as efficient and environment-friendly tools in eradicating plant pathogenic bacteria. However, recent research also highlights the potential negative aspects of this bacterium, including its virulence traits in infecting crops like peach, onion, and potato. Therefore, caution should be exercised when using B. velezensis in novel crop cultivation techniques.
Article
Medicine, General & Internal
Jorge Calderon Parra, Daniel De Castro-Campos, Patricia Munoz Garcia, Maria Olmedo Samperio, Mercedes Marin Arriaza, Aristides De Alarcon, Encarnacion Gutierrez-Carretero, Maria Carmen Farinas Alvarez, Jose Maria Miro Meda, Miguel Angel Goneaga Sanchez, Raquel Rodriguez Garcia, Guillermo Ojeda Burgos, Zeltia Valcarce-Gonzalez, Antonio Ramos-Martinez
Summary: IE caused by non-HACEK Gram-Negative Bacilli is a rare infection affecting elderly patients with high comorbidity, nosocomial acquisition, and unfavorable outcome. Factors associated with mortality include age, prosthetic valve, and failure to undergo indicated surgery. Patients treated with quinolone combination therapy had lower mortality rates.
EUROPEAN JOURNAL OF INTERNAL MEDICINE
(2021)
Article
Multidisciplinary Sciences
Paul W. Chrystal, Nils J. Lambacher, Lance P. Doucette, James Bellingham, Elena R. Schiff, Nicole C. L. Noel, Chunmei Li, Sofia Tsiropoulou, Geoffrey A. Casey, Yi Zhai, Nathan J. Nadolski, Mohammed H. Majumder, Julia Tagoe, Fabiana D'Esposito, Maria Francesca Cordeiro, Susan Downes, Jill Clayton-Smith, Jamie Ellingford, Omar A. Mahroo, Jennifer C. Hockin, Michael E. Cheetham, Andrew R. Webster, Gert Jansen, Oliver E. Blacque, W. Ted Allison, Ping Yee Billie Au, Ian M. MacDonald, Gavin Arno, Michel R. Leroux
Summary: Motile and non-motile cilia have distinct functions and CFAP20 protein plays a critical role in both types. This study reveals the importance of CFAP20 in maintaining motile cilia function and the structural integrity of non-motile cilia inner junctions.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Malgorzata Brauncajs, Filip Bielec, Anna Macieja, Dorota Pastuszak-Lewandoska
Summary: Gram-negative fermenting and non-fermenting bacteria, especially those that produce carbapenemases, are important etiological factors of nosocomial and community infections. New antibiotics and treatment regimens offer hope against these infections.
Article
Microbiology
Rohit Ruhal, Rashmi Kataria
Summary: Biofilms formed by Gram-positive and Gram-negative bacteria are the root cause of industrial biofouling and antimicrobial resistance during infections. To understand the mechanisms of biofilm formation better, it is essential to study common components and genetic regulations that are shared among the two types of bacteria.
MICROBIOLOGICAL RESEARCH
(2021)
Article
Immunology
Qingliang Wang, Xiaojie Li, Wenting Tang, Xiaoling Guan, Zhiyong Xiong, Yong Zhu, Jiao Gong, Bo Hu
Summary: This study explored the gene differences between Gram-negative, Gram-positive, and mixed infections in sepsis using genome-wide techniques. The results showed molecular heterogeneity between Gram-negative and Gram-positive sepsis, which was confirmed in the validation dataset.共有40个共同的差异基因集识别. The findings offer new insights into investigating the pathophysiology of bacterial sepsis.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Immunology
Sunish Shah, Lloyd G. Clarke, Ryan K. Shields
Summary: This study describes the changing epidemiology of gram-negative infective endocarditis (GNIE) and identifies factors associated with treatment failure and death. Serratia spp. is found to be the most common pathogen causing GNIE, especially among persons who inject drugs. Patients infected with P. aeruginosa have higher microbiologic failure rates. Combination antimicrobial therapy does not improve clinical outcomes.
OPEN FORUM INFECTIOUS DISEASES
(2023)
Article
Medicine, General & Internal
Sharan Silvarajoo, Chan Jan Bond, Embong Zunaina
Summary: A 42-year-old male presented with generalized redness and painless blurring of vision in the left eye, with subsequent fever and left leg abscess. Despite multiple treatments including antibiotics and vitrectomy, his left eye vision deteriorated to nonperception of light due to non-sporulating fungal infection.
CUREUS JOURNAL OF MEDICAL SCIENCE
(2021)
Article
Microbiology
Svetlana Sadyrbaeva-Dolgova, Maria del Mar Sanchez-Suarez, Juan Antonio Reguera Marquez, Carmen Hidalgo-Tenorio
Summary: Nosocomial infections caused by non-fermenting Gram-negative bacteria, including bloodstream infections, are a significant therapeutic management challenge for clinicians. This retrospective study analyzed the clinical characteristics, empirical antibiotic therapy, and risk factors related to clinical failure. The study found low accuracy of empirical treatment, especially for S. maltophilia and A. baumanii, and identified factors such as ICU admission, sepsis or shock septic, age, previous antibiotic treatment, and contact with healthcare facilities associated with clinical failure.
Article
Multidisciplinary Sciences
Kumar Sachin Singh, Rishabh Sharma, Poli Adi Narayana Reddy, Prashanthi Vonteddu, Madeline Good, Anjana Sundarrajan, Hyeree Choi, Kar Muthumani, Andrew Kossenkov, Aaron R. Goldman, Hsin-Yao Tang, Maxim Totrov, Joel Cassel, Maureen E. Murphy, Rajasekharan Somasundaram, Meenhard Herlyn, Joseph M. Salvino, Farokh Dotiwala
Summary: Isoprenoids are essential for maintaining cellular functions and IspH is a crucial enzyme in their synthesis pathway. Through structure-guided design, a class of IspH inhibitors with nanomolar potency were identified, showing efficacy against multidrug-resistant bacteria while being relatively non-toxic to mammalian cells. These prodrugs also induce expansion and activation of human V gamma 9V delta 2 T cells, suggesting a potential strategy to limit antibiotic-resistant bacterial populations.
Review
Immunology
Arsheena Yassin, Mariya Huralska, Jason M. Pogue, Deepali Dixit, Robert G. Sawyer, Keith S. Kaye
Summary: The prevalence of multidrug-resistant gram-negative bacterial infections has significantly increased in the past decade, leading to higher rates of morbidity and mortality. Treating these infections presents challenges, particularly for critically ill patients with limited margin for error. The availability of new therapies has improved treatment options, but optimal clinical and therapeutic approaches for managing these infections still need to be established.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Infectious Diseases
Richard G. Wunderink, Yuko Matsunaga, Mari Ariyasu, Philippe Clevenbergh, Roger Echols, Keith S. Kaye, Marin Kollef, Anju Menon, Jason M. Pogue, Andrew F. Shorr, Jean-Francois Timsit, Markus Zeitlinger, Tsutae D. Nagata
Summary: Cefiderocol was found to be non-inferior to high-dose, extended-infusion meropenem in terms of all-cause mortality on day 14 in patients with Gram-negative nosocomial pneumonia, with similar tolerability. This suggests that cefiderocol is a potential option for the treatment of patients with nosocomial pneumonia, including those caused by multidrug-resistant Gram-negative bacteria.
LANCET INFECTIOUS DISEASES
(2021)
Article
Infectious Diseases
Faduma Nur Adan, Mohamed Osman Omar Jeele, Nasteho Mohamed Sheikh Omar
Summary: This study analyzes the epidemiology of MDR-NFGNB among HAP patients in a tertiary care hospital in Somalia. The prevalence rate of NFGNB in HAP patients was 8%, with higher rates in men and the elderly. Acinetobacter baumannii and Stenotrophomonas maltophilia exhibited the highest antibiotic resistance rate.
INFECTION AND DRUG RESISTANCE
(2022)
Article
Immunology
Andrew Bock, Blake M. Hanson, Felicia Ruffin, Joshua B. Parsons, Lawrence P. Park, Batu Sharma-Kuinkel, Michael Mohnasky, Cesar A. Arias, Vance G. Fowler, Joshua T. Thaden
Summary: Recurrent gram-negative bacterial bloodstream infections (GNB-BSI) are mainly caused by relapse, and pulsed-field gel electrophoresis accurately differentiates relapse from reinfection. Having a cardiac device is a risk factor for relapse.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Infectious Diseases
Cristina Corsini Campioli, Natalia E. Castillo Almeida, John C. O'Horo, Walter R. Wilson, Edison Cano, Daniel C. DeSimone, Larry M. Baddour, M. Rizwan Sohail
Summary: This retrospective study investigated adult patients with monomicrobial brain abscesses caused by gram-positive and gram-negative bacteria. The study found that brain abscesses caused by gram-negative bacteria were more likely to occur in patients with a history of head and neck surgery. In terms of treatment failure, gram-negative bacteria had a higher rate compared to gram-positive bacteria.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Hematology
Naser Ansari-Pour, Mehmet Samur, Erin Flynt, Sarah Gooding, Fadi Towfic, Nicholas Stong, Maria Ortiz Estevez, Konstantinos Mavrommatis, Brian Walker, Gareth Morgan, Nikhil Munshi, Herve Avet-Loiseau, Anjan Thakurta
Summary: Large-scale analysis of relapsed/refractory multiple myeloma (rrMM) shows significant genomic variation compared to newly diagnosed multiple myeloma (ndMM). This variation may be associated with therapeutic exposures and clonal structure. Genomic aberrations associated with resistance to immunomodulatory agent (IMiD) therapy are identified and their role in therapy evasion should be further evaluated.
Article
Entomology
Saraswoti Neupane, Brandon Hall, Grant Brooke, Dana Nayduch
Summary: House flies mechanically vector disease-causing microorganisms. This study found that the preference for different foods varied with the sex of the flies, with females preferring protein and carbohydrate-rich milk, and males preferring carbohydrate-rich sugar. The preference for milk was higher in mated females. The presence of multiple food types reduced the influence of food color on fly feeding preference.
JOURNAL OF MEDICAL ENTOMOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Benjamin D. Lee, Uri Neri, Simon Roux, Yuri I. Wolf, Antonio Pedro Camargo, Mart Krupovic, Peter Simmonds, Nikos Kyrpides, Uri Gophna, Valerian V. Dolja, Eugene V. Koonin
Summary: We developed a computational pipeline to identify viroid-like cccRNAs and found a 5-fold increase in the number of identified elements compared to previous studies. The presence of viroid-like cccRNAs in diverse transcriptomes and ecosystems suggests that their host range is broader than currently known.
Article
Ecology
Antonio P. Camargo, Rafael S. C. de Souza, Juliana Jose, Isabel R. Gerhardt, Ricardo A. Dante, Supratim Mukherjee, Marcel Huntemann, Nikos C. Kyrpides, Marcelo F. Carazzolle, Paulo Arruda
Summary: The grassland ecosystem of Brazilian campos rupestres has low concentrations of phosphorus and nitrogen, yet supports a high plant diversity. This study explores the taxonomic profile and functional potential of microbial communities associated with two plant species of the campos rupestres. The results show that the soil and rock communities associated with these plants share a core group of efficient colonizers enriched in certain bacterial families. The microbial populations associated with plant roots have a genetic repertoire for organic compound intake, phosphorus and nitrogen turnover, highlighting their role in nutrient availability.
Article
Biochemistry & Molecular Biology
Antonio Pedro Camargo, Stephen Nayfach, I-Min A. Chen, Krishnaveni Palaniappan, Anna Ratner, Ken Chu, Stephan J. Ritter, T. B. K. Reddy, Supratim Mukherjee, Frederik Schulz, Lee Call, Russell Y. Neches, Tanja Woyke, Natalia N. Ivanova, Emiley A. Eloe-Fadrosh, Nikos C. Kyrpides, Simon Roux
Summary: Viruses play critical roles in all microbiomes and their genomic diversity and impacts on biological processes are extensively explored through metagenomics. IMG/VR is a platform providing access to a large collection of viral sequences along with functional annotation and metadata. The latest version, IMG/VR v4, contains over 15 million virus genomes and genome fragments.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
I-Min A. Chen, Ken Chu, Krishnaveni Palaniappan, Anna Ratner, Jinghua Huang, Marcel Huntemann, Patrick Hajek, Stephan J. Ritter, Cody Webb, Dongying Wu, Neha J. Varghese, T. B. K. Reddy, Supratim Mukherjee, Galina Ovchinnikova, Matt Nolan, Rekha Seshadri, Simon Roux, Axel Visel, Tanja Woyke, Emiley A. Eloe-Fadrosh, Nikos C. Kyrpides, Natalia N. Ivanova
Summary: The Integrated Microbial Genomes & Microbiomes system (IMG/M) at the Department of Energy Joint Genome Institute (JGI) provides support for comparative analysis of various genomes, metagenomes, and metatranscriptomes. It includes datasets from JGI, as well as imported datasets from public sources and user-submitted datasets. In recent years, efforts have been made to improve annotation pipeline, upgrade reference database versions, and add new analysis functionalities.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Genetics & Heredity
Saraswoti Neupane, Travis Davis, Dana Nayduch, Bethany L. L. McGregor
Summary: This study found that microbial communities play an important role in midge larval habitat utilization. Habitat and grazing type significantly influenced the composition of bacterial, protistan, fungal, and metazoan communities. Soil properties also influenced microbial communities and the presence of midges. Grazed areas had higher prevalence of midges, possibly due to the abundance of hosts and food.
ENVIRONMENTAL MICROBIOME
(2023)
Article
Mycology
Aaron Robinson, Michal Babinski, Yan Xu, Julia Kelliher, Reid Longley, Patrick Chain
Summary: Research on bacterial-fungal interactions (BFIs) has shown that fungi and bacteria often interact with each other in various ecosystems and microbiomes. However, assessing the current state of BFI research is challenging due to a lack of centralized resources. To address this issue, we have developed a publicly accessible database to document previously reported interactions between bacterial and fungal taxa, serving as a centralized resource for the field.
Review
Microbiology
Dana Nayduch, Saraswoti Neupane, Victoria Pickens, Tanya Purvis, Cassandra Olds
Summary: House flies are recognized as filth-associated organisms causing public nuisances. They bridge the gap between breeding environments and habitations, creating sanitation issues. Scientific surveys show that fly carriage of bacterial pathogens is more widespread and dangerous than thought, including antimicrobial resistance genes. Flies not only harbor but also transmit viable and infectious bacterial pathogens. The extent of fly dissemination of pathogens is extensive. The house fly's role as a reservoir, disseminator, and vector for pathogens has been greatly underestimated.
Article
Entomology
Saraswoti Neupane, Justin L. Talley, David B. Taylor, Dana Nayduch
Summary: This study reveals that the bacterial composition of house flies is influenced by farm type and location, with variation in microbial communities among flies from different geographical areas. House flies play a significant role in the transmission of pathogenic bacteria and antibiotic resistance genes.
JOURNAL OF MEDICAL ENTOMOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Antonio Pedro Camargo, Lee Call, Simon Roux, Stephen Nayfach, Marcel Huntemann, Krishnaveni Palaniappan, Anna Ratner, Ken Chu, Supratim Mukherjeep, T. B. K. Reddy, I-Min A. Chen, Natalia N. Ivanova, Emiley A. Eloe-Fadrosh, Tanja Woyke, David A. Baltrus, Salvador Castaneda-Barba, Fernando de la Cruz, Barbara E. Funnell, James P. J. Hall, Aindrila Mukhopadhyay, Eduardo P. C. Rocha, Thibault Stalder, Eva Top, Nikos C. Kyrpides
Summary: This study introduces the IMG/PR database, which collects a large number of plasmid sequences from various microbiome samples and provides rich metadata and multiple browsing methods.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Mathematical & Computational Biology
Supratim Mukherjee, Galina Ovchinnikova, Dimitri Stamatis, Cindy Tianqing Li, I-Min A. Chen, Nikos C. Kyrpides, T. B. K. Reddy
Summary: The power of next-generation sequencing has led to a massive increase in projects aiming to understand the diversity of complex microbial environments. However, the lack of standardized reporting standards for microbiome data and samples poses a challenge for follow-up studies. The Genomes OnLine Database (GOLD) has developed a standardized naming system for microbiome samples to address this issue and has continued to enrich the research community with well-curated and understandable names for metagenomes and metatranscriptomes. This naming system should be adopted as a best practice to improve the interoperability and reusability of microbiome data.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)
Article
Microbiology
Michelle Qiu Carter, Beatriz Quinones, Xiaohua He, Antares Pham, Diana Carychao, Michael B. Cooley, Chien-Chi Lo, Patrick S. G. Chain, Rebecca L. Lindsey, James L. Bono
Summary: Through comparative genomics and phenotypic characterization, this study assessed the pathogenic potential of Escherichia albertii strains isolated from wild birds in California. The results showed that these strains have high pathogenicity potential and could cause severe diseases in humans.
