Latest Articles
Research Article | Host-Microbe BiologyRNA Sequencing-Based Genome Reannotation of the Dermatophyte Arthroderma benhamiae and Characterization of Its Secretome and Whole Gene Expression Profile during InfectionDermatophytoses (ringworm, jock itch, athlete’s foot, and nail infections) are the most common fungal infections, but their virulence mechanisms are poorly understood. Combining transcriptomic data obtained from growth under various culture conditions with data obtained during infection led to a significantly improved genome annotation. About 65% of the protein-encoding genes predicted with our protocol did not match the existing...
Editor's Pick Minireview | Applied and Environmental ScienceWhat Have We Learned about the Microbiomes of Indoor Environments?The advent and application of high-throughput molecular techniques for analyzing microbial communities in the indoor environment have led to illuminating findings and are beginning to change the way we think about human health in relation to the built environment. Here I review recent studies on the microbiology of the built environment, organize their findings into 12 major thematic categories, and comment on how these studies have or...
Research Article | Applied and Environmental ScienceMultiplexed Metagenomic Deep Sequencing To Analyze the Composition of High-Priority Pathogen ReagentsBoth the integrity and reproducibility of experiments using select agents depend in large part on unbiased validation to ensure the correct identity and purity of the species in question. Metagenomic deep sequencing (MDS) provides the required level of validation by allowing for an unbiased and comprehensive assessment of all the microbes in a laboratory stock.
Research Article | Clinical Science and Epidemiology16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in WildlifeSeveral recent public health crises have shown that the surveillance of zoonotic agents in wildlife is important to prevent pandemic risks. High-throughput sequencing (HTS) technologies are potentially useful for this surveillance, but rigorous experimental processes are required for the use of these effective tools in such epidemiological contexts. In particular, HTS introduces biases into the raw data set that might lead to incorrect...
Editor's Pick Research Article | Applied and Environmental ScienceZonal Soil Type Determines Soil Microbial Responses to Maize Cropping and FertilizationMicrobial communities are essential drivers of soil functional processes such as nitrification and heterotrophic respiration. Although there is initial evidence revealing the importance of soil type in shaping microbial communities, there has been no in-depth, comprehensive survey to robustly establish it as a major determinant of microbial community composition, functional gene structure, or ecosystem functioning. We examined bacterial...
Research Article | Molecular Biology and PhysiologyProteome Remodeling in Response to Sulfur Limitation in “Candidatus Pelagibacter ubique”“Ca. Pelagibacter ubique” is a key driver of marine biogeochemistry cycles and a model for understanding how minimal genomes evolved in free-living anucleate organisms. This study explores the unusual sulfur acquisition strategy that has evolved in these cells, which lack assimilatory sulfate reduction and instead rely on reduced sulfur compounds found in oxic marine environments to meet their cellular quotas. Our findings...
Editor's Pick Research Article | Host-Microbe BiologyIdentification of Novel Host Interactors of Effectors Secreted by Salmonella and CitrobacterDuring infection, pathogenic bacteria face an adverse environment of factors driven by both cellular and humoral defense mechanisms. To help evade the immune response and ultimately proliferate inside the host, many bacteria evolved specialized secretion systems to deliver effector proteins directly into host cells. Translocated effector proteins function to subvert host defense mechanisms. Numerous pathogenic bacteria use a specialized...
EditorialASM Journals Eliminate Impact Factor Information from Journal WebsitesMany scientists attempt to publish their work in a journal with the highest possible journal impact factor (IF). Despite widespread condemnation of the use of journal IFs to assess the significance of published work, these numbers continue to be widely misused in publication, hiring, funding, and promotion decisions (1, 2...
Research Article | Host-Microbe BiologyA Simple Screening Approach To Prioritize Genes for Functional Analysis Identifies a Role for Interferon Regulatory Factor 7 in the Control of Respiratory Syncytial Virus DiseaseMaking the most of “big data” is one of the core challenges of current biology. There is a large array of heterogeneous data sets of host gene responses to infection, but these data sets do not inform us about gene function and require specialized skill sets and training for their utilization. Here we describe an approach that combines and simplifies these data sets, distilling this information into a single list of genes commonly...
Commentary | Applied and Environmental ScienceAvoiding Pandemic Fears in the Subway and Conquering the PlatypusMetagenomics is increasingly used not just to show patterns of microbial diversity but also as a culture-independent method to detect individual organisms of intense clinical, epidemiological, conservation, forensic, or regulatory interest. A widely reported metagenomic study of the New York subway suggested that the pathogens Yersinia pestis and...