Latest Articles
Research Article | Applied and Environmental SciencePreservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field StudiesOur study, spanning 15 individuals and over 1,200 samples, provides our most comprehensive view to date of storage and stabilization effects on stool. We tested five methods for preserving human and dog fecal specimens for periods of up to 8 weeks, including the types of variation often encountered under field conditions, such as freeze-thaw cycles and high temperature fluctuations. We show that several cost-effective methods provide...
Research Article | Molecular Biology and PhysiologyOsdR of Streptomyces coelicolor and the Dormancy Regulator DevR of Mycobacterium tuberculosis Control Overlapping RegulonsDormancy is a state of growth cessation that allows bacteria to escape the host defense system and antibiotic challenge. Understanding the mechanisms that control dormancy is of key importance for the treatment of latent infections, such as those from Mycobacterium tuberculosis. In mycobacteria, dormancy is controlled by the response regulator DevR, which responds to...
Research Article | Novel Systems Biology TechniquesFrom Sample to Multi-Omics Conclusions in under 48 HoursPolymicrobial infections are difficult to diagnose due to the challenge in comprehensively cultivating the microbes present. Omics methods, such as 16S rRNA sequencing, metagenomics, and metabolomics, can provide a more complete picture of a microbial community and its metabolite production, without the biases and selectivity of microbial culture. However, these advanced methods have not been applied to clinical or industrial...
Commentary | Applied and Environmental ScienceApplication of a Database-Independent Approach To Assess the Quality of Operational Taxonomic Unit Picking MethodsAssignment of 16S rRNA gene sequences to operational taxonomic units (OTUs) allows microbial ecologists to overcome the inconsistencies and biases within bacterial taxonomy and provides a strategy for clustering similar sequences that do not have representatives in a reference database.
Editor's Pick Research Article | Applied and Environmental ScienceProteomic Stable Isotope Probing Reveals Taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine BacterioplanktonAn estimated 50 gigatons of carbon is annually fixed within marine systems, of which heterotrophic microbial populations process nearly half. These communities vary in composition and activity across spatial and temporal scales, so understanding how these changes affect global processes requires the delineation of functional roles for individual members. In a step toward ascertaining these roles, we applied proteomic stable isotope...
Commentary | Applied and Environmental ScienceThe Built Environment Is a Microbial WastelandHumanity’s transition from the outdoor environment to the built environment (BE) has reduced our exposure to microbial diversity. The relative importance of factors that contribute to the composition of human-dominated BE microbial communities remains largely unknown.
Editor's Pick Research Article | Applied and Environmental ScienceGeography and Location Are the Primary Drivers of Office Microbiome CompositionOur study highlights several points that should impact the design of future studies of the microbiology of BEs. First, projects tracking changes in BE bacterial communities should focus sampling efforts on surveying different locations in offices and in different cities but not necessarily different materials or different offices in the same city. Next, disturbance due to repeated sampling, though detectable, is small compared to that...
Research Article | Molecular Biology and PhysiologyComprehensive Transcriptome Profiles of Streptococcus mutans UA159 Map Core Streptococcal Competence GenesS. mutans has the hard surfaces of the oral cavity as its natural habitat, where it depends on its ability to form biofilms in order to survive. The comprehensive identification of S. mutans regulons activated in response to peptide pheromones provides an important basis for understanding how...
Editor's Pick Perspective | Host-Microbe BiologyGetting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their MicrobiomesGiven the complexity of host-microbiota symbioses, scientists and philosophers are asking questions at new biological levels of hierarchical organization—what is a holobiont and hologenome? When should this vocabulary be applied? Are these concepts a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Critical discourse is necessary in this nascent area...
Editor's Pick Research Article | Host-Microbe BiologyLocal Action with Global Impact: Highly Similar Infection Patterns of Human Viruses and BacteriophagesWhile host-virus interaction interfaces have been previously investigated, relatively little is known about the indirect interactions of pathogen and host proteins required for viral infection and host cell function. Therefore, we investigated the topological relationships of human and bacterial viruses and how they interact with their hosts. We focused on those host proteins that are directly targeted by viruses, those that are...