Latest Articles
Research Article | Molecular Biology and PhysiologyHfq Globally Binds and Destabilizes sRNAs and mRNAs in Yersinia pestisDiscovered in 1968 as an Escherichia coli host factor that was essential for replication of the bacteriophage Qβ, the Hfq protein is a ubiquitous and highly abundant RNA-binding protein in many bacteria. With the assistance of Hfq, small RNAs in bacteria play important roles in regulating the stability and translation of mRNAs by base pairing. In this study, we want...
Research Article | Novel Systems Biology TechniquesSpecies Deletions from Microbiome Consortia Reveal Key Metabolic Interactions between Gut MicrobesGut microbes associate, compete for, and specialize in specific metabolic tasks. These interactions are dictated by the cross-feeding of degradation or fermentation products. However, the individual contribution of microbes to the function of the gut microbiome is difficult to evaluate. It is essential to understand the complexity of microbial interactions and how the presence or absence of specific microorganisms affects the stability...
Editor's Pick Research Article | Host-Microbe BiologyA Cross-Sectional Study of Compositional and Functional Profiles of Gut Microbiota in Sardinian CentenariansThe gut microbiota has been proposed as a promising determinant for human health. Centenarians as a model for extreme aging may help us understand the correlation of gut microbiota with healthy aging and longevity. Here we confirmed that centenarians had microbiota elements usually associated with benefits to health. Our finding of a high capacity of glycolysis and related SCFA production represented a healthy microbiome and environment...
Research Article | Host-Microbe BiologyBrlA and AbaA Govern Virulence-Required Dimorphic Switch, Conidiation, and Pathogenicity in a Fungal Insect PathogenDimorphic insect mycopathogens infect the host by hyphal penetration through the host cuticle and switch from the penetrating hyphae to unicellular blastospores after entry into the host hemocoel, where blastospore propagation by yeast-like budding accelerates host mummification to death. The fungal virulence-required dimorphic switch is confirmed as a process of asexual development directly regulated by BrlA and AbaA, two key...
Research Article | Applied and Environmental ScienceTime Series Genome-Centric Analysis Unveils Bacterial Response to Operational Disturbance in Activated SludgeDisturbance is a key determinant of community assembly and dynamics in natural and engineered ecosystems. Microbiome response to disturbance is thought to be influenced by bacterial growth traits and life history strategies. In this time series observational study, the response to disturbance of microbial communities in a full-scale activated sludge wastewater treatment plant was assessed by computing specific cellular traits of genomes...
Commentary | Applied and Environmental ScienceA Lot on Your Plate? Well-to-Well Contamination as an Additional Confounder in Microbiome Sequence AnalysesDNA sequence-based microbiome studies can be impacted by a range of different methodological artefacts. Contamination originating from laboratory kits and reagents can lead to erroneous results, particularly in samples containing a low microbial biomass.
Observation | Novel Systems Biology Techniquesredbiom: a Rapid Sample Discovery and Feature Characterization SystemAlthough analyses that combine many microbiomes at the whole-community level have become routine, searching rapidly for microbiomes that contain a particular sequence has remained difficult. The software we present here, redbiom, dramatically accelerates this process, allowing samples that contain microbiome features to be rapidly identified. This is especially useful when taxonomic annotation is limited, allowing users to identify...
Research Article | Novel Systems Biology TechniquesQuantifying and Understanding Well-to-Well Contamination in Microbiome ResearchMicrobiome research has uncovered magnificent biological and chemical stories across nearly all areas of life science, at times creating controversy when findings reveal fantastic descriptions of microbes living and even thriving in what were once thought to be sterile environments. Scientists have refuted many of these claims because of contamination, which has led to robust requirements, including the use of controls, for validating...
Research Article | Ecological and Evolutionary ScienceProteomic Response of Three Marine Ammonia-Oxidizing Archaea to Hydrogen Peroxide and Their Metabolic Interactions with a Heterotrophic AlphaproteobacteriumAmmonia-oxidizing archaea (AOA) are the most abundant chemolithoautotrophic microorganisms in the oxygenated water column of the global ocean. Although H2O2 appears to be a universal by-product of aerobic metabolism, genes encoding the hydrogen peroxide (H2O2)-detoxifying enzyme catalase are largely absent in genomes of marine AOA. Here, we provide evidence that closely related marine AOA have...
Research Article | Host-Microbe BiologyMultipartner Symbiosis across Biological Domains: Looking at the Eukaryotic Associations from a Microbial PerspectiveThe symbiotic lifestyle represents a fundamental cryptic contribution to the diversity of marine ecosystems. Sponges are ideal targets to improve understanding the symbiotic relationships from evolutionary and ecological points of view, because they are the most ancient metazoans on earth, are ubiquitous in the marine benthos, and establish complex symbiosis with both prokaryotes and animals, which in turn also harbor their own...