Latest Articles
Research Article | Molecular Biology and PhysiologyRedox-Regulated Adaptation of Streptococcus oligofermentans to Hydrogen Peroxide StressThe catalase-negative streptococci produce as well as tolerate high levels of H2O2. This work reports the molecular mechanisms of low-H2O2-concentration-induced adaptation to higher H2O2 stress in a Streptococcus species, in which the peroxide-responsive repressor PerR and its redox regulons play the major role. Distinct from the...
Author Reply | Host-Microbe BiologyReply to Kenyon, “Are Differences in the Oral Microbiome Due to Ancestry or Socioeconomics?”
Research Article | Molecular Biology and PhysiologyProton Nuclear Magnetic Resonance Metabolomics Corroborates Serine Hydroxymethyltransferase as the Primary Target of 2-Aminoacrylate in a ridA Mutant of Salmonella entericaThe accumulation of the reactive enamine intermediate 2-aminoacrylate (2AA) elicits global metabolic stress in many prokaryotes and eukaryotes by simultaneously damaging multiple pyridoxal 5′-phosphate (PLP)-dependent enzymes. This work employed 1H NMR to expand our understanding of the consequence(s) of 2AA stress on metabolite pools and effectively identify the metabolic changes stemming from one damaged target: GlyA. This...
Letter to the Editor | Host-Microbe BiologyAre Differences in the Oral Microbiome Due to Ancestry or Socioeconomics?
Research Article | Ecological and Evolutionary ScienceComplementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest SoilMicrobial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of...
Research Article | Ecological and Evolutionary ScienceIndigenous Ammonia-Oxidizing Archaea in Oxic Subseafloor Oceanic CrustRidge flanks represent the major avenue of chemical and heat exchange between the Earth’s oceans and the lithosphere and are thought to harbor an enormous and understudied biosphere. However, little is known about the diversity and functionality of the crustal biosphere. Here, we report an indigenous community of archaea specialized in ammonia oxidation (i.e., AOA) in the oxic oceanic crust at North Pond. These AOA are the dominant...
Research Article | Host-Microbe BiologyMetabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive CheetahsMetabolome-informed analyses can enhance omics studies by enabling the correct partitioning of samples by identifying hidden confounders inadvertently misrepresented or omitted from carefully curated metadata. We demonstrate here the utility of metabolomics in a study characterizing the microbiome associated with liver disease in cheetahs. Metabolome-informed reinterpretation of metagenome and metabolome profiles factored in an...
Research Article | Ecological and Evolutionary ScienceCarbon Assimilation Strategies in Ultrabasic Groundwater: Clues from the Integrated Study of a Serpentinization-Influenced AquiferThis study describes the potential metabolic pathways by which microbial communities in a serpentinite-influenced aquifer may produce biomass from the products of serpentinization. Serpentinization is a widespread geochemical process, taking place over large regions of the seafloor and at continental margins, where ancient seafloor has accreted onto the continents. Because of the difficulty in delineating abiotic and biotic processes in...
Research Article | Molecular Biology and PhysiologyThe Entner-Doudoroff and Nonoxidative Pentose Phosphate Pathways Bypass Glycolysis and the Oxidative Pentose Phosphate Pathway in Ralstonia solanacearum
Editor's Pick Research Article | Novel Systems Biology TechniquesSystematic Localization of Escherichia coli Membrane ProteinsCurrent knowledge of protein localization, particularly outer membrane proteins, is highly dependent on bioinformatic predictions. To date, no systematic experimental studies have directly compared protein localization spanning the inner and outer membranes of E. coli. By combining sucrose density gradient fractionation of inner membrane (IM) and outer membrane (OM)...