mass spectrometry
Editor's Pick Research Article | Applied and Environmental ScienceExometabolite Dynamics over Stationary Phase Reveal Strain-Specific ResponsesNongrowth states are common for bacteria that live in environments that are densely populated and predominantly nutrient exhausted, and yet these states remain largely uncharacterized in cellular metabolism and metabolite output. Here, we investigated and compared stationary-phase exometabolites and RNA transcripts for each of three environmental bacterial strains.
Research Article | Ecological and Evolutionary ScienceChemical Profiling Provides Insights into the Metabolic Machinery of Hydrocarbon-Degrading Deep-Sea MicrobesHigh-throughput technologies and emerging informatics tools have significantly advanced knowledge of hydrocarbon metabolism by marine microbes. However, research into microbes inhabiting deep-sea sediments (>1,000 m) is limited compared to those found in shallow waters. In this study, a nontargeted and nonclassical approach was used to examine the diversity of bacterial taxa and the metabolic profiles of hydrocarbon-degrading deep-...
Observation | Novel Systems Biology TechniquesEvaluating Organism-Wide Changes in the Metabolome and Microbiome following a Single Dose of AntibioticWe are just beginning to understand the unintended effects of antibiotics on our microbiomes and health. In this study, we aimed to define an approach by which one could obtain a comprehensive picture of (i) how antibiotics spatiotemporally impact commensal microbes throughout the gut and (ii) how these changes influence host chemistry throughout the body. We found that just a single dose of antibiotic altered host chemistry in a...
Research Article | Novel Systems Biology TechniquesHigh-Throughput Stool Metaproteomics: Method and Application to Human SpecimensWidely available technologies based on DNA sequencing have been used to describe the kinds of microbes that might correlate with health and disease. However, mechanistic insights might be best achieved through careful study of the dynamic proteins at the interface between the foods we eat, our microbes, and ourselves. Mass spectrometry-based proteomics has the potential to revolutionize our understanding of this complex system, but its...
Research Article | Applied and Environmental ScienceNitrogen Source Governs Community Carbon Metabolism in a Model Hypersaline Benthic Phototrophic BiofilmAnthropogenic inputs of nitrogen into aquatic ecosystems, and especially those of agricultural origin, involve a mix of chemical species. Although it is well-known in general that nitrogen eutrophication markedly influences the metabolism of aquatic phototrophic communities, relatively little is known regarding whether the specific chemical form of nitrogen inputs matter. Our data suggest that the nitrogen form alters the rate of...
Research Article | Molecular Biology and PhysiologyIn Vivo Thermodynamic Analysis of Glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Using 13C and 2H TracersThermodynamics constitutes a key determinant of flux and enzyme efficiency in metabolic networks. Here, we provide new insights into the divergent thermodynamics of the glycolytic pathways of C. thermocellum and T. saccharolyticum, two industrially relevant thermophilic bacteria whose metabolism still is not well understood. We report that while the glycolytic pathway in T. saccharolyticum is as...
Editor's Pick Research Article | Novel Systems Biology TechniquesA Metabolome- and Metagenome-Wide Association Network Reveals Microbial Natural Products and Microbial Biotransformation Products from the Human MicrobiotaExperimental advances have enabled the acquisition of tandem mass spectrometry and metagenomics sequencing data from tens of thousands of environmental/host-oriented microbial communities. Each of these communities contains hundreds of microbial features (corresponding to microbial species) and thousands of molecular features (corresponding to microbial natural products). However, with the current technology, it is very difficult to...
Research Article | Host-Microbe BiologySalmonella Proteomic Profiling during Infection Distinguishes the Intracellular Environment of Host CellsSalmonella Typhimurium is one of the leading causes of foodborne bacterial infection. Nevertheless, how Salmonella adapts to distinct types of host cells during infection remains poorly understood. By contrasting intracellular Salmonella proteomes from both infected macrophages and epithelial cells, we found striking proteomic signatures specific to particular types of host cells. Notably, Salmonella...
Research Article | Host-Microbe BiologyMultiplatform Physiologic and Metabolic Phenotyping Reveals Microbial ToxicityThe gut microbiota is modulated physiologically, compositionally, and metabolically by xenobiotics, potentially causing metabolic consequences to the host. We recently reported that tempol, a stabilized free radical nitroxide, can exert beneficial effects on the host through modulation of the microbiome community structure and function. Here, we investigated a multiplatform phenotyping approach that combines high-throughput global...
Special Issue Perspective | Molecular Biology and PhysiologyThe Tripod for Bacterial Natural Product Discovery: Genome Mining, Silent Pathway Induction, and Mass Spectrometry-Based Molecular NetworkingNatural products are the richest source of chemical compounds for drug discovery. Particularly, bacterial secondary metabolites are in the spotlight due to advances in genome sequencing and mining, as well as for the potential of biosynthetic pathway manipulation to awake silent (cryptic) gene clusters under laboratory cultivation.