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mass spectrometry

  • Open Access
    Exometabolite Dynamics over Stationary Phase Reveal Strain-Specific Responses
    Editor's Pick Research Article | Applied and Environmental Science
    Exometabolite Dynamics over Stationary Phase Reveal Strain-Specific Responses

    Nongrowth 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.

    John L. Chodkowski, Ashley Shade
  • Open Access
    Chemical Profiling Provides Insights into the Metabolic Machinery of Hydrocarbon-Degrading Deep-Sea Microbes
    Research Article | Ecological and Evolutionary Science
    Chemical Profiling Provides Insights into the Metabolic Machinery of Hydrocarbon-Degrading Deep-Sea Microbes

    High-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-...

    Aldo Moreno-Ulloa, Victoria Sicairos Diaz, Javier A. Tejeda-Mora, Marla I. Macias Contreras, Fernando Díaz Castillo, Abraham Guerrero, Ricardo Gonzalez Sanchez, Omar Mendoza-Porras, Rafael Vazquez Duhalt, Alexei Licea-Navarro
  • Open Access
    Evaluating Organism-Wide Changes in the Metabolome and Microbiome following a Single Dose of Antibiotic
    Observation | Novel Systems Biology Techniques
    Evaluating Organism-Wide Changes in the Metabolome and Microbiome following a Single Dose of Antibiotic

    We 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...

    Alison Vrbanac, Kathryn A. Patras, Alan K. Jarmusch, Robert H. Mills, Samuel R. Shing, Robert A. Quinn, Fernando Vargas, David J. Gonzalez, Pieter C. Dorrestein, Rob Knight, Victor Nizet
  • Open Access
    High-Throughput Stool Metaproteomics: Method and Application to Human Specimens
    Research Article | Novel Systems Biology Techniques
    High-Throughput Stool Metaproteomics: Method and Application to Human Specimens

    Widely 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...

    Carlos G. Gonzalez, Hannah C. Wastyk, Madeline Topf, Christopher D. Gardner, Justin L. Sonnenburg, Joshua E. Elias
  • Open Access
    Nitrogen Source Governs Community Carbon Metabolism in a Model Hypersaline Benthic Phototrophic Biofilm
    Research Article | Applied and Environmental Science
    Nitrogen Source Governs Community Carbon Metabolism in a Model Hypersaline Benthic Phototrophic Biofilm

    Anthropogenic 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...

    Christopher R. Anderton, Jennifer M. Mobberley, Jessica K. Cole, Jamie R. Nunez, Robert Starke, Amy A. Boaro, Yasemin Yesiltepe, Beau R. Morton, Alexandra B. Cory, Hayley C. Cardamone, Kirsten S. Hofmockel, Mary S. Lipton, James J. Moran, Ryan S. Renslow, James K. Fredrickson, Stephen R. Lindemann
  • Open Access
    <em>In Vivo</em> Thermodynamic Analysis of Glycolysis in <span class="named-content genus-species" id="named-content-1">Clostridium thermocellum</span> and <span class="named-content genus-species" id="named-content-2">Thermoanaerobacterium saccharolyticum</span> Using <sup>13</sup>C and <sup>2</sup>H Tracers
    Research Article | Molecular Biology and Physiology
    In Vivo Thermodynamic Analysis of Glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Using 13C and 2H Tracers

    Thermodynamics 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...

    Tyler B. Jacobson, Travis K. Korosh, David M. Stevenson, Charles Foster, Costas Maranas, Daniel G. Olson, Lee R. Lynd, Daniel Amador-Noguez
  • Open Access
    A Metabolome- and Metagenome-Wide Association Network Reveals Microbial Natural Products and Microbial Biotransformation Products from the Human Microbiota
    Editor's Pick Research Article | Novel Systems Biology Techniques
    A Metabolome- and Metagenome-Wide Association Network Reveals Microbial Natural Products and Microbial Biotransformation Products from the Human Microbiota

    Experimental 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...

    Liu Cao, Egor Shcherbin, Hosein Mohimani
  • Open Access
    <em>Salmonella</em> Proteomic Profiling during Infection Distinguishes the Intracellular Environment of Host Cells
    Research Article | Host-Microbe Biology
    Salmonella Proteomic Profiling during Infection Distinguishes the Intracellular Environment of Host Cells

    Salmonella 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...

    Zezhou Li, Yanhua Liu, Jiaqi Fu, Buyu Zhang, Sen Cheng, Mei Wu, Zhen Wang, Jiezhang Jiang, Cheng Chang, Xiaoyun Liu
  • Open Access
    Multiplatform Physiologic and Metabolic Phenotyping Reveals Microbial Toxicity
    Research Article | Host-Microbe Biology
    Multiplatform Physiologic and Metabolic Phenotyping Reveals Microbial Toxicity

    The 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...

    Jingwei Cai, Robert G. Nichols, Imhoi Koo, Zachary A. Kalikow, Limin Zhang, Yuan Tian, Jingtao Zhang, Philip B. Smith, Andrew D. Patterson
  • Open Access
    The Tripod for Bacterial Natural Product Discovery: Genome Mining, Silent Pathway Induction, and Mass Spectrometry-Based Molecular Networking
    Special Issue Perspective | Molecular Biology and Physiology
    The Tripod for Bacterial Natural Product Discovery: Genome Mining, Silent Pathway Induction, and Mass Spectrometry-Based Molecular Networking

    Natural 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.

    Daniela B. B. Trivella, Rafael de Felicio

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