metabolomics
Research Article | Novel Systems Biology TechniquesMetabolomics and Machine Learning Approaches Combined in Pursuit for More Accurate Paracoccidioidomycosis DiagnosesParacoccidioidomycosis (PCM) is a fungal infection typically found in Latin American countries, especially in Brazil. The identification of this disease is based on techniques that may fail sometimes. Intending to improve PCM detection in patient samples, this study used the combination of two of the newest technologies, artificial intelligence and metabolomics. This combination allowed PCM detection, independently of disease form,...
Research Article | Applied and Environmental ScienceComparative Genomics and Metabolomics in the Genus NocardiaOur work emphasizes that Nocardia represent a prolific source for natural products rivaling better-characterized genera such as Streptomyces or Amycolatopsis. Furthermore, we showed that large-scale analysis of biosynthetic gene clusters using similarity networks with high stringency allows the distinction and prediction of natural product structural variations. This will facilitate future genomics-driven drug...
Research Article | Therapeutics and PreventionThe Killing Mechanism of Teixobactin against Methicillin-Resistant Staphylococcus aureus: an Untargeted Metabolomics StudyAntimicrobial resistance is one of the greatest threats to the global health system. It is imperative that new anti-infective therapeutics be developed against problematic “superbugs.” The cyclic depsipeptide teixobactin holds much promise as a new class of antibiotics for highly resistant Gram-positive pathogens (e.g., methicillin-resistant Staphylococcus aureus [...
Research Article | Applied and Environmental ScienceStructural and Functional Changes in Prokaryotic Communities in Artificial Pit Mud during Chinese Baijiu ProductionStrong-flavor baijiu (SFB) accounts for more than 70% of all Chinese liquor production. In the Chinese baijiu brewing industry, artificial pit mud (APM) has been widely used since the 1960s to construct fermentation cellars for production of high-quality SFB. To gain insights at the systems level into the mechanisms driving APM prokaryotic taxonomic and functional dynamics and into how this variation is connected with high-quality SFB...
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...
Research Article | Novel Systems Biology TechniquesDefining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association StudiesIdentifying the key microbial taxa responsible for metabolic differences between microbiomes is an important step toward understanding and manipulating microbiome metabolism. To achieve this goal, researchers commonly conduct microbiome-metabolome association studies, comprehensively measuring both the composition of species and the concentration of metabolites across a set of microbial community samples and then testing for...
Research Article | Host-Microbe BiologyEnvironmental Chemical Diethylhexyl Phthalate Alters Intestinal Microbiota Community Structure and Metabolite Profile in MiceSeveral previous studies have pointed to environmental chemical exposure during windows of development as a contributing factor in neurodevelopmental disorders and correlated these disorders with microbiota dysbiosis; however, little is known about how the chemicals specifically alter the microbiota to interfere with development. The findings reported in this paper unambiguously establish that a pollutant linked with neurodevelopmental...
Editor's Pick Methods and Protocols | Applied and Environmental ScienceMarine Metabolomics: a Method for Nontargeted Measurement of Metabolites in Seawater by Gas Chromatography–Mass SpectrometryNontargeted approaches using metabolomics to analyze metabolites that occur in the oceans is less developed than those for terrestrial and limnic ecosystems. One of the challenges in marine metabolomics is that salt limits metabolite analysis in seawater to methods requiring salt removal. Building on previous sample preparation methods for metabolomics, we developed SeaMet, which overcomes the limitations of salt on metabolite detection...
Research Article | Host-Microbe BiologyMolecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic FibrosisMicrobial infections are now recognized to be polymicrobial and personalized in nature. Comprehensive analysis and understanding of the factors underlying the polymicrobial and personalized nature of infections remain limited, especially in the context of the host. By visualizing microbiomes and metabolomes of diseased human lungs, we reveal how different the chemical environments are between hosts that are dominated by the same...
Research Article | Synthetic BiologySystems Analyses Reveal the Resilience of Escherichia coli Physiology during Accumulation and Export of the Nonnative Organic Acid CitramalateCitramalate is an attractive biotechnology target because it is a precursor of methylmethacrylate, which is used to manufacture Perspex and other high-value products. Engineered E. coli strains are able to produce high titers of citramalate, despite having to express a foreign enzyme and tolerate the presence of a nonnative biochemical. A systems analysis of the...