metabolomics
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...
Research Article | Host-Microbe BiologyA Multi-omics Approach to Unraveling the Microbiome-Mediated Effects of Arabinoxylan Oligosaccharides in Overweight HumansThe use of dietary fiber food supplementation as a strategy to reduce the burden of diet-related diseases is a matter of study given its cost-effectiveness and the positive results demonstrated in clinical trials. This multi-omics assessment, on different biological samples of overweight subjects with signs of metabolic syndrome, sheds light on the early and less evident effects of short-term AXOS intake on intestinal microbiota and...
Research Article | Molecular Biology and PhysiologyCarbon Fate and Flux in Prochlorococcus under Nitrogen LimitationPhotosynthetic microbes are the predominant sources of organic carbon in the sunlit regions of the ocean. During photosynthesis, nitrogen and carbon metabolism are coordinated to synthesize nitrogen-containing organics such as amino acids and nucleic acids. In large regions of the ocean, nitrogen is thought to limit the growth of phytoplankton. The impact of nitrogen limitation on the synthesis of organic carbon is not well understood,...
Research Article | Molecular Biology and PhysiologyMinor Isozymes Tailor Yeast Metabolism to Carbon AvailabilityGene duplication is one of the main evolutionary paths to new protein function. Typically, duplicated genes either accumulate mutations and degrade into pseudogenes or are retained and diverge in function. Some duplicated genes, however, show long-term persistence without apparently acquiring new function. An important class of isozymes consists of those that catalyze the same reaction in the same compartment, where knockout of one...