Quantitative Bioreactor Monitoring of Intracellular Bacterial Metabolites in Using Liquid Chromatography-Isotope Dilution Mass Spectrometry.

We report a liquid chromatography-isotope dilution mass spectrometry method for the simultaneous quantification of 131 intracellular bacterial metabolites of . A comprehensive mixture of uniformly C-labeled internal standards (U-C IS) was biosynthesized from the closely related bacterium using 4% C-glucose as a carbon source. The U-C IS mixture combined with C authentic standards was used to validate the linearity, precision, accuracy, repeatability, limits of detection, and quantification for each metabolite.

Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions.

Metabolic engineering in the post-genomic era is characterised by the development of new methods for metabolomics and fluxomics, supported by the integration of genetic engineering tools and mathematical modelling. Particularly, constraint-based stoichiometric models have been widely studied: (i) flux balance analysis (FBA) (in silico), and (ii) metabolic flux analysis (MFA) (in vivo). Recent studies have enabled the incorporation of thermodynamics and metabolomics data to improve the predictive capabilities of these approaches.

Engineering of vitamin prototrophy in Clostridium ljungdahlii and Clostridium autoethanogenum.

Clostridium autoethanogenum and Clostridium ljungdahlii are physiologically and genetically very similar strict anaerobic acetogens capable of growth on carbon monoxide as sole carbon source. While exact nutritional requirements have not been reported, we observed that for growth, the addition of vitamins to media already containing yeast extract was required, an indication that these are fastidious microorganisms. Elimination of complex components and individual vitamins from the medium revealed that the only organic compounds required for growth were pantothenate, biotin and thiamine.

Gsmodutils: a python based framework for test-driven genome scale metabolic model development.

Motivation: Genome scale metabolic models (GSMMs) are increasingly important for systems biology and metabolic engineering research as they are capable of simulating complex steady-state behaviour. Constraints based models of this form can include thousands of reactions and metabolites, with many crucial pathways that only become activated in specific simulation settings. However, despite their widespread use, power and the availability of tools to aid with the construction and analysis of large scale models, little methodology is suggested for their continued management.

Progress towards platform chemical production using .

Since 2013, there has been an explosion in the number of research articles published on , an acetogen capable of producing platform chemicals such as ethanol and 2,3-butanediol from greenhouse gases. However, no review focusing solely on has appeared in the literature. This review outlines the research conducted into this organism in three broad categories (Enzymology, Genetics, and Systems Biology) and suggestions for future research are offered.

Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium.

Background: Clostridium autoethanogenum is an acetogenic bacterium capable of producing high value commodity chemicals and biofuels from the C1 gases present in synthesis gas. This common industrial waste gas can act as the sole energy and carbon source for the bacterium that converts the low value gaseous components into cellular building blocks and industrially relevant products via the action of the reductive acetyl-CoA (Wood-Ljungdahl) pathway. Current research efforts are focused on the enhancement and extension of product formation in this organism via synthetic biology approaches.