Quantitative metabolic network profiling of Escherichia coli: An overview of analytical methods for measurement of intracellular metabolites

Shen, Yang; Tohidi, Fatemeh; Tang, Lei-Han; Cai, Zongwei

doi:10.1016/j.trac.2015.07.006

Cited by 18 publications

(15 citation statements)

References 91 publications

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“…Efforts have begun to optimise analytical methods for metabolome identification, e.g. in Escherichia coli [16], Saccharomyces cerevisiae [17] and Caenorhabditis elegans [18], as well as to mine the literature for existing knowledge, e.g. in S. cerevisiae [19].…”

Section: Introductionmentioning

confidence: 99%

How close are we to complete annotation of metabolomes?

Viant

Kurland

Jones

et al. 2017

Current Opinion in Chemical Biology

238

211

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The metabolome describes the full complement of the tens to hundreds of thousands of low molecular weight metabolites present within a biological system. Identification of the metabolome is critical for discovering the maximum amount of biochemical knowledge from metabolomics datasets. Yet no exhaustive experimental characterisation of any organismal metabolome has been reported to date, dramatically contrasting with the genome sequencing of thousands of plants, animals and microbes. Here we review the status of metabolome annotation and describe advances in the analytical methodologies being applied. In part through new international coordination, we conclude that we are now entering a new era of metabolome annotation.

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Section: Introductionmentioning

confidence: 99%

How close are we to complete annotation of metabolomes?

Viant

Kurland

Jones

et al. 2017

Current Opinion in Chemical Biology

238

211

View full text Add to dashboard Cite

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“…), and it is important that these environmental parameters be kept stable (Shen et al . ). For this reason, it is imperative that the cultivation conditions for metabolomics studies are optimized to ensure that the maximum amounts of significant metabolites are produced to ensure detectability.…”

Section: Optimum Cultivation Conditions For Metabolite Productionmentioning

confidence: 97%

“…This method of cultivation occurs in a bioreactor consisting of various components such as a feed reservoir, pump, fermenter, stirrer and weir (Shen et al . ). Jin et al .…”

Section: Optimum Cultivation Conditions For Metabolite Productionmentioning

confidence: 97%

“…However, few studies have investigated the influence of culture conditions on specifically metabolite production. The metabolic status of micro-organisms is culture condition-sensitive (Shen et al 2016). Consequently, the use of microbial cells for metabolomics can be problematic during analysis since cells require cultivation in growth media and specific media components could artificially increase metabolite levels (Marcinowska et al 2011).…”

Section: Optimum Cultivation Conditions For Metabolite Productionmentioning

confidence: 99%

“…Consequently, the use of microbial cells for metabolomics can be problematic during analysis since cells require cultivation in growth media and specific media components could artificially increase metabolite levels (Marcinowska et al 2011). The production of metabolites by micro-organisms is influenced by various environmental factors such as the cultivation media used (complex media vs a minimal media), cultivation method (batch culture vs continuous culture), temperature, the period of incubation, pH, light and moisture (Tyc et al 2017), and it is important that these environmental parameters be kept stable (Shen et al 2016). For this reason, it is imperative that the cultivation conditions for metabolomics studies are optimized to ensure that the maximum amounts of significant metabolites are produced to ensure detectability.…”

Section: Optimum Cultivation Conditions For Metabolite Productionmentioning

confidence: 99%

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Microbial metabolomics: essential definitions and the importance of cultivation conditions for utilizing Bacillus species as bionematicides

Horak

Engelbrecht

Rensburg

et al. 2019

J of Applied Microbiology

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Root‐knot nematodes are destructive phytopathogens that damage agricultural crops globally, and there is growing interest in the use of biocontrol based on rhizobacteria such as Bacillus to combat Meloidogyne species. It is hypothesized that nematicidal activity of Bacillus can be attributed to the production of secondary metabolites and hydrolytic enzymes. Yet, few studies have characterized these metabolites and their identities remain unknown. Others are speculative or fail to elaborate on how secondary metabolites were detected or distinguished from primary metabolites. Metabolites can be classified based on their origin as either intracellular or extracellular and based on their function, as either primary or secondary. Although this classification is in general use, the boundaries are not always well defined. An understanding of the secondary metabolite and hydrolytic enzyme classification of Bacillus species will facilitate investigations aimed at bionematicide development. This review summarizes the significance of Bacillus hydrolytic enzymes and secondary metabolites in bionematicide research and provides an overview of known classifications. The importance of appropriate cultivation conditions for optimum metabolite and enzyme production is also discussed. Finally, the use of metabolomics for the detection and identification of nematicidal compounds is considered.

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