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It links gene information to phenotypic information from microbial pathogens on their hosts. Information is manually curated from peer-reviewed literature. RGD Rat Genome Database: genomic and phenotype data for Rattus norvegicus; PomBase database: manually curated phenotypic data for the yeast Schizosaccharomyces pombe
For example, EcoCyc is a highly detailed bioinformatics database on the genome and metabolic reconstruction of Escherichia coli, including thorough descriptions of E. coli signaling pathways and regulatory network. The EcoCyc database can serve as a paradigm and model for any reconstruction.
The E. coli Metabolome Database (ECMDB) [1] is a freely accessible, online database of small molecule metabolites found in or produced by Escherichia coli (E. coli strain K12, MG1655). Escherichia coli is perhaps the best studied bacterium on earth and has served as the "model microbe" in microbiology research for more than 60 years.
Microme: a platform that integrates a database, tools and browsers for studying bacterial metabolism. MBGD: Microbial Genome Database for Comparative Analysis; Virtual Institute for Microbial Stress and Survival (VIMSS): the supporter for an integrated program to study how microbes respond to and survive environmental stresses.
The database is designed to contain or link three kinds of data: Chemical data, Clinical data and; Molecular biology/biochemistry data. The database contains 220,945 metabolite entries including both water-soluble and lipid soluble metabolites. Additionally, 8,610 protein sequences (enzymes and transporters) are linked to these metabolite entries.
Syntrophy, in the context of microbial metabolism, refers to the pairing of multiple species to achieve a chemical reaction that, on its own, would be energetically unfavorable. The best studied example of this process is the oxidation of fermentative end products (such as acetate, ethanol and butyrate) by organisms such as Syntrophomonas ...
The metabolite structure data is linked to chemical databases, including ChemSpider, PubChem, and ChEBI. Links to metabolite databases, however, seem to be missing. MetaboLights consists of two components: a repository, that enables the metabolomic community to share experimental findings, data and protocols for any metabolomic study. (Fig. 1-2)
As an analytical technique, MS is a very sensitive method that requires very little sample (<1 ng of material or <10 μL of a biofluid) and can generate signals for thousands of metabolites from a single sample. MS instruments can also be configured for very high throughput metabolome analyses (hundreds to thousands of samples a day).