Bacterial strains identification

While this chapter has described two examples of our efforts in bacterial strain identification, a number of other groups have contributed to this research area. It remains to be seen whether mathematical algorithms such as the modified correlation approach described herein are always more effective for strain assignments than the simple use of distinctive biomarker peaks. Nilsson reported MALDI mass spectra of Helicobacter pylori with three different matrices and solvent conditions.59 She showed that some strains of this bacteria yield rather similar mass spectra while others are quite different. Nevertheless, each strain appears to exhibit some unique peaks that might be used for distinguishing strains. 

The refractory nature of some pollutants, notably, persistent polyhalogenated compounds, has raised problems of bioremediation of contaminated sites (e.g., sediments and dumping sites). There has been interest in the identification, or the production by genetic manipulation, of strains of microorganisms that can metabolically degrade recalcitrant molecules. For example, there are bacterial strains that can reductively dechlorinate PCBs under anaerobic conditions. 

Witschel M, S Nagel, T Egli (1997) Identification and characterization of the two-enzyme system catalyzing the oxidation of EDTA in the EDTA-degrading bacterial strain DSM 9103. J Bacterial 179 6937-6943. 

Further research in improving the BDS activity of the biocatalysts was targeted towards the search of co-catalysts and co-factors to enhance overall desulfurization rates as well as promoters to enhance enzyme expression. This research resulted in identification of NADH and FMNH2 as co-factors essential for electron transfer and related oxidoreductase enzymes as co-catalysts as described in detail below. Additionally, other bacterial strains were also investigated as hosts and are reported below. 

Identification of azo dye degrading bacterial strains for use in bioaugmentation typically involves a stepwise process to isolate potential strains and screen them for their ability to degrade different dyes. A number of strategies have been devised to isolate such bacteria to achieve consistent and reproducible results in biotreatment systems (Fig. 2). Specific methods that have been employed for the isolation of microbial strains capable of degrading azo dyes are summarized in Table 2. 

Indications for the formation of analogous species in microbial metabolism of LAS were found by Knepper and Kruse [33] during biotransformation of commercial LAS surfactant on an FBBR. However, the low concentrations of the tentative metabolites in the test liquor, which eluted under the applied reversed-phase (RP)-HPLC conditions somewhat earlier than the normal SPC, did not permit acquisition of full-scan mass spectra as was needed for unequivocal identification. Further evidence for the formation of the intermediate with a double bond in the alkanoate moiety was reported by Bird [103]. During biodegradation of Cn-LAS by a bacterial strain, a new UV adsorption band centred near 260 nm was detected, which was assumed to result from a double bond, although a definite confirmation could not be provided. 

Similar work was performed by Maquelin et al.6 in 2000. They used con-focal Raman microspectroscopy to obtain spectra directly from microbial microcolonies on solid culture medium. The spectra were obtained after 6 h of culmring and were of most commonly encountered organisms. While depth studies showed varying quantitative levels of success, the qualitative (identification) of various bacterial strains was deemed a success. 

For classification (e.g. identification of country of origin or variety of a sample, or the bacterial strain), it is not quite so straightforward, as it is difficult to know within a class (country of origin, etc.) which data fie at the edge of the spectrum. This may, however, be achieved, by examining the data for each... 

Characterization and Identification of Bacterial Strains Isolated From BC1. 

Natural product extracts and bacterial culture collections do not necessarily work well together on drug discovery platforms. The separation, identification, characterization, scale-up, and purification of natural products for large-scale libraries suitable for these HTS are daunting, and rational arguments for the selection of organisms and/or natural product molecules are often absent, especially given the poor taxonomic characterization of strains in natural product bacterial strain collections. 

Four bacterial strains which grow on mercurial plates were isolated from mercury contaminated sludge. These mercury resistant bacteria were subjected to Gram stain and all were Gram-negative. The results of identification of these mercury volatilizing bacteria were Klebsiella pneumoniae, Pseudomonas putida, Enterobacter agglomerans and Proteus mirabilis. 

SNPs and InDei (Insertion/deletion) are distributed equally over the total genome of animals, plants, fungi, and bacteria. They have very low mutation rates and therefore can be used for animal or plant species determination, identification of fungi or bacterial strains, proof of identity, and authenticity testing. Detection of SNPs can be carried out on both genomic and mitochondrial DNA. 

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