DGGE

Application of denaturing gradient gel electrophoresis for detection of bacterial and yeast communities along a salinity gradient in the estuary of the Cachoeira River in Brazil

C. S. P. Rodrigues, Souza, S. S., Rezende, R. P., Silva, A., Andrioli, J. L., Costa, H., Fontana, R., and Dias, J. C. T., Application of denaturing gradient gel electrophoresis for detection of bacterial and yeast communities along a salinity gradient in the estuary of the Cachoeira River in Brazil, vol. 12, pp. 1752-1760, 2013.

An estuary is a transition zone between freshwater and marine ecosystems, resulting in dilution of seawater. Estuaries are also considered environments of intense biological activity related to the processes of nutrient cycling. The aim of this study was to evaluate the microbial community composition along a salinity gradient in the estuary of the Cachoeira River, located in southern Bahia, Brazil. The analysis of bacterial and yeast communities was performed by determining the denaturing gradient gel electrophoresis band richness.

Denaturing gradient gel electrophoresis analysis of 16S ribosomal DNA to monitor changes in mouse gut bacterial communities during Salmonella enterica serovar Enteritidis latent infection

B. M. Maciel, Marques, E. L. S., Dias, J. C. T., Santos, T. F., Romano, C. C., Brendel, M., and Rezende, R. P., Denaturing gradient gel electrophoresis analysis of 16S ribosomal DNA to monitor changes in mouse gut bacterial communities during Salmonella enterica serovar Enteritidis latent infection, vol. 12, pp. 2611-2617, 2013.

Changes in intestinal microbial flora during a 4-week period of Salmonella enterica serovar Enteritidis colonization in resistant mice (latent carrier animals) were evaluated using a culture independent method involving denaturing gradient gel electrophoresis. The contents of the ileocecal portion of the intestines produced 26 bands. Fifty-seven percent of the bands were expressed in more than 80% of the samples.

Lactic acid bacteria dynamics during spontaneous fermentation of cocoa beans verified by culture-independent denaturing gradient gel electrophoresis

T. F. Santos, Santana, L. K. A., Santos, A. C. F., Silva, G. S., Romano, C. C., Dias, J. C. T., and Rezende, R. P., Lactic acid bacteria dynamics during spontaneous fermentation of cocoa beans verified by culture-independent denaturing gradient gel electrophoresis, vol. 10, pp. 2702-2709, 2011.

Cocoa is naturally fermented in the field before the cocoa seeds are removed for processing. We assessed the dynamics of lactic acid bacteria during cocoa fermentation in Bahia, Brazil. During five days of fermentation, temperature and pH were measured and beans were collected for genomic DNA extraction every 12 h. The DNA was used as a template for amplification with Lac1-Lac2 and Lac3-Lac2 for denaturing gradient gel electrophoresis analyses. pH values ranged from 3.34 to 4.98, while the temperature varied from 23° to 50°C.

Simple DNA extraction protocol for a 16S rDNA study of bacterial diversity in tropical landfarm soil used for bioremediation of oil waste

B. M. Maciel, Santos, A. C. F., Dias, J. C. T., Vidal, R. O., Dias, R. J. C., Gross, E., Cascardo, J. C. M., and Rezende, R. P., Simple DNA extraction protocol for a 16S rDNA study of bacterial diversity in tropical landfarm soil used for bioremediation of oil waste, vol. 8, pp. 375-388, 2009.

Landfarm soil is used to bioremediate oil wastes from petrochemical industries. We developed a simplified protocol for microbial DNA extraction of tropical landfarm soil using only direct lysis of macerated material. Two samples of tropical landfarm soil from a Brazilian refinery were analyzed by this protocol (one consisted of crude oil-contaminated soil; the other was continuously enriched for nine months with petroleum). The soil samples were lysed by maceration with liquid nitrogen, eliminating the need for detergents, organic solvents and enzymatic cell lysis.

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