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#16S rDNA Sequencing and Analysis (Organism Identification)  Following the second dilution streaking, the organisms need to be identified. This is accomplished by Sanger sequencing of a 16S rDNA PCR product.  The samples can be prepared for 16S rDNA PCR via direct PCR (using the liquid culture as the template for the PCR reaction) or following DNA extraction. Direct PCR significantly decreases the amount of work needed for preparation, but it can yield poorer Sanger results, both in terms of PCR success and resultant sequence quality. We However, we  recommend direct PCR when screening a large number of samples. DNA extraction can then be used for any recalcitrant samples. DNA extraction is significantly more work, but it often generates better Sanger sequences allowing for more accurate identification. ##DNA Extraction  There are a number of different options for DNA isolation and which one should use depends on many factors including available equipment, experience, and cost. A standard approach in microbiology involves the use of phenol and chloroform extraction followed by ethanol precipitation, and any number of protocols for this approach can be found in books, articles and on the internet. A common alternative approach is to use a commercially available kit - there are many advantages to such kits - notably ease and lack of toxic chemicals. A disadvantage of kits is that they typically are more expensive per sample than other approaches (especially if one is only doing a few samples since most kits include materials for at a minimum 50 samples). For most projects, we use kits - especially the Promega-Wizard Genomic DNA Purification Kit or the MO BIO-Power Soil DNA Isolation Kit.