Abstract: Cottonseed meal is one of the important forage protein raw materials. Microbial fermentation is one of the most efficient methods for detoxification. In order to monitor the microbial fermentation process and optimize the fermentation parameters of cottonseed meal, an efficient DNA extraction method was established. Decoloration buffer was used to remove free gossypol and other polyphenolic pigment from fermented cottonseed, and then lysozyme, SDS and proteinase K were combined for fragmentation. As a result, the total DNA yields ranged from 1.8 to 6.4 μg per gram of wet fermented cottonseed meal, the DNA extraction efficiency was more than 89%, and the fragment size was about 23 kb. The extracted DNA could be used directly for PCR amplification and restriction enzyme digestion without additional purification. In addition, using the extracted DNA as template, the 16S rRNA V3 fragments were amplified and then analyzed by DGGE to investigate the diversity and change of microbial community structure of the fermented cottonseed meal. Therefore, this is a simple, reliable protocol of DNA extraction from the fermented cottonseed meal．

Key words: cottonseed meal, microbial fermentation, DNA extraction, PCR-DGGE