Hi

Thank you for your response. Actually I do not work with metagenomics but happens to attend a talk by Dr Bhabatosh Das from THSTI India. At THSTI they do a lot of metagenomics work and developed a protocol for DNA extraction from stool. When they did the 16s analysis using DNA extracted by their method and Kit based method (QIagen stool mini kit) the result had wide variation. His recommendation was using the manual method for extraction because by using a column based kit method you tend to miss out bacterial populations present at low levels and those could be the ones that makes an actual difference to your result .  

I hope I was of help.