babu u better try with metagenomics that's good instead of wasting time in DNA isolation already we had a experience. metagenomics gives good result than normal method
People usually use Qiagen DNA isolation kits. We tested them in CIGESMED Project, as well as Macherey-Nagel, and chelex extraction methods: none gives visible amounts of DNa, but all work for DNA amplification.
You can find more information on http://www.cigesmed.eu/