We are having problems with this kit. Low DNA yield, as we obtain 5 ng/ul of DNA from a sediment sample and biofilms. Samples are quite different so we think that there is some problems with the solutions, but we don't know what they contain.
Few years back, i also faced the same problems....But i couldn't find out the problems as everything was hidden in specific codewords...I will suggest you to go with either conventional method of DNA extraction or PowerSoil® DNA Isolation Kit (50 Preps-12888-50)..
Try the new PureLink Microbiome DNA Purification Kit – it has protocols for stool and soil, and also urine, saliva, misc swabs, transport media, growth media http://www.thermofisher.com/order/catalog/product/A29790?ICID=search-product. consistently high yields