here's a good article on the topic.

http://www.rei.com/expertadvice/articles/water+risks.html
There are an estimated 99 million cases of intestinal infectious disease annually in the United States from a wide variety of pathogens, so treating backcountry water won't necessarily reduce your risk by much.
http://www.ncbi.nlm.nih.gov/pubmed/3128825?dopt=Abstract