2) Yes there have been some positive results in trials of probiotics for crohn's disease. 'Evidence for the use of probiotics and prebiotics in inflammatory bowel disease: a review of clinical trials' is a good review article. Looks like the pdf is available free - http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=1209192

4) The paper you are thinking of is 'Enterotypes of the human gut microbiome' which appeared in Nature - pdf from http://tinyurl.com/74n6xnp