Sorting bacteria from stool

Does anyone have any experience sorting bacteria from stool samples?   
Specifically, what dyes were used to identify the bacteria, how much  
debris impacted the sorting, and whether or not you could distinguish  
between bacteria aggregates and single bacteria?  Currently, we are  
attempting to use a DNA stain like DAPI or PI on fixed samples, but  
are running into problems with aggregated bacteria due to the presence	
of biofilms in the sample.  I'm sure the fixation process is not  
helping, but from a biohazard standpoint, we'd prefer to fix.  The  
ability to accurately sort a single bacteria is of most concern.  We'd	
prefer the ability to get rid of any aggregates at the cost of yield.	
We have a MoFlo with a 488, 633, and an unreliable I90-K and a	
FACSAria with a 405nm, 488nm and 633nm.  Any help would be greatly  
appreciated

thanks,
Ryan

-----------------------------------------------
Ryan Duggan
Technical Director
Flow Cytometry Facility
University of Chicago

Ph:  773.702.9212 or .5582
Web:  http://ucflow.uchicago.edu

Main Facility
910 E. 58th, Room 037
Chicago, IL 60637
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