Prepare sample containers , presterilized, disposable Whirl-pak® bags can be used to sample, plastic tubes of 5 ml can also use. Use scalpel to collect a sizable amount,  Remember to wash your hands thoroughly after collecting samples suspected of containing fecal contamination. Also, be careful not to touch your eyes, ears, nose, or mouth until you've washed your hands. No you should go for 5 insect cage, collect the whole feces and divide it by five. It is very difficult to collect individual insect feces. Use plastic thin film for finding a place to resting insects. 

Dear Raquel,

            The main point is to have a good media /substrate to be able to collect. I think filter paper or para-film might be fine. 

Best, A.

Well, I do not think that you will be able to sample a sufficient amount of faeces from living bees in cages at all (because of their special rectum). In our cage studies bees hardly ever defecated, although we kept them for more then four weeks. The only exception was, when bees were infected with gut parasites like Nosema apis or ceranae. I think you should go for your second suggestion and use cohort representatives for each measuring interval.

I agree with dr Richard Odemer,

Best way if feasible (e.g. you don’t want to keep them longer) is to dissect them in this way you could find difference between the gut to rectum at different interval

Sheet of glass in the flight path at the hive's entrance.  Remove from glass with a razor blade or scalpel. 

Dear Raquel,

I have not an experience in the study of the honeybee feces, but I collected Osmia rufa, Megachile rotundata and Bombus terrestris faeces for pollen analyses.

Below you will find links to these publications.

It may come in handy.

Best regards

Dariusz

http://www.jas.org.pl/Food-plants-of-Bombus-terrestris-L-as-determined-by-pollen-analysis-of-faeces,0,93.html

http://www.jas.org.pl/Food-plants-of-the-red-mason-bee-Osmia-rufa-L-determined-based-on-a-palynological-analysis-of-faeces,0,117.html

http://www.jas.org.pl/Food-plants-of-Megachile-rotundata-L-determined-based-on-palinological-analysis-of-faece,0,149.html