When I collected fecal samples from wild animals, there were two important precautions that I took to minimize environmental contamination. First, I only collected fresh samples (usually, I waited until I saw the animal defecate, though I understand that this might not be possible for some species/ecosystems). The second important precaution to take is to make an effort not to collect any portion of the sample that is in contact with the ground.

The best option is to collect the faeces directly from hunted animals, as you will reduce contamination. If this does not apply to your case and you can only collect faeces from the ground, be sure that the faeces are fresh (fresh faeces are recognized as being fresh if they are soft with a greenish shiny surface, without any signs of decomposition or coprophagous activity) and to prevent contamination from the soil, collect only the uppermost of the faeces.

Hello Qayoom,

It really depends on the type of bacteria you are working with and its prevalence in the environment.

I know some people working on these issues, please have a look. Hopefully you will find something useful.

PhD thesis on pathogens in chimpanzee faeces:

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CCwQFjAB&url=http%3A%2F%2Fopus4.kobv.de%2Fopus4-tuberlin%2Ffiles%2F3166%2Fkoendgen_sophie.pdf&ei=eJsQU7a3EerR4QS36YFY&usg=AFQjCNHcnYgg21DAPkEdbvibb_SgZfap9w&bvm=bv.62286460,d.bGE

-There are a number of published papers which she has completed as well.

Research group:

http://www.envs.emory.edu/faculty/GILLESPIE/Lab.html

-They work with faeces as well as environmental samples.

Best

~adeelia

I agree with most of the previous comments. I tend to try to collect almost directly after deposition on the ground (our groups are followed by telemetry or domestic animals). If you want to implement a protocol to test for contamination I would suggest that 1) If possible you compare fecal material directly taken form the animal and from the same animal on the ground; 2) you regularly sample the same fecal material through time to assess if contamination increases with time; 3) you repeat sampling of the same fecal material (multiple swabs at different place of the same dung for example). This can be difficult on wild animals but you can try your protocol on domestic animals (birds, livestock, rates etc. depending what's your wild species). Hope this helps.

Best,

AleX