Well, I fear the answer is not a simple yes or no!

Sure, the big advantage of collecting fecal samples to evaluate adrenocortical activity (and thus stress) is that it can be achieved without handling the animals (=non-invasive).

BUT:

In order to fully validate (a prerequisite for a successful application!) methods which measure fecal cortisol/corticosterone metabolites (FCM) you have to perform some sort of a physiological/biological validation experiment. I mean that you have to prove that your method measures something biologically meaningful (ie an increase in adrenocortical activity = higher plasma levels - is reflected in an increase of FCM concentrations). This is best achieved by performing an ACTH test (you may also use animals kept in a zoo), but you can also take advantage of some other stressful conditions where you collect samples before and after that event and measure FCM levels with your method.

So, which species do you deal with and which method do you want to use? If someone else has performed such a validation experiment in your species you might use their method and analyse fecal samples to evaluate baseline values from your wild animals.  

Hope this short answer is somewhat helpful! Please see some of my papers for more details about the necessity of such validations and how to best perform them (ie Touma & Palme, 2005; Sheriff et al., 2011 - both available via ResearchGate).

..and don't hesitate to contact me if you have further questions.

Best wishes

Rupert

Full references of above citations:

Sheriff, MJ., Dantzer, B., Delehanty, B., Palme, R., Boonstra, R. (2011): Measuring stress in wildlife: techniques for quantifying glucocorticoids. Oecologia 166, 869-887. 

Touma, C., Palme, R. (2005): Measuring fecal glucocorticoid metabolites in mammals and birds: The importance of validation. Annals New York Acad. Sci. 1046, 54-74.

I think you can,  since this is a baseline wild life study and not a controlled study in a laboratory. In your comparisons or analysis of data those limitations should be considered.

Yes.  If you cant touch the animal that may be the only option.  You will have higher sample variation than in the lab, but it certainly would give you a baseline for the field. 

Well, I fear the answer is not a simple yes or no!

Sure, the big advantage of collecting fecal samples to evaluate adrenocortical activity (and thus stress) is that it can be achieved without handling the animals (=non-invasive).

BUT:

In order to fully validate (a prerequisite for a successful application!) methods which measure fecal cortisol/corticosterone metabolites (FCM) you have to perform some sort of a physiological/biological validation experiment. I mean that you have to prove that your method measures something biologically meaningful (ie an increase in adrenocortical activity = higher plasma levels - is reflected in an increase of FCM concentrations). This is best achieved by performing an ACTH test (you may also use animals kept in a zoo), but you can also take advantage of some other stressful conditions where you collect samples before and after that event and measure FCM levels with your method.

So, which species do you deal with and which method do you want to use? If someone else has performed such a validation experiment in your species you might use their method and analyse fecal samples to evaluate baseline values from your wild animals.  

Hope this short answer is somewhat helpful! Please see some of my papers for more details about the necessity of such validations and how to best perform them (ie Touma & Palme, 2005; Sheriff et al., 2011 - both available via ResearchGate).

..and don't hesitate to contact me if you have further questions.

Best wishes

Rupert

Full references of above citations:

Sheriff, MJ., Dantzer, B., Delehanty, B., Palme, R., Boonstra, R. (2011): Measuring stress in wildlife: techniques for quantifying glucocorticoids. Oecologia 166, 869-887. 

Touma, C., Palme, R. (2005): Measuring fecal glucocorticoid metabolites in mammals and birds: The importance of validation. Annals New York Acad. Sci. 1046, 54-74.

What is your study subject ? as previously mentioned a proper validation is needed to validate if your methods are indeed measured the intended response. Beside ACTH challenge other biological validation can also be use. You could measure samples before and after a known stress event (ie Weingrill et al 2011 & Shutt et al 2012).

Weingrill T, Willems EP, Zimmermann N, Steinmetz H, Heistermann M. 2011. Species-Specific Patterns in Fecal Glucocorticoid and Androgen Levels in Zoo-Living Orangutans (Pongo Spp.). Gen. Comp. Endocr. 172, 446-457.

Shutt K, Setchell JM, Heistermann M. 2012. Non-Invasive Monitoring of Physiological Stress in the Western Lowland Gorilla (Gorilla Gorilla Gorilla): Validation of a Fecal Glucocorticoid Assay and Methods for Practical Application in the Field. Gen. Comp. Endocr. 179, 167-177.

Thank you for the answer and the papers! 

To answer most of the questions: I'm doing studies of orangutans, but at different set of management (captive, semi wild, wild). I shall get back in touch with you guys with more questions! 

We have validated the assay for orangutan stress in our lab see Weingrill et all 2011 for more detail.

This article may be interesting for you as well! Good luck with your study!