Faecal samples may be collected using a metabolic cage or, if fresh material is required, the animal should be removed from its cage or pen and, in the case of larger species (cat, rabbit, dog, non-human primates and farm species), small quantities removed from the rectum using a swab.
Use of a small speculum enables larger quantities of material to be removed. Small rodents will almost invariably pass one or more faecal pellets when manually restrained for a few minutes.
Collection of total faecal output is complicated by the occurrence of coprophagy in rodents and rabbits. If total faecal output is required, special apparatus is needed to prevent the animal ingesting faeces as they are passed. It must also be remembered that prevention of this activity may interfere with normal growth and metabolism. Suitable apparatus includes restraining harnesses that prevent access to faeces as they are voided, coupled with a grid floor to prevent accumulation of faeces in the cage. An alternative technique is to attach an anal cup, and a variety of designs of these can be obtained.