The November edition of Emerging Infectious Diseases contains a commentary about probiotic safety. The paper, entitled "Regulatory Oversight and Safety of Probiotic Use" (Venugopalan et al. 2010), focuses on a probiotic yeast, Saccharomyces boulardii, which is increasingly being used for treatment or prevention of Clostridium difficile infection in people. Because it is marketed as a dietary supplement, this yeast doesn't have the same requirements for demonstration of safety and effectiveness as a "drug" would. Systemic Saccharomyces infections have been reported, predominantly in people who are critically ill or who have other risk factors for an infection caused by a microorganism that is typically harmless.
The lack of regulatory oversight limits the identification and reporting of problems associated with probiotic administration, and means that safety testing is not required, even if the product will be used by high risk individuals. Often people consider probiotics completely innocuous, and they don't think about the potential for complications. While very low, the risk of infection caused by the probiotic organism itself needs to be considered, especially when dealing with high risk patients and situations for which there is little proof that probiotics might be effective.
Are probiotics safe for use in animals such as pets and horses? Probably. For the vast majority of animals, the majority of probiotics are likely safe. Given the very lax nature of licensing and poor reporting of complications, it's hard to be definitive, but the likelihood of a significant problem occurring from giving an animal a probiotic is pretty limited. The fact that most commercial products actually contain few live organisms, a fraction of what is claimed on the label, probably increases safety (while also decreasing the chance that they work).
My general line is that probiotics are unlikely to do any harm for your average healthy animal. I have no problem with people trying probiotics in those cases, with the understanding that we really have little evidence that they work, but that they might. I am hesitant to use them (or recommend them) in very young animals, very old animals and animals with compromised immune systems. These types of animals are at increased risk of infection by even rather innocuous organisms that would not likely cause disease in other animals. Since the evidence that probiotics might work is lacking, I'm more careful when dealing with such high-risk groups. What we really need is sound research to provide the required evidence of probiotic safety and effectiveness.
Image: Coloured scanning electron micrograph of Saccharomyces boulardii (source: www.vub.ac.be)