How pro are probiotics for non-model animal species? Novel data, lack of evidence, and future directions - Ferret 16S data

Treatments that aim to purposefully manipulate host-associated microbiomes are now prevalent in human and animal medicine. Probiotics that contain live bacteria are purported to improve microbiome function and host health. Although research is advancing, commercial probiotic development has outpaced empirical study of probiotic efficacy. Probiotics are widely used in ex-situ wildlife care despite a lack of empirical study or support. We interrogate the relevance of commercial probiotics in ex-situ wildlife by (a) sequencing the composition of commercial probiotics used to treat wildlife, (b) comparing the probiotic sequences to data on the microbiomes of > 900 animal species, and (c) characterizing the effects of a commercial probiotic on probiotic colonization, pathogen prevalence (Clostridium perfringens), and metagenomic function in endangered black-footed ferrets (Mustela nigripes). We found mislabeling and potential contaminants in probiotics marketed for a range of species. The probiotic bacteria were rare or absent in published animal microbiomes. In ferrets, probiotic treatment induced minimal probiotic colonization, negligible functional change, and limited influence on the enteric pathogen. Given our findings that commercial probiotics do not consider the microbial ecology of non-model animals, greater effort must be put towards identifying species-specific probiotic candidates and studying alternative microbial therapies for wildlife species.