How pro are probiotics for non-model animal species? Novel data, lack of evidence, and future directions - black-footed ferret metagenomics

Black-footed ferret metagenomic sequences - 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.

黑足雪貂宏基因组序列——旨在人为调控宿主相关微生物组的治疗手段，目前已广泛应用于人类与动物医学领域。含有活性细菌的益生菌制剂据称可改善微生物组功能与宿主健康状况。尽管相关研究持续推进，但商业益生菌的开发速度已远超其功效的实证研究水平。尽管缺乏实证依据与研究支持，益生菌仍被广泛应用于野生动物迁地保护护理工作中。本研究通过以下三方面探究商业益生菌在野生动物迁地保护中的适用性：(a) 对用于野生动物治疗的商业益生菌制剂的组成进行测序；(b) 将益生菌序列与超过900种动物的微生物组数据进行比对；(c) 解析一款商业益生菌对濒危黑足雪貂（Mustela nigripes）的益生菌定植情况、病原菌（产气荚膜梭菌（Clostridium perfringens））感染率以及宏基因组功能的影响。研究发现，面向多物种发售的益生菌制剂存在标签标注错误与潜在污染物问题；在已发表的动物微生物组数据中，该类益生菌所含细菌十分罕见甚至未被检出。在黑足雪貂实验中，益生菌定植效果极弱，对微生物组功能的改变可忽略不计，且对肠道病原菌的影响有限。鉴于本研究发现商业益生菌未考虑非模式动物的微生物生态特征，未来应投入更多精力筛选物种特异性益生菌候选株，并研究适用于野生动物的新型微生物治疗手段。