Monger Xavier C, Saucier Linda, Gilbert Alex-An, Vincent Antony T
Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Quebec City, QC G1V 0A6, Canada.
Institut sur la nutrition et les aliments fonctionnels, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Quebec City, QC G1V 0A6, Canada.
MethodsX. 2022 Apr 29;9:101716. doi: 10.1016/j.mex.2022.101716. eCollection 2022.
Studies on the microbiome of different species are on the rise, due to a growing interest in animal health and the safety of food products of animal origin. A challenge with studying animals' microbiomes is to find methods that obtain a good representation of the microbial community of interest. Good unbiased sampling protocols are the basis for a solid experimental design, but may need to be done in environments where sample preservation could be difficult. In this study, we evaluate by shotgun sequencing the impact of stabilizing swine faeces samples using a commercial stabilizer (PERFORMAbiome • GUT | PB-200, DNA Genotek). Using stabilizer makes it possible to obtain DNA that is significantly less degraded than when the samples are not stabilized. Also, the results on the taxonomy and on the bacterial functions encoded in the microbiome are impacted by whether or not the samples are stabilized. Finally, the stabilization of samples that had already been frozen and stored at -80°C led to extraction and DNA quality results similar to those obtained from samples that were stabilized before freezing.
由于对动物健康和动物源食品安全性的兴趣日益浓厚，针对不同物种微生物组的研究正在增加。研究动物微生物组面临的一个挑战是找到能够很好地代表目标微生物群落的方法。良好的无偏差采样方案是坚实实验设计的基础，但可能需要在样品保存困难的环境中进行。在本研究中，我们通过鸟枪法测序评估了使用商业稳定剂（PERFORMAbiome • GUT | PB - 200，DNA Genotek）稳定猪粪便样本的影响。使用稳定剂能够获得比未稳定样本降解程度显著更低的DNA。此外，样本是否稳定会影响微生物组中分类学和编码细菌功能的结果。最后，对已经冷冻并储存在-80°C的样本进行稳定处理，其提取和DNA质量结果与冷冻前进行稳定处理的样本相似。
