采用高通量测序技术研究抗生素对小鼠肠道菌群的影响

目的 探讨不同浓度抗生素对小鼠肠道菌群多样性和结构的影响，并预测相关功能变化。方法 15只SPF级ICR小鼠随机分为正常组、低浓度抗生素组和高浓度抗生素组，连续灌胃5 d后，采集小鼠新鲜粪便样本。利用Illumina MiSeq测序平台，对细菌的16S rRNA V3‒V4区进行高通量测序，并对测序结果进行生物信息学分析。结果 高、低浓度抗生素组小鼠肠道菌群组成与正常组存在明显差异。与正常组相比，高剂量组小鼠肠道肠球菌属、志贺埃希菌属相对丰度显著升高（t=‒2.71，P=0.026；t=‒2.30，P<0.05）；分节丝状菌属、拟普雷沃菌属相对丰度显著降低（t=2.88，P=0.020；t=2.49，P=0.037），理研菌属极显著降低（t=3.79，P=0.005）。低剂量组小鼠肠道菌群变形菌纲成为优势菌，芽胞杆菌属、粪球菌_2、苏黎世杆菌属、普雷沃菌属_2、普雷沃菌属_7、志贺埃希菌属、沙雷菌属和放线菌属等相对丰度显著升高（均P<0.05）；梭杆菌属、泛菌属极显著升高（t=‒3.19，P=0.013；t=‒3.50，P=0.008）；分节丝状菌属、理研菌属相对丰度显著降低（t=2.69，P=0.028；t=2.33，P=0.048）。PICRUSt功能预测分析显示，抗生素组显著增加人类疾病、细胞过程和环境信息处理功能层的基因拷贝数，显著降低有机系统、遗传信息处理和代谢功能层的基因拷贝数。结论 广谱抗生素能破坏小鼠肠道的微生态平衡，有必要深入研究抗生素对心血管、免疫性、感染性及神经退行性疾病发展的潜在作用。

Impact of antibiotics on the murine gut microbiota determined byhigh-throughput sequencing

Abstract: Objective To investigate the impact of antibiotics at different concentrations on gut microbial composition in mice, and identify the related functional changes. Methods Fifteen SPF mice were randomly divided into control group, low-dose antibiotic group [Gentamycin sulfate 0.75 g/(kg·d) + Cefotaxime sodium 3.00 g/(kg·d)] or high-dose antibiotic group [Gentamycin sulfate 2.25 g/(kg·d) + Cefotaxime sodium 9.00 g/(kg·d)]. After 5 days of administration, 15 fecal samples were collected and total DNA was extracted from the faecal samples. The primers were designed on bacterial 16S rRNA V3 - V4 region sequences and Illumina Miseq platform was used for high-throughput sequencing. The obtained data were analyzed using bioinformatics. Results Compared with the control group, the relative abundances of Enterococcus and Escherichia_Shigella in high-dose antibiotic group significantly increased (all P<0.05), while those of Candidatus_Arthromitus, Alloprevotella and other genera significantly decreased (all P<0.05), and that of Alistpes extremely significantly decreased (P<0.01). Compared with the control group, Proteobacteria in the low-dose group became dominant; the relative abundances of Bacillus, Coprococcus_2, Turicibacter, Prevotella_2, Prevotella_7, Escherichia_Shigella, Serratia and Actinomyces significantly increased (all P<0.05), those of Fusobacterium and Pantoea extremely significantly increased (all P<0.01) while those of Candidatus_Arthromitus and Alistpes significantly decreased (all P<0.05). PICRUSt analysis showed that the metabolic pathways were potentially affected by antibiotics use. Conclusion Broad-spectrum antibiotics may disrupt gut microbiota, which warrants further studies on the potential role of antibiotics in the development of cardiovascular, immune system, infectious and neurodegenerative disorders.