不同环境微生物暴露对小鼠生命早期肠道菌群定植的影响

Influences of different microbial environment on gut microbiota colonization in early life of mice

目的探讨不同环境微生物暴露对生命早期小鼠肠道菌群定植的影响。方法选取无特殊病原体6-8周BALB/c小鼠24只（雌16只，雄8只），雌雄2︰1合笼，受孕后按子代不同时期（胎儿期、哺乳期、儿童期）的饲养环境分为4组。A组：胎儿期、哺乳期、儿童期均于清洁环境中饲养；B组：胎儿期、哺乳期于清洁环境中饲养，儿童期于普通环境中饲养；C组：胎儿期于清洁环境中饲养，哺乳期、儿童期于普通环境中饲养；D组：胎儿期、哺乳期、儿童期均于普通环境中饲养。采集小鼠生后3周末和5周末粪便样本，提取样本细菌总DNA，采用Illumina MiSeq高通量测序仪对细菌的16S rDNA V4区进行测序及生物信息学分析。采用Kruskal-Wallis及Dunn-Bonferroni检验进行统计学分析。结果1、生后3周末：（1）物种组成分析：①门水平：4组间厚壁菌门、疣微菌门、变形菌门和放线菌门相对丰度比较，差异均有统计学意义（P值均〈0.05）；A和B组厚壁菌门相对丰度分别低于C和D组[30.876（23.448-41.218）×10－2、3.317（1.116-4.641）×10－2与71.936（53.587-86.713）×10－2、79.105（56.305-82.736）×10－2]，而疣微菌门、变形菌门相对丰度高于C和D组[疣微菌门：17.249（9.748-35.106）×10－2、58.883（0.017-6.047）×10－2与0.152（0.066-1.890）×10－2、0.003（0.000-0.016）×10－2；变形菌门：12.640（0.336-15.070）×10－2、3.653（3.362-4.596）×10－2与0.219（0.134-0.325）×10－2、0.124（0.116-0.165）×10－2]，差异均有统计学意义（P值均〈0.05或0.01）；②属水平：4组间乳酸杆菌属、阿克曼菌属、拟杆菌属等相对丰度比较差异均有统计学意义（P值均〈0.01）；A和B组乳酸杆菌属相对丰度低于C和D组[19.283（8.618-31.541）×10－2、0.339（0.264-22.278）×10－2与58.414（34.874-71.942）×10－2、66.007（55.141-76.940）×10－2]，而阿克曼菌属、拟杆菌属、克雷伯杆菌属相对丰度高于C和D组[阿克曼菌属：17.247（9.748-35.106）×10－2、58.883（0.017-60.475）×10－2与0.152（0.066-1.890）×10－2、0.003（0.000-0.017）×10－2；拟杆菌属：3.978（0.683-25.171）×10－2、8.216（6.023-9.946）×10－2与0.141（0.061-0.281）×10－2、0.568（0.149-1.455）×10－2；克雷伯杆菌属：0.209（0.050-8.888）×10－2、1.402（0.865-1.692）×10－2与0.003（0.000-0.039）×10－2、0.000（0.000-0.001）×10－2]，差异均有统计学意义（P值均〈0.05或〈0.01）。（2）α多样性分析：4组间操作分类单位（operational taxonomic unit，OTU）数量、Chao1指数比较差异有统计学意义（P值均〈0.05），Shannon指数差异无统计学意义（P值〉0.05）；A和B组OTU数量低于D组[246（221-348）和257（209-280）与387（324-478），P值分别为0.045和0.0082]。2、生后5周末：（1）物种组成分析：①门水平：4组间厚壁菌门、疣微菌门、变形菌门相对丰度比较差异有统计学意义（P值均〈0.05或0.01）；A组厚壁菌门相对丰度低于B、C和D组[13.765（64.181-24.238）×10－2与48.912（37.280-59.466）×10－2、86.065（50.149-89.856）×10－2、53.847（31.946-72.936）×10－2]，而疣微菌门相对丰度高于B、C和D组[58.089（22.459-61.285）×10－2与0.001（0.000-0.005）×10－2、0.000（0.000-0.001）×10－2、0.003（0.000-0.006）×10－2]，差异均有统计学意义（P值均〈0.05或0.01）；②属水平：4组间乳酸杆菌属、阿克曼菌属相对丰度比较差异均有统计学意义（P值均〈0.01）。A组乳酸杆菌属相对丰度低于B、C和D组[1.755（0.805-8.833）×10－2与26.391（17.550-37.265）×10－2、70.688（45.713-77.953）×10－2、28.675（15.660-57.224）×10－2]，而阿克曼菌属相对丰度高于B、C和D组[58.089（22.460-61.285）×10－2与0.000（0.000-0.006）×10－2、0.000（0.000-0.001）×10－2、0.003（0.000-0.006）×10－2]，差异均有统计学意义（P值均〈0.05或0.01）。（2）α多样性分析：4组间OTU数量、Chao1指数、Shannon指数比较差异均有统计学意义（P值均〈0.05或0.01）；A组OTU数量低于B、C、D组[268（241-410）与438（380-516）、562（533-588）、546（473-599）]，B组OTU数量、Chao1指数、Shannon指数均低于C和D组[OTU数量：438（380-516）与562（533-588）、546（473-599）；Chao1指数：1 033（883-1 181）与1 285（1 220-1 338）、1 328（1 155-1 516）；Shannon指数：3.85（3.25-4.50）与4.28（3.30-5.11）、4.17（3.62-4.38）]，差异有统计学意义（P值均〈0.05或0.01）。结论不同环境微生物暴露会影响生命早期小鼠肠道菌群的多样性与结构；环境清洁度越高，肠道菌群多样性越低，菌群结构组成也有一定差异；哺乳期可能是肠道菌群定植的重要＂时间窗＂。

ObjectiveTo investigate the influences of exposure to different environmental microbes on early-life gut microbiota colonization in mice.MethodsMale （n=8） and female （n=16） adult specific pathogen free （SPF） BALB/c mice were caged together at a ratio of 2∶1. After conception, the mice were divided into four groups according to the environments where the offsprings were reared at three different periods （fetal period, breastfeeding period and childhood）. Group A： Offsprings were kept in a SPF environment throughout the study; group B： SPF environment during fetal and breastfeeding periods, and then ordinary environment during childhood; group C： SPF environment during fetal period, and then ordinary environment during breastfeeding period and childhood; group D： ordinary environment all the time. Fecal samples were collected at the end of week 3 and 5. Total bacterial DNA was extracted from each sample and analyzed by high throughput analysis. Kruskal-Wallis and Dunn-Bonferroni test were applied for statistical anaysis.Results1. At the end of three weeks： （1） Diversity：① Phylum level： There were significant differences in the abundance of Firmicutes, Verrucomicrobia, Proteobacteria and Actinobacteria among the four group （all P〈0.01）. Compared with group C and D, group A and B showed significantly decreased abundance of Firmicutes [30.876（23.448-41.218）×10-2, 3.317（1.116-4.641）×10-2 vs 71.936（53.587-86.713）×10-2, 79.105（56.305-82.736）×10-2], but increased abundance of Verrucomicrobia and Proteobacteria [Verrucomicrobia： 17.249（9.748-35.106）×10-2, 58.883（0.017-6.047）×10-2 vs 0.152（0.066-1.890）×10-2, 0.003（0.000-0.016）×10-2; Proteobacteria： 12.640（0.336-15.070）×10-2, 3.653（3.362-4.5955）×10-2 vs 0.219（0.134-0.325）×10-2, 0.124（0.116-0.165）×10-2, all P〈0.05 or 0.01].② Genus level： There were significant differences in the abundance of Lactobacillus, Akkermansia and Bacteroides among the four groups （all P〈0.01）. Compared with group C and D, group A and B showed significantly decreased abundance of Lactobacillus [19.283（8.618-31.541）×10-2, 0.339（0.264-22.278）×10-2 vs 58.414（34.874-71.942）×10-2, 66.007（55.141-76.940）×10-2], but increased abundance of Akkermansia, Bacteroides and Klebsiella [Akkermansia： 17.247（9.748-35.106）×10-2, 58.883（0.017-60.475）×10-2 vs 0.152（0.066-1.890）×10-2, 0.003（0.000-0.017）×10-2; Bacteroides： 3.978（0.683-25.171）×10-2, 8.216（6.023-9.946）×10-2 vs 0.141（0.061-0.281）×10-2, 0.568（0.149-1.455）×10-2; Klebsiella： 0.209（0.050-8.888）×10-2, 1.402（0.865-1.692）×10-2 vs 0.003（0.000-0.039）×10-2, 0.000（0.000-0.001）×10-2, all P〈0.05 or 0.01]. （2） Alpha diversity： Significant differences were found in operational taxonomic unit （OTU） and Chao1 index （P〈0.05）, but not in Shannon index among the four groups （P〉0.05）. The OTUs of group A and B were significantly lower than that of group D [246（221-348）, 257（209-280） vs 387（324-478）, P=0.045 and 0.008, respectively]. 2. At the end of five weeks： （1） Diversity：① Phylum level： There were significant differences in the abundance of Firmicutes, Verrucomicrobia and Proteobacteria among the four groups （P〈0.05 or 0.01）. The abundance of Firmicutes in gut microbiota in group A was lower than that in group B, C and D [13.765（64.181-24.238）×10-2 vs 48.912（37.280-59.466）×10-2, 86.065（50.149-89.856）×10-2, 53.847（31.946-72.936）×10-2], while that of Verrucomicrobia was higher [58.089（22.459-61.285）×10-2 vs 0.001（0.000-0.005）×10-2, 0.000（0.000-0.001）×10-2, 0.003（0.000-0.006）×10-2], all P〈0.05 or 0.01.② Genus level： There were significant differences in the abundance of Lactobacillus and Akkermansia among the four groups （P〈0.01）.The abundance of Lactobacillus in gut microbiota in group A was lower than that in group B, C and D[1.755（0.805-8.833）×10-2 vs 26.391（17.550-37.265）×10-2, 70.688（45.713-77.953）×10-2, 28.675（15.660-57.224）×10-2], while that of Akkermansia was higher [58.089（22.460-61.285）×10-2 vs 0.000（0.000-0.006）×10-2, 0.000（0.000-0.001）×10-2, 0.003（0.000-0.006）×10-2, all P〈0.05 or 0.01]. （2） Alpha diversity： There were significant differences in OTU, Chao1 and Shannon index among the four groups （P〈0.05 or 0.01）. The OTU of group A was lower than that of group B, C and D [268（241-410） vs 438（380-516）, 562（533-588）, 546（473-599）], and the OTU, Chao1 and Shannon index of group B were all lower than those of group C and D [OTU： 438（380-516） vs 562（533-588）, 546（473-599）; Chao1 index： 1 033（883-1 181） vs 1 285（1 220-1 338）, 1 328（1 155-1 516）; Shannon index： 3.85（3.25-4.50） vs 4.28（3.30-5.11）, 4.17（3.62-4.38）, all P〈0.05 or 0.01].ConclusionsEarly-life exposure to different environments has an obvious impact on the diversity and composition of intestinal microbiota in mice. The less clean the living environment is, the more diverse the gut microflora will be. Furthermore, the window of opportunity for gut microbiota colonization seems to be related to breastfeeding period.