Alterations in Ileal Mucosa Bacteria Related to Diet Complexity and Growth Performance in Young Pigs

BackgroundEvaluation of the prolonged impact of weaning diet on ileal mucosa bacteria and during periods of reduced and improved growth was conducted using 454 pyrosequencing.Methodology/Principal FindingsWeaned pigs were fed HIGH or LOW complexity diets, with or without antibiotics, for 6 weeks, followed by a common grower diet. Pigs were killed at 2 (n = 4 or 5) and 8 (n = 6) weeks post-weaning (periods of reduced and improved growth, respectively). Mucosal bacteria were removed; DNA was extracted and amplified using the V1–V3 region of the 16S rRNA gene. Mucosal bacteria clustered more closely by week post-weaning than diet but 44% of bacterial species did not change from week 2 to 8. There was no effect of diet complexity or antibiotic inclusion on indices of bacterial diversity. Firmicutes made up 91 and 96% of total reads at week 2 and 8, respectively. The proportion of Clostridium paraputrificum increased (P = 0.003) from week 2 to 8 in pigs fed LOW but didn’t change in pigs fed HIGH; whereas Clostridium leptum decreased (P = 0.02) from week 2 to 8 in pigs fed LOW but didn’t change in pigs fed HIGH. The proportion of Sarcina genus was 3-fold higher in pigs fed A+ compared to A− at week 2 and 5-fold higher at week 8 despite the lack of in-feed antibiotics at that time.Conclusions/SignificanceShifts in mucosal bacteria populations may be related to dietary induced changes in growth performance during reduced and improved growth but further studies are required to confirm causative relationship. Weaning diet results in species specific prolonged alterations in mucosal bacteria, particularly where high levels of in-feed antibiotics are used. A considerable portion of ileal mucosal bacteria colonize early and remain stable over time despite changes in diet.**背景** 本研究采用454焦磷酸测序技术，探究断奶日粮对回肠黏膜菌群的长期影响，以及该效应在生长受限与生长改善阶段的表现。 **材料与方法/主要结果** 断奶仔猪被饲喂高复杂度或低复杂度日粮，添加或不添加抗生素，持续6周，随后饲喂通用育肥日粮。分别于断奶后2周（对应生长受限阶段，样本量n=4或5）和8周（对应生长改善阶段，样本量n=6）处死仔猪。收集回肠黏膜菌群，提取基因组DNA并以16S核糖体RNA（16S rRNA）基因的V1-V3可变区为靶点进行扩增。聚类分析结果显示，回肠黏膜菌群的聚类模式与断奶后周龄的相关性强于日粮类型，但44%的细菌物种在断奶后2周至8周间未发生丰度变化。日粮复杂度与抗生素添加与否均未对细菌多样性指数产生显著影响。厚壁菌门（Firmicutes）在断奶后2周和8周的测序读段占比分别为91%和96%。饲喂低复杂度日粮的仔猪，其副产气荚膜梭菌（Clostridium paraputrificum）的相对丰度在断奶后2周至8周间显著升高（P=0.003），而饲喂高复杂度日粮的仔猪该菌丰度无明显变化；与此同时，柔嫩梭菌（Clostridium leptum）的相对丰度在饲喂低复杂度日粮的仔猪中显著降低（P=0.02），饲喂高复杂度日粮的仔猪则无显著变化。在断奶后2周，饲用抗生素添加组（A+）仔猪的八叠球菌属（Sarcina）相对丰度是未添加组（A−）的3倍；断奶后8周时，尽管此时日粮中未添加抗生素，添加抗生素组的八叠球菌属相对丰度仍为未添加组的5倍。 **结论与意义** 回肠黏膜菌群的结构变化可能与生长受限及生长改善阶段日粮诱导的生长性能变化相关，但仍需进一步研究以明确二者的因果关系。断奶日粮会对黏膜菌群产生物种特异性的长期改变，尤其是在日粮中添加高水平饲用抗生素的情况下。尽管日粮会发生变更，但相当一部分回肠黏膜菌群会在早期定植并随时间保持稳定。