Shen Junshi, Li Zhipeng, Yu Zhongtang, Zhu Weiyun
Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China.
National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095 China.
J Anim Sci Biotechnol. 2020 Sep 7;11:93. doi: 10.1186/s40104-020-00499-2. eCollection 2020.
Diet has a profound impact on the rumen microbiota, and the impact can vary among the different rumen ecological niches (REN). This study investigated the effects of dietary replacement of soybean meal (SBM) with dried distillers grains with solubles (DDGS) on the rumen microbiota occupying different REN of growing Hu lambs. After a 9-week feeding trial, 6 lambs from each dietary treatment (SBM vs. DDGS-based diets) were slaughtered for sample collection. The microbiota of the rumen solid, liquid, and epithelium fractions was examined using amplicon sequencing analysis of bacterial 16S rRNA gene, functional prediction, and qPCR.
No interaction of dietary protein source (PS) and REN were detected for virtually all the measurements made in this study. The DDGS substitution resulted in very limited influence on bacterial community structure. However, the metabolic pathways predicted from 16S rRNA gene sequences varied greatly between SBM- and DDGS-based diets. The populations of rumen total bacteria, fungi, sulfate-reducing bacteria (SRB), and methanogens were not influenced by DDGS substitution, but the population of protozoa was reduced. The bacterial communities in rumen solid (RS) and liquid (RL) were similar in taxonomic composition but were different in relative abundance of some taxa. In contrast, the bacterial composition and relative abundance of rumen epithelium (RE) were greatly distinct from those of the RS and the RL. In alignment with the bacterial relative abundance, the metabolic pathways predicted from 16S rRNA genes also varied greatly among the different REN. The populations of total bacteria, protozoa, and methanogens attached to the RE were smaller than those in the RS and RL, and the fungal population on the rumen epithelium was smaller than that in the RS but similar to that in the RL. On the contrary, the SRB population on the RE was greater than that in the RS and RL.
Substitution of SBM with DDGS had greater impact to the protozoa than to the other microbes, and the microbial community structure and functions at different REN are distinct and niche-adapted.
日粮对瘤胃微生物群有深远影响，且这种影响在不同的瘤胃生态位（REN）之间可能存在差异。本研究调查了用含可溶物的干酒糟（DDGS）替代生长中的湖羊日粮中的豆粕（SBM）对占据不同REN的瘤胃微生物群的影响。经过9周的饲养试验，对每种日粮处理（基于SBM与基于DDGS的日粮）的6只羔羊进行屠宰以采集样本。使用细菌16S rRNA基因的扩增子测序分析、功能预测和qPCR检测瘤胃固体、液体和上皮部分的微生物群。
在本研究进行的几乎所有测量中，均未检测到日粮蛋白质来源（PS）与REN之间的相互作用。DDGS替代对细菌群落结构的影响非常有限。然而，基于SBM和基于DDGS的日粮之间，根据16S rRNA基因序列预测的代谢途径差异很大。瘤胃总细菌、真菌、硫酸盐还原菌（SRB）和产甲烷菌的数量不受DDGS替代的影响，但原生动物数量减少。瘤胃固体（RS）和液体（RL）中的细菌群落在分类组成上相似，但某些分类群的相对丰度不同。相比之下，瘤胃上皮（RE）的细菌组成和相对丰度与RS和RL的有很大差异。与细菌相对丰度一致，根据16S rRNA基因预测的代谢途径在不同的REN之间也有很大差异。附着在RE上的总细菌、原生动物和产甲烷菌数量低于RS和RL中的数量，瘤胃上皮上的真菌数量低于RS中的数量，但与RL中的数量相似。相反，RE上的SRB数量高于RS和RL中的数量。
用DDGS替代SBM对原生动物的影响大于对其他微生物的影响，且不同REN处的微生物群落结构和功能是不同的且适应各自生态位。
