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.

中文翻译：

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含可溶物干酒糟替代豆粕日粮对生长胡羊瘤胃不同生态位微生物群落的影响[J].

饮食对瘤胃微生物群有深远的影响，并且影响在不同的瘤胃生态位 (REN) 之间可能有所不同。本研究调查了用干酒糟和可溶物 (DDGS) 替代豆粕 (SBM) 的日粮对占据生长中的胡羊不同 REN 的瘤胃微生物群的影响。在为期 9 周的喂养试验后，每种日粮处理（SBM 与 DDGS 日粮）的 6 只羔羊被屠宰以进行样本收集。使用细菌 16S rRNA 基因的扩增子测序分析、功能预测和 qPCR 检查瘤胃固体、液体和上皮部分的微生物群。对于本研究中进行的几乎所有测量，均未检测到膳食蛋白质源 (PS) 和 REN 的相互作用。DDGS 替代对细菌群落结构的影响非常有限。然而，从 16S rRNA 基因序列预测的代谢途径在基于 SBM 和 DDGS 的饮食之间差异很大。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，但原生动物的数量减少。瘤胃固体（RS）和液体（RL）中的细菌群落分类组成相似，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 有很大不同。与细菌相对丰度一致，从 16S rRNA 基因预测的代谢途径在不同 REN 之间也有很大差异。细菌总数、原生动物、附着在RE上的产甲烷菌和产甲烷菌比RS和RL中的少，瘤胃上皮上的真菌数量比RS中的少，但与RL中的相似。相反，RE 上的 SRB 数量大于 RS 和 RL。用DDGS替代SBM对原生动物的影响大于对其他微生物的影响，并且不同REN的微生物群落结构和功能是不同的并且具有生态位适应。