PDF(Pubmed)
Abstract：
Emus (Dromaius novaehollandiae), a large flightless omnivorous ratite, are farmed for their fat and meat. Emu fat can be rendered into oil for therapeutic and cosmetic use. They are capable of gaining a significant portion of its daily energy requirement from the digestion of plant fibre. Despite of its large body size and low metabolic rate, emus have a relatively simple gastroinstetinal (GI) tract with a short mean digesta retention time. However, little is known about the GI microbial diversity of emus. The objective of this study was to characterize the intraluminal intestinal bacterial community in the different segments of small intestine (duodenum, jejunum, and ileum) using pyrotag sequencing and compare that with the ceca. Gut content samples were collected from each of four adult emus (2 males, 2 females; 5-6 years old) that were free ranged but supplemented with a barley-alfalfa-canola based diet. We amplified the V3-V5 region of 16S rRNA gene to identify the bacterial community using Roche 454 Junior system. After quality trimming, a total of 165,585 sequence reads were obtained from different segments of the small intestine (SI). A total of 701 operational taxonomic units (OTUs) were identified in the different segments of small intestine. Firmicutes (14-99%) and Proteobacteria (0.5-76%) were the most predominant bacterial phyla in the small intestine. Based on species richness estimation (Chao1 index), the average number of estimated OTUs in the small intestinal compartments were 148 in Duodenum, 167 in Jejunum, and 85 in Ileum, respectively. Low number of core OTUs identified in each compartment of small intestine across individual birds (Duodenum: 13 OTUs, Jejunum: 2 OTUs, Ileum: 14 OTUs) indicated unique bacterial community in each bird. Moreover, only 2 OTUs (Escherichia and Sinobacteraceae) were identified as core bacteria along the whole small intestine. PICRUSt analysis has indicated that the detoxification of plant material and environmental chemicals seem to be performed by SI microbiota, especially those in the jejunum. The emu cecal microbiome has more genes than SI segments involving in protective or immune response to enteric pathogens. Microbial digestion and fermentation is mostly in the jejunum and ceca. This is the first study to characterize the microbiota of different compartments of the emu intestines via gut samples and not fecal samples. Results from this study allow us to further investigate the influence of the seasonal and physiological changes of intestinal microbiota on the nutrition of emus and indirectly influence the fatty acid composition of emu fat.
摘要：
Emus(Dromaiusnovaehollandiae)，一个巨大的不会飞的杂食性平胸，是为了他们的脂肪和肉而养殖的。emu脂肪可以制成油用于治疗和美容用途。它们能够从植物纤维的消化中获得其日常能量需求的很大一部分。尽管它体型大，代谢率低，emus具有相对简单的胃肠（GI）道，平均消化保留时间短。然而,对emus的GI微生物多样性知之甚少。本研究的目的是表征小肠不同节段（十二指肠，空肠,和回肠）使用pyrotag测序并将其与盲肠进行比较。从四个成年emus（2个雄性，2名女性；5-6岁），自由放养，但补充了基于大麦-苜蓿-油菜的饮食。我们使用Roche454Junior系统扩增了16SrRNA基因的V3-V5区域以鉴定细菌群落。质量修整后，从小肠(SI)的不同区段获得总共165,585个序列读数。在小肠的不同部分中总共鉴定出701个操作分类单位（OTU）。厚壁菌（14-99％）和变形杆菌（0.5-76％）是小肠中最主要的细菌门。基于物种丰富度估计(Chao1指数)，十二指肠小肠隔室中估计的OTU的平均数量为148，167在空肠，85在回肠，分别。在单个鸟类的小肠的每个隔室中识别出的核心OTU数量较少(十二指肠：13个OTU，空肠：2个OTU，回肠：14个OTU）表明每只鸟中独特的细菌群落。此外，在整个小肠中，只有2个OTUs（埃希氏菌和中细菌科）被鉴定为核心细菌。PICRUSt分析表明，植物材料和环境化学物质的解毒似乎是由SI微生物群进行的，尤其是空肠里的.emu盲肠微生物组比SI片段具有更多的基因，涉及对肠道病原体的保护性或免疫反应。微生物消化和发酵大多在空肠和盲肠。这是第一项通过肠道样品而不是粪便样品表征the肠不同区室微生物群的研究。这项研究的结果使我们能够进一步研究肠道菌群的季节性和生理变化对emus营养的影响，并间接影响emu脂肪的脂肪酸组成。
