Salmonella Enteritidis (SE) is one of the major causes of human foodborne intoxication resulting from consumption of contaminated poultry products. Genetic selection of animals that are more resistant to Salmonella carriage and modulation of the gut microbiota are two promising ways to decrease individual Salmonella carriage. The aims of this study were to identify the main genetic and microbial factors that control the level of Salmonella carriage in chickens (Gallus gallus) under controlled experimental conditions. Two-hundred and forty animals from the White Leghorn inbred lines N and 61 were infected by SE at 7 days of age. After infection, animals were kept in isolators to reduce recontamination of birds by Salmonella. Caecal contents were sampled at 12 days post-infection and used for DNA extraction. Microbiota DNA was used to measure individual counts of SE by digital PCR and to determine the bacterial taxonomic composition, using a 16S rRNA gene high-throughput sequencing approach. Our results confirmed that the N line is more resistant to Salmonella carriage than the 61 line, and that intra-line variability is higher for the 61 line. Furthermore, the 16S analysis showed strong significant differences in microbiota taxonomic composition between the two lines. Among the 617 operational taxonomic units (OTU) observed, more than 390 were differentially abundant between the two lines. Furthermore, within the 61 line, we found a difference in the microbiota taxonomic composition between the high and low Salmonella carriers, with 39 differentially abundant OTU. Using metagenome functional prediction based on 16S data, several metabolic pathways that are potentially associated to microbiota taxonomic differences (e.g. short chain fatty acids pathways) were identified between high and low carriers. Overall, our findings demonstrate that the caecal microbiota composition differs between genetic lines of chickens. This could be one of the reasons why the investigated lines differed in Salmonella carriage levels under experimental infection conditions.

中文翻译：

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实验感染鸡自交系之间盲肠微生物群组成和沙门氏菌携带的差异

肠炎沙门氏菌 (SE) 是因食用受污染的家禽产品而导致人类食源性中毒的主要原因之一。对沙门氏菌携带更具抵抗力的动物的基因选择和肠道微生物群的调节是减少个体沙门氏菌携带的两种有希望的方法。本研究的目的是确定在受控实验条件下控制鸡（原鸡）沙门氏菌携带水平的主要遗传和微生物因素。来自白来航近交系 N 和 61 的 240 只动物在 7 日龄时被 SE 感染。感染后，动物被饲养在隔离器中，以减少沙门氏菌对鸟类的再次污染。感染后12天对盲肠内容物进行取样并用于DNA提取。使用微生物群 DNA 通过数字 PCR 测量 SE 个体计数，并使用 16S rRNA 基因高通量测序方法确定细菌分类组成。我们的结果证实，N 系比 61 系对沙门氏菌携带具有更强的抵抗力，并且 61 系的系内变异性更高。此外，16S 分析显示这两个品系之间的微生物群分类组成存在显着差异。在观察到的 617 个操作分类单位 (OTU) 中，两个品系之间有超过 390 个的丰度存在差异。此外，在 61 个品系中，我们发现高沙门氏菌携带者和低沙门氏菌携带者之间的微生物群分类组成存在差异，其中 39 个 OTU 丰度存在差异。使用基于 16S 数据的宏基因组功能预测，在高携带者和低携带者之间确定了可能与微生物群分类差异相关的几种代谢途径（例如短链脂肪酸途径）。总体而言，我们的研究结果表明，鸡的遗传系之间的盲肠微生物群组成存在差异。这可能是实验感染条件下所研究的品系沙门氏菌携带水平不同的原因之一。