Background Chickens are a highly important source of protein for a large proportion of the human population. The caecal microbiota plays a crucial role in chicken nutrition through the production of short-chain fatty acids, nitrogen recycling, and amino acid production. In this study, we sequence DNA from caecal content samples taken from 24 chickens belonging to either a fast or a slower growing breed consuming either a vegetable-only diet or a diet containing fish meal. Results We utilise 1.6 T of Illumina data to construct 469 draft metagenome-assembled bacterial genomes, including 460 novel strains, 283 novel species, and 42 novel genera. We compare our genomes to data from 9 European Union countries and show that these genomes are abundant within European chicken flocks. We also compare the abundance of our genomes, and the carbohydrate active enzymes they produce, between our chicken groups and demonstrate that there are both breed- and diet-specific microbiomes, as well as an overlapping core microbiome. Conclusions This data will form the basis for future studies examining the composition and function of the chicken caecal microbiota.

中文翻译：

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来自鸡盲肠的数百种新型细菌基因组的组装

背景 对于大部分人口而言，鸡是非常重要的蛋白质来源。盲肠微生物群通过短链脂肪酸的产生、氮循环和氨基酸的产生在鸡营养中起着至关重要的作用。在这项研究中，我们对 24 只鸡的盲肠内容物样本进行 DNA 测序，这些鸡属于快速或生长较慢的品种，它们食用纯植物饮食或含有鱼粉的饮食。结果 我们利用 1.6 T 的 Illumina 数据构建了 469 个宏基因组组装的细菌基因组草图，包括 460 个新菌株、283 个新物种和 42 个新属。我们将我们的基因组与来自 9 个欧盟国家的数据进行比较，并表明这些基因组在欧洲鸡群中非常丰富。我们还比较了我们基因组的丰度，以及它们产生的碳水化合物活性酶，在我们的鸡群之间，并证明存在品种和饮食特定的微生物组，以及重叠的核心微生物组。结论 该数据将构成未来研究鸡盲肠微生物群的组成和功能的基础。