Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian, UK.
Microbes in the Food Chain, Quadram Institute Bioscience, Norwich, UK.
Genome Biol. 2020 Feb 12;21(1):34. doi: 10.1186/s13059-020-1947-1.
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.
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.
This data will form the basis for future studies examining the composition and function of the chicken caecal microbiota.
对于很大一部分人类来说，鸡是一种非常重要的蛋白质来源。盲肠微生物群通过产生短链脂肪酸、氮循环和氨基酸生产，在鸡的营养中起着至关重要的作用。在这项研究中，我们从属于快速生长或缓慢生长品种的 24 只鸡的盲肠内容物样本中提取 DNA，这些鸡分别食用只含蔬菜的饮食或含有鱼粉的饮食。
我们利用 1.6 太字节的 Illumina 数据构建了 469 个草图宏基因组组装细菌基因组，包括 460 个新菌株、283 个新物种和 42 个新属。我们将这些基因组与来自 9 个欧盟国家的数据进行比较，表明这些基因组在欧洲鸡群中非常丰富。我们还比较了我们的基因组及其产生的碳水化合物活性酶在我们的鸡群之间的丰度，并证明存在既具有品种特异性又具有饮食特异性的微生物组，以及一个重叠的核心微生物组。
这些数据将为未来研究鸡盲肠微生物组的组成和功能奠定基础。
