College of Veterinary Medicine, Qingdao Agricultural Universitygrid.412608.9, Qingdao, Shandong Province, China.
Heilongjiang Provincial Key Laboratory of the Prevention and Control of Bovine Diseases, College of Animal Science, Heilongjiang Bayi Agriculture University, Daqing, Heilongjiang Province, China.
Microbiol Spectr. 2022 Dec 21;10(6):e0221122. doi: 10.1128/spectrum.02211-22. Epub 2022 Nov 2.
Most microbiome studies regarding the ruminant digestive tract have focused on the rumen microbiota, whereas only a few studies were performed on investigating the gut microbiota of ruminants, which limits our understanding of this important component. Herein, the gut microbiota of 30 Caprinae animals (sheep and goats) from six provinces in China was characterized using ultradeep (>100 Gbp per sample) metagenome shotgun sequencing. An inventory of Caprinae gut microbial species containing 5,046 metagenomic assembly genomes (MAGs) was constructed. Particularly, 2,530 of the genomes belonged to uncultured candidate species. These genomes largely expanded the genomic repository of the current microbes in the Caprinae gut. Several enzymes and biosynthetic gene clusters encoded by these Caprinae gut species were identified. In summary, our study extends the gut microbiota characteristics of Caprinae and provides a basis for future studies on animal production and animal health. We constructed a microbiota catalog containing 5,046 MAGs from Caprinae gut from six regions of China. Most of the MAGs do not overlap known databases and appear to be potentially new species. We also characterized the functional spectrum of these MAGs and analyzed the differences between different regions. Our study enriches the understanding of taxonomic, functional, and metabolic diversity of Caprinae gut microbiota. We are confident that the manuscript will be of utmost interest to a wide range of readers and be widely applied in future research.
大多数关于反刍动物消化道微生物组的研究都集中在瘤胃微生物群上，而只有少数研究致力于调查反刍动物的肠道微生物群，这限制了我们对这一重要组成部分的理解。本研究采用超高深度（每个样本>100Gbp）宏基因组 shotgun 测序技术，对来自中国六个省份的 30 只反刍动物（绵羊和山羊）的肠道微生物组进行了研究。构建了包含 5046 个宏基因组组装基因组（MAG）的反刍动物肠道微生物物种清单。特别是，其中 2530 个基因组属于未培养的候选物种。这些基因组极大地扩展了反刍动物肠道中当前微生物的基因组存储库。鉴定出了这些反刍动物肠道物种编码的几种酶和生物合成基因簇。总之，我们的研究扩展了反刍动物肠道微生物组的特征，并为未来的动物生产和动物健康研究提供了基础。我们构建了一个包含来自中国六个地区反刍动物肠道的 5046 个 MAG 的微生物组目录。大多数 MAG 与已知数据库不重叠，似乎是潜在的新物种。我们还对这些 MAG 的功能谱进行了表征，并分析了不同地区之间的差异。我们的研究丰富了对反刍动物肠道微生物组的分类、功能和代谢多样性的理解。我们相信，该手稿将引起广大读者的极大兴趣，并在未来的研究中得到广泛应用。
