Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
College of Animal Science and Technology, Jilin Agricultural University, Changchun, China.
Microbiome. 2021 Jun 12;9(1):137. doi: 10.1186/s40168-021-01078-x.
Gastrointestinal tract (GIT) microbiomes in ruminants play major roles in host health and thus animal production. However, we lack an integrated understanding of microbial community structure and function as prior studies. are predominantly biased towards the rumen. Therefore, to acquire a microbiota inventory of the discrete GIT compartments, In this study, we used shotgun metagenomics to profile the microbiota of 370 samples that represent 10 GIT regions of seven ruminant species.
Our analyses reconstructed a GIT microbial reference catalog with > 154 million nonredundant genes and identified 8745 uncultured candidate species from over 10,000 metagenome-assembled genomes. The integrated gene catalog across the GIT regions demonstrates spatial associations between the microbiome and physiological adaptations, and 8745 newly characterized genomes substantially expand the genomic landscape of ruminant microbiota, particularly those from the lower gut. This substantially expands the previously known set of endogenous microbial diversity and the taxonomic classification rate of the GIT microbiome. These candidate species encode hundreds of enzymes and novel biosynthetic gene clusters that improve our understanding concerning methane production and feed efficiency in ruminants. Overall, this study expands the characterization of the ruminant GIT microbiota at unprecedented spatial resolution and offers clues for improving ruminant livestock production in the future.
Having access to a comprehensive gene catalog and collections of microbial genomes provides the ability to perform efficiently genome-based analysis to achieve a detailed classification of GIT microbial ecosystem composition. Our study will bring unprecedented power in future association studies to investigate the impact of the GIT microbiota in ruminant health and production. Video abstract.
反刍动物的胃肠道（GIT）微生物群在宿主健康中起着重要作用，因此也影响动物生产。然而，我们缺乏对微生物群落结构和功能的综合理解，因为之前的研究主要偏向瘤胃。因此，为了获得离散 GIT 区室的微生物群落图谱，在本研究中，我们使用宏基因组学对来自 7 个反刍动物物种的 10 个 GIT 区室的 370 个样本的微生物组进行了分析。
我们的分析构建了一个包含> 1.54 亿个非冗余基因的 GIT 微生物参考目录，并从 10000 多个宏基因组组装基因组中鉴定出 8745 个未培养的候选种。整个 GIT 区室的综合基因目录展示了微生物组与生理适应之间的空间关联，而 8745 个新特征化的基因组极大地扩展了反刍动物微生物组的基因组景观，特别是那些来自下消化道的基因组。这极大地扩展了先前已知的内源性微生物多样性集合和 GIT 微生物组的分类分类率。这些候选种编码了数百种酶和新的生物合成基因簇，这有助于我们了解反刍动物的甲烷生成和饲料效率。总体而言，本研究以前所未有的空间分辨率扩展了反刍动物 GIT 微生物组的特征描述，并为未来提高反刍动物养殖生产提供了线索。
获得全面的基因目录和微生物基因组集合使我们能够有效地进行基于基因组的分析，以实现对 GIT 微生物生态系统组成的详细分类。我们的研究将为未来的关联研究带来前所未有的力量，以研究 GIT 微生物群在反刍动物健康和生产中的影响。视频摘要。
