中文摘要：

人和动物胃肠道存在大量微生物群落，这些微生物是与宿主长期共同进化的结果，并且同宿主的健康和疾病密切相关，因此胃肠道微生物研究已成为当今的热点研究领域。宏基因组学技术在这一领域的应用，使我们不仅能够对胃肠道微生物群落结构及多样性进行分析，还能进一步深入了解其代谢功能，开发和利用潜在的微生物及其基因资源。文中结合我们的研究工作，综述了宏基因组学在人和动物胃肠道微生物研究中的应用，同时着重介绍宏基因组研究的生物信息学技术。

英文摘要：

Animal gastrointestinal tract contains a complex community of microbes, whose composition ultimately reflects the co-evolution of microorganisms with their animal host. The gut microbial community of humans and animals has received significant attention from researchers because of its association with health and disease. The application of metagenomics technology enables researchers to study not only the microbial composition but also the function of microbes in the gastrointestinal tract. In this paper, combined with our own findings, we summarized advances in studying gastrointestinal tract microorganism with metagenomics and the bioinformatics technology.