元基因组或总体基因体学（英语：Metagenomics）是一门直接取得环境中所有遗传物质的研究。研究领域广泛，也可称为环境基因体学、生态基因体学或群落基因体学。在早期研究微生物基因体必须将环境基因DNA或RNA转殖进入大肠杆菌体内，利用复制选殖方式，分析在自然环境中复制选殖特定基因(通常为16S rRNA)的多样性。但是，以复制选殖的方式得不到精准的微生物多样性。近十年，研究学者利用DNA定序或焦磷酸定序的方式取得环境中所有样本基因，此新技术有助于我们取得微观下的生物多样性。总体基因体学提供一个更客观的方式发现微生物的世界，有可能改变之前我们所认知的微生物世界。

Metagenomics is the study of genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. While traditional microbiology and microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods. Recent studies use either "shotgun" or PCR directed sequencing to get largely unbiased samples of all genes from all the members of the sampled communities. Because of its ability to reveal the previously hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world. As the price of DNA sequencing continues to fall, metagenomics now allows microbial ecology to be investigated at a much greater scale and detail than before.